schrodinger.infra.canvas module

Canvas C++ wrappers

class schrodinger.infra.canvas.AtomData

::AtomData

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

cachedCoords

constrained

declareAromatic

fixed

hasCoords

hidden

ignored

next()

returns the next ‘this’ object

owner

class schrodinger.infra.canvas.AtomicInvariant

::AtomicInvariant

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getAtomicCharge() → char

getAtomicMass() → uchar

getAtomicNumber() → uchar

getBondsToNonHydrogen() → uchar

getTotalHydrogens() → uchar

getTotalValence() → uchar

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.BondData

::BondData

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

owner

schrodinger.infra.canvas.CHMSTRING(p) → std::string

schrodinger.infra.canvas.CHM_FORCE2D(mol, force2D, arg3) → bool

schrodinger.infra.canvas.CHM_OUTPUT2D(os, mol, v3SDF, force2D, arg5, withprops)

CHM_OUTPUT2D(os, mol, v3SDF, force2D, arg5) CHM_OUTPUT2D(os, mol, v3SDF, force2D)

class schrodinger.infra.canvas.CMWC

::CMWC

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.Chm2DCoordGen

::Chm2DCoordGen

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static assignCoordsForHiddenAtoms(mol)

static assignCoordsForNullAtoms(mol)

static assignMissingCoords(mol)

static center(mol) → ChmPoint

static centerAndRescale(mol, desiredBondLength=1.3)

centerAndRescale(mol)

static checkForNAN(mol) → bool

static exportCoordinatesFromMinimizer(min, mol)

static flipHorizontal(mol)

static flipVertical(mol)

static generateAndApply(mol, arg2, arg3)

generateAndApply(mol, arg2) generateAndApply(mol)

static generateCoordinates(mol, precision)

generateCoordinates(mol)

static generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5, arg6, fixup=False, completelyByPassCoordgen=False, copyOverOriginalTemplateCoordinates=False)

generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5, arg6, fixup=False, completelyByPassCoordgen=False) generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5, arg6, fixup=False) generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5, arg6) generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers, arg5) generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers)

static generateFromTemplateAndApply2(mol, templateMol, matches, arg4, arg5, fixup=False, completelyByPassCoordgen=False, copyOverOriginalTemplateCoordinates=False)

generateFromTemplateAndApply2(mol, templateMol, matches, arg4, arg5, fixup=False, completelyByPassCoordgen=False) generateFromTemplateAndApply2(mol, templateMol, matches, arg4, arg5, fixup=False) generateFromTemplateAndApply2(mol, templateMol, matches, arg4, arg5) generateFromTemplateAndApply2(mol, templateMol, matches, arg4) generateFromTemplateAndApply2(mol, templateMol, matches)

static getBounds(mol) → std::pair< ChmPoint,ChmPoint >

static getCoordgenTemplateDir() → std::string

static getScale(mol) → float

static hasCorrectScale(mol, desiredBondLength=1.3, relativeTolerance=0.05) → bool

hasCorrectScale(mol, desiredBondLength=1.3) -> bool hasCorrectScale(mol) -> bool

static initializeMinimizerFromMolecule(min, mol)

static isAvailable() → bool

next()

returns the next ‘this’ object

static rotate(mol, degrees)

static rotateAbout(mol, degrees, center)

static sketcherBondStereoFromChmBond(chmBond, bond) → sketcherMinimizerBondStereoInfo

static sketcherChiralityFromChmChirality(info, atoms) → sketcherMinimizerAtomChiralityInfo

static translate(mol, offset)

static visibleAtomsAtOrigin(mol) → ChmBitset

schrodinger.infra.canvas.Chm2DCoordGen_assignCoordsForHiddenAtoms(mol)

schrodinger.infra.canvas.Chm2DCoordGen_assignCoordsForNullAtoms(mol)

schrodinger.infra.canvas.Chm2DCoordGen_assignMissingCoords(mol)

schrodinger.infra.canvas.Chm2DCoordGen_center(mol) → ChmPoint

schrodinger.infra.canvas.Chm2DCoordGen_centerAndRescale(mol)

schrodinger.infra.canvas.Chm2DCoordGen_checkForNAN(mol) → bool

schrodinger.infra.canvas.Chm2DCoordGen_exportCoordinatesFromMinimizer(min, mol)

schrodinger.infra.canvas.Chm2DCoordGen_flipHorizontal(mol)

schrodinger.infra.canvas.Chm2DCoordGen_flipVertical(mol)

schrodinger.infra.canvas.Chm2DCoordGen_generateAndApply(mol)

schrodinger.infra.canvas.Chm2DCoordGen_generateCoordinates(mol)

schrodinger.infra.canvas.Chm2DCoordGen_generateFromTemplateAndApply(mol, templateMol, molAtomNumbers, templateAtomNumbers)

schrodinger.infra.canvas.Chm2DCoordGen_generateFromTemplateAndApply2(mol, templateMol, matches)

schrodinger.infra.canvas.Chm2DCoordGen_getBounds(mol) → std::pair< ChmPoint,ChmPoint >

schrodinger.infra.canvas.Chm2DCoordGen_getCoordgenTemplateDir() → std::string

schrodinger.infra.canvas.Chm2DCoordGen_getScale(mol) → float

schrodinger.infra.canvas.Chm2DCoordGen_hasCorrectScale(mol) → bool

schrodinger.infra.canvas.Chm2DCoordGen_initializeMinimizerFromMolecule(min, mol)

schrodinger.infra.canvas.Chm2DCoordGen_isAvailable() → bool

schrodinger.infra.canvas.Chm2DCoordGen_rotate(mol, degrees)

schrodinger.infra.canvas.Chm2DCoordGen_rotateAbout(mol, degrees, center)

schrodinger.infra.canvas.Chm2DCoordGen_sketcherBondStereoFromChmBond(chmBond, bond) → sketcherMinimizerBondStereoInfo

schrodinger.infra.canvas.Chm2DCoordGen_sketcherChiralityFromChmChirality(info, atoms) → sketcherMinimizerAtomChiralityInfo

schrodinger.infra.canvas.Chm2DCoordGen_translate(mol, offset)

schrodinger.infra.canvas.Chm2DCoordGen_visibleAtomsAtOrigin(mol) → ChmBitset

class schrodinger.infra.canvas.ChmABProperty

::ChmABProperty

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

key

next()

returns the next ‘this’ object

value

class schrodinger.infra.canvas.ChmAdaptor

::ChmAdaptor

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static calcCategoryTrainList(percent, randSeed, categories, index1based=True) → std::vector< uint,std::allocator< uint > >

calcCategoryTrainList(percent, randSeed, categories) -> std::vector< uint,std::allocator< uint > >

static calcDuplexTrainList(percent, randSeed, activities) → std::vector< size_t,std::allocator< size_t > >

static checkMemory(mem)

static divEqualPortions(responseData, nEqualP, responseCutOffs)

static genRandomNumber(irand)

getExcludedList(freader, stVec, toEnd)

getReport() → ChmModelReporter

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTrainListByPercentage() → std::vector< size_t,std::allocator< size_t > >

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

getVariableNames() → std::vector< std::string,std::allocator< std::string > >

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmAdaptor_calcCategoryTrainList(percent, randSeed, categories) → std::vector< uint,std::allocator< uint > >

schrodinger.infra.canvas.ChmAdaptor_calcDuplexTrainList(percent, randSeed, activities) → std::vector< size_t,std::allocator< size_t > >

schrodinger.infra.canvas.ChmAdaptor_checkMemory(mem)

schrodinger.infra.canvas.ChmAdaptor_divEqualPortions(responseData, nEqualP, responseCutOffs)

schrodinger.infra.canvas.ChmAdaptor_genRandomNumber(irand)

class schrodinger.infra.canvas.ChmAssignments

::ChmIterator< int64 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< long long,std::allocator< long long > > const &

asVector() -> std::vector< long long,std::allocator< long long > >

at(index) → long long &

at(index) -> long long const

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → long long

prev() → long long

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmAtom

::ChmAtom

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

canBeChiral() → bool

chmtostring() → std::string

clone() → ChmAtom

countNeighborsByAtomicNumber(filterBy) → int

debug() → std::string

static dummyAtom() → ChmAtom

findNeighbor(neighbor) → int

firstNeighbor() → ChmAtom

fixBondLength()

flipChirality()

getAtomicNumber() → periodicTable::atomicNumber

getAttachedHydrogens() → ChmAtoms

getBond(index) → ChmBond

getBondCount(wantImplicitHydrogens=False) → int

getBondCount() -> int

getBondTo(otherAtom) → ChmBond

getBonds(wantImplicitHydrogens=False) → ChmBonds

getBonds() -> ChmBonds

getChiralCenters() → ChmAtoms

getChiralDeterminant(atomOrdering, mappedAtomsCount, force3D) → double

getChiralDeterminant(permutation) -> double getChiralDeterminant() -> double

getChiralityInfo() → ChmChiralityInfo

getChiralityType() → ChmChiralityType

getCoords() → ChmPoint

getElementalInfo() → ChmElement

getFormalCharge() → int

getHeavyBondCount() → int

getHeavyBonds() → ChmBonds

getHeavyNeighbors() → ChmAtoms

getHybridization() → ChmAtomHybridization

getHydrogenCount() → int

getImplicitHydrogenCount() → int

getImplicitNeighbors() → ChmAtoms

getInvariant() → AtomicInvariant

getIsotope(specified=None) → int

getIsotope() -> int

getLabel(oneBased=False) → std::string

getLabel() -> std::string

getLonePairCount(considerConjugation=False) → int

getLonePairCount() -> int

getMDLParity() → int

getMol() → ChmMol

getMolIndex() → int

getMolSize() → int

getNeighbors(wantImplicitHydrogens=False, wantExplicitHydrogens=True) → ChmAtoms

getNeighbors(wantImplicitHydrogens=False) -> ChmAtoms getNeighbors() -> ChmAtoms

getNeighborsByAtomicNumber(filterBy) → ChmAtoms

getNeighborsMasked(exclude) → ChmAtoms

getPartialCharge() → float

getRGroup() → int

getReactionAtomIndex() → int

getRingBondCount() → int

getRingSize() → int

getSmilesChirality() → ChmSmilesChirality

getSymbol() → std::string

getSymbolForSMARTS() → std::string

getTotalValence() → int

getUID() → size_t

getUnpairedElectronCount() → uint

getUserData() → int

getVisibleHydrogenCount() → int

getX() → float

getY() → float

getZ() → float

getZeroOrderBondCount() → int

has3DCoords() → bool

hasCommonNeighbor(toCheck, commonNeighbor) → bool

hasCoords() → bool

hasMetallicNeighbor() → bool

hasNeighborOfElementType(an) → bool

hasOnlyWedge() → bool

hasPolarNeighbor() → bool

hasRingNeighbor() → bool

hasSpecifiedIsotope(specified=None) → bool

hasSpecifiedIsotope() -> bool

hasWedge() → bool

isAcid() → bool

isAliphatic() → bool

isAromatic() → bool

isBondedTo(rhs) → bool

isCarbon() → bool

isCarbonyl() → bool

isChiral() → bool

isChiralAttachment() → bool

isConjugated() → bool

isConnectedToAliphaticRing() → bool

isConnectedToAromaticRing() → bool

isConnectedToRing() → bool

isConstrained() → bool

isDegenerateHydrogen() → bool

isDummy() → bool

isEZAttachment() → bool

isEZAttachmentToN() → bool

isEster() → bool

isFixed() → bool

isHalogen() → bool

isHeavy() → bool

isHetero() → bool

isHidden() → bool

isHydrogen(excludeIsotopicVariants=False) → bool

isHydrogen() -> bool

isIgnored() → bool

isImplicit() → bool

isInMol() → bool

isInRing() → bool

isMetal() → int

isNitrogen() → bool

isOxygen() → bool

isPhosphorous() → bool

isPolar() → bool

isPolarHydrogen() → bool

isPyroleN() → bool

isSP() → bool

isSP2() → bool

isSP3() → bool

isSulfur() → bool

isTerminal() → bool

isValid() → bool

isVisible() → bool

isWildcard() → bool

next()

returns the next ‘this’ object

perceiveTetrahedralChirality()

setAtomicNumber(arg2)

setChiralityType(chirality)

setConstrained(on)

setCoords(point)

setCoordsFrom(atom)

setFixed(on)

setFormalCharge(charge)

setHidden(on)

setHybridization(hyb)

setHydrogensHidden(on)

setIgnored(on)

setIsotope(val)

setPartialCharge(charge)

setRGroup(group)

setReactionAtomIndex(rxn)

setSmilesChirality(code)

setSmilesChiralityInfo(info)

setUnpairedElectronCount(unpaired) → uint

setUserData(data)

setVisibility(arg2) → bool

setXYZ(x, y, z)

testVisibility(arg2) → bool

validateChirality()

wedgeCount() → int

class schrodinger.infra.canvas.ChmAtomHybridizationTyper

::ChmAtomHybridizationTyper

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, arg3=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomIterator

::ChmIterator< ChmAtom >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmAtom,std::allocator< ChmAtom > > const &

asVector() -> std::vector< ChmAtom,std::allocator< ChmAtom > >

at(index) → ChmAtom

at(index) -> ChmAtom

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmAtom

prev() → ChmAtom

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmAtomOption

::ChmAtomOption

H_All = 8

H_AsIs = -1

H_Chiral = 4

H_Default = 1

H_ExplicitChiral = 5

H_ExplicitOnly = 1

H_ExplicitPolar = 3

H_ExplicitPolarAndChiral = 6

H_Never = 0

H_Polar = 2

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmAtomTyper

::ChmAtomTyper

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperAlogP

::ChmAtomTyperAlogP

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperEstate

::ChmAtomTyperEstate

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getFallOffPower() → int

getMaxPath() → int

getUID() → size_t

getWeights() → std::vector< double,std::allocator< double > > const &

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setParam(maxPath, fallOffPower)

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperEstateBinned

::ChmAtomTyperEstateBinned

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getFallOffPower() → int

getMaxPath() → int

getUID() → size_t

getWeights() → std::vector< double,std::allocator< double > > const &

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setParam(maxPath, fallOffPower)

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperMR

::ChmAtomTyperMR

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperPSA

::ChmAtomTyperPSA

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmAtomTyperPolarMiller

::ChmAtomTyperPolarMiller

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getAtomicPolarizabilities() → std::vector< double,std::allocator< double > >

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

schrodinger.infra.canvas.ChmAtom_dummyAtom() → ChmAtom

class schrodinger.infra.canvas.ChmAtoms

::ChmAtoms

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmAtom,std::allocator< ChmAtom > > const &

asVector() -> std::vector< ChmAtom,std::allocator< ChmAtom > >

at(index) → ChmAtom

at(index) -> ChmAtom

barycenterOf() → ChmPointT< float,true >

centerOf() → ChmPointT< float,true >

centerOf(include) -> ChmPointT< float,true >

chmtostring() → std::string

distanceTo(pt) → float

distanceTo(atom) -> float

getMW() → double

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmAtom

prev() → ChmAtom

rewind()

size() → int

sort()

toBitset() → ChmBitset

class schrodinger.infra.canvas.ChmAtomsAndBonds

::ChmAtomsAndBonds

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atoms

bonds

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmBaseModelReporter

::ChmBaseModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getStatus() → ChmModelStatus

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setStatus(s)

success() → bool

static translateCode(st) → std::string

schrodinger.infra.canvas.ChmBaseModelReporter_translateCode(st) → std::string

class schrodinger.infra.canvas.ChmBayesModelReporter

::ChmBayesModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getStatus() → ChmModelStatus

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTestYObsBins() → std::vector< int,std::allocator< int > >

getTestYPredBins() → std::vector< int,std::allocator< int > >

getTestYPredLabels() → std::vector< std::string,std::allocator< std::string > >

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

getTrainingYObsBins() → std::vector< int,std::allocator< int > >

getTrainingYObsLabels() → std::vector< std::string,std::allocator< std::string > >

getTrainingYPredBins() → std::vector< int,std::allocator< int > >

getTrainingYPredLabels() → std::vector< std::string,std::allocator< std::string > >

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setStatus(s)

setTestYObsBins(bin)

setTestYPredBins(bin)

setTestYPredLabels(labels)

setTrainingYObsBins(bin)

setTrainingYObsLabels(labels)

setTrainingYPredBins(bin)

setTrainingYPredLabels(labels)

success() → bool

static translateCode(st) → std::string

class schrodinger.infra.canvas.ChmBitComparable32

::ChmBitComparable< uint >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

count() → uint64

countCommonOff(rhs) → uint64

countCommonOn(rhs) → uint64

countDifference(rhs) → uint64

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

getType() → int

next()

returns the next ‘this’ object

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

class schrodinger.infra.canvas.ChmBitComparable64

::ChmBitComparable< uint64 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

count() → uint64

countCommonOff(rhs) → uint64

countCommonOn(rhs) → uint64

countDifference(rhs) → uint64

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

getType() → int

next()

returns the next ‘this’ object

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

class schrodinger.infra.canvas.ChmBitset

::ChmBitset

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__() → uint64

all() → bool

any() → bool

append()

appends another ‘this’ object

blockReverse()

chmtostring() → std::string

clear()

clear(index)

compare(rhs) → int

contains(rhs) → bool

count() → uint64

countCommonOff(rhs) → uint64

countCommonOff(rhs) -> uint64

countCommonOn(rhs) → uint64

countCommonOn(rhs) -> uint64

countDifference(rhs) → uint64

countDifference(rhs) -> uint64

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

empty() → bool

flip()

flip(index)

static fromBinary(onesAndZeros) → ChmBitset

static fromBlob(raw) → ChmBitset

get(index) → bool

getHash() → uint

getHash64() → uint64

getType() → int

getWord(index) → uint &

hasDifference(rhs) → bool

intersects(rhs) → bool

isContainedBy(rhs) → bool

isSubsetOf(rhs) → bool

next()

returns the next ‘this’ object

none() → bool

physicalSize() → size_t

reserve(blocks)

resize(logicalSize)

reverse()

set()

set(index) set(index, on)

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

store(inputStream)

storeRaw(inputStream)

swap(rhs)

toBitString() → std::string

toBlob() → std::string

toHexString() → std::string

toHexString(arg2)

toMmbs(base=1) → int

toMmbs() -> int

toString(oneBased=False, wantCounts=False) → std::string

toString(oneBased=False) -> std::string toString() -> std::string

toVector(oneBased=False) → std::vector< uint,std::allocator< uint > >

toVector() -> std::vector< uint,std::allocator< uint > > toVector(dest) toVector(dest)

class schrodinger.infra.canvas.ChmBitset64

::ChmBitset64

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__() → uint64

all() → bool

any() → bool

append()

appends another ‘this’ object

blockReverse()

chmtostring() → std::string

clear()

clear(index)

compare(rhs) → int

contains(rhs) → bool

count() → uint64

countCommonOff(rhs) → uint64

countCommonOff(rhs) -> uint64

countCommonOn(rhs) → uint64

countCommonOn(rhs) -> uint64

countDifference(rhs) → uint64

countDifference(rhs) -> uint64

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

flip()

flip(index)

static fromBinary(onesAndZeros) → ChmBitset64

static fromBlob(raw) → ChmBitset64

static fromHex(hexstring) → ChmBitset64

fromHex(hexstring, len) -> ChmBitset64

get(index) → bool

getHash() → uint

getHash64() → uint64

getType() → int

getWord(index) → uint64 &

hasDifference(rhs) → bool

intersects(rhs) → bool

isContainedBy(rhs) → bool

isSubsetOf(rhs) → bool

next()

returns the next ‘this’ object

none() → bool

physicalSize() → size_t

reserve(blocks)

resize(logicalSize)

reverse()

set()

set(index) set(index, on)

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

store(outputStream)

storeRaw(outputStream)

swap(rhs)

toBitString() → std::string

toBlob() → std::string

toHexString() → std::string

toHexString(arg2)

toString(oneBased=False, wantCounts=False) → std::string

toString(oneBased=False) -> std::string toString() -> std::string

toVector(oneBased=False) → std::vector< uint64,std::allocator< uint64 > >

toVector() -> std::vector< uint64,std::allocator< uint64 > > toVector(dest, oneBased=False) toVector(dest)

schrodinger.infra.canvas.ChmBitset64_fromBinary(onesAndZeros) → ChmBitset64

schrodinger.infra.canvas.ChmBitset64_fromBlob(raw) → ChmBitset64

schrodinger.infra.canvas.ChmBitset64_fromHex(hexstring, len) → ChmBitset64

class schrodinger.infra.canvas.ChmBitsetIterator

::ChmIterator< ChmBitset >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → ChmBitsetVector

asVector() -> ChmBitsetVector

at(index) → ChmBitset

at(index) -> ChmBitset

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmBitset

prev() → ChmBitset

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmBitsetVector

std::vector< ChmBitset >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append(x)

assign(n, x)

back() → ChmBitset

begin() → std::vector< ChmBitset >::iterator

capacity() → std::vector< ChmBitset >::size_type

clear()

empty() → bool

end() → std::vector< ChmBitset >::iterator

erase(pos) → std::vector< ChmBitset >::iterator

erase(first, last) -> std::vector< ChmBitset >::iterator

front() → ChmBitset

get_allocator() → std::vector< ChmBitset >::allocator_type

insert(pos, x) → std::vector< ChmBitset >::iterator

insert(pos, n, x)

iterator() → SwigPyIterator

next()

returns the next ‘this’ object

pop() → ChmBitset

pop_back()

push_back(x)

rbegin() → std::vector< ChmBitset >::reverse_iterator

rend() → std::vector< ChmBitset >::reverse_iterator

reserve(n)

resize(new_size)

resize(new_size, x)

size() → std::vector< ChmBitset >::size_type

swap(v)

schrodinger.infra.canvas.ChmBitset_fromBinary(onesAndZeros) → ChmBitset

schrodinger.infra.canvas.ChmBitset_fromBlob(raw) → ChmBitset

class schrodinger.infra.canvas.ChmBond

::ChmBond

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atom1() → ChmAtom

atom2() → ChmAtom

chmtostring() → std::string

clearBondDirectionHint()

directionDown = 6

directionNone = 0

directionUp = 1

flipBondDirectionHint()

getBondDirectionHint() → ChmBond::bondDirectionHint

getBondLength() → float

getCis(atomIndex1, atomIndex4)

getMaeOrder() → int

getMolIndex() → int

getMolSize() → int

getOrder() → ChmBondOrder

getRingSize() → int

getStereo() → ChmBondStereo

getStereoDeterminant(externalOrder, f1, f2, f3, f4) → double

getSymbolForSMARTS() → std::string

getTrans(atomIndex1, atomIndex4)

getUserData() → int

hasBondDirectionHint() → bool

idealLength() → double

isAromatic() → bool

isChiral() → bool

isConjugated() → bool

isDouble() → bool

isDown() → bool

isHidden() → bool

isInRing() → bool

isRotatable() → bool

isSingle() → bool

isStereo() → bool

isTerminal() → bool

isTriple() → bool

isUp() → bool

isVisible() → bool

mate(reference) → ChmAtom

next()

returns the next ‘this’ object

noHint = 15

otherAtom(reference) → ChmAtom

setBondDirectionHint(hint)

setCis(atomIndex1, atomIndex4)

setCis(atom1, atom4)

setOrder(arg2)

setRingSize(arg2)

setStereo(arg2)

setTrans(atomIndex1, atomIndex4)

setTrans(atom1, atom4)

setUserData(data)

validateStereo()

class schrodinger.infra.canvas.ChmBondIterator

::ChmIterator< ChmBond >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmBond,std::allocator< ChmBond > > const &

asVector() -> std::vector< ChmBond,std::allocator< ChmBond > >

at(index) → ChmBond

at(index) -> ChmBond

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmBond

prev() → ChmBond

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmBonds

::ChmBonds

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmBond,std::allocator< ChmBond > > const &

asVector() -> std::vector< ChmBond,std::allocator< ChmBond > >

at(index) → ChmBond

at(index) -> ChmBond

bondsToAtoms() → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmBond

prev() → ChmBond

rewind()

size() → int

sort()

toBitset() → ChmBitset

class schrodinger.infra.canvas.ChmCSVBinaryOut

::ChmCSVBinaryOut

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

static parseHeader(items, binPref) → ChmSparseBitset

parseHeader(items) -> ChmSparseBitset

static parseHeader64(items, binPref) → ChmSparseBitset64

parseHeader64(items) -> ChmSparseBitset64

schrodinger.infra.canvas.ChmCSVBinaryOut_parseHeader(items) → ChmSparseBitset

schrodinger.infra.canvas.ChmCSVBinaryOut_parseHeader64(items) → ChmSparseBitset64

class schrodinger.infra.canvas.ChmCSVDataChecker

::ChmCSVDataChecker

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

hasRepeats(filename, filter, nameColIndex, dem, hasHeader=True) → bool

hasRepeats(filename, filter, nameColIndex, dem) -> bool hasRepeats(filename, filter, nameColIndex) -> bool

hasRepeatsColumn(filename, filter, colIndex, dem, hasHeader=True) → bool

hasRepeatsColumn(filename, filter, colIndex, dem) -> bool hasRepeatsColumn(filename, filter, colIndex) -> bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmCSVFileLineReader

::ChmCSVFileLineReader

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

close()

directorySeparator = '/'

getCumulativeLinesRead() → uint64

getFilename() → std::string const &

getLastPos() → uint64

getLineNumber() → uint64

getPos() → uint64

getStream() → std::istream &

hasNextLine() → bool

static isCompressedFileName(filename) → bool

static isZipped(filename) → bool

next()

returns the next ‘this’ object

nextLine() → std::string

nextLine(line)

open(filename, isZipped=False)

open(filename)

peekNextLine(line) → bool

reset()

rewind()

seekg(pos)

setPos(pos)

tellg() → uint64

totalBytes() → uint64

class schrodinger.infra.canvas.ChmCSVFormatIn

::ChmCSVFormatIn

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

format(str, wasQuoted=None) → std::string

format(str) -> std::string

next()

returns the next ‘this’ object

tokenize(line, nTokenExp=0, quotes=None) → std::vector< std::string,std::allocator< std::string > >

tokenize(line, nTokenExp=0) -> std::vector< std::string,std::allocator< std::string > > tokenize(line) -> std::vector< std::string,std::allocator< std::string > >

tokenizeFirstN(line, n) → std::vector< std::string,std::allocator< std::string > >

class schrodinger.infra.canvas.ChmCSVFormatOut

::ChmCSVFormatOut

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

format(str, overrideForceQuote=False) → std::string

format(str) -> std::string

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmCheckedAllocate(size, alignment) → void *

schrodinger.infra.canvas.ChmCheckedDeallocate(p, size)

class schrodinger.infra.canvas.ChmChiralityInfo

::ChmChiralityInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atom1

atom2

atomLookingFrom

centralAtom

direction

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmCholesky

::ChmCholesky

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getL() → ChmMatrix< double > const &

isSymPosDefinite() → bool

next()

returns the next ‘this’ object

solve(B) → std::vector< double,std::allocator< double > >

solve(B) -> ChmMatrix< double >

class schrodinger.infra.canvas.ChmClusterGrouper

::ChmClusterGrouper

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

group(source, info_file, out_file, numGroups, skipSingletons, collectDuplicates)

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmColumnUIDFilter

::ChmColumnUIDFilter

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

contains(rhs) → bool

containsKey(key) → bool

count() → uint64

static fromBlob(raw) → ChmRangeUIDFilter

static fromFile(filename) → ChmColumnUIDFilter

getAutoScaleInfo() → std::map< uint64,std::pair< double,double >,std::less< uint64 >,std::allocator< std::pair< uint64 const,std::pair< double,double > > > > const &

getFirstItem() → uint64

getHash() → uint

getOrder() → std::vector< uint64,std::allocator< uint64 > > const *

hasAutoScaleInfo() → bool

hasNext() → bool

isEOF() → bool

isSorted() → bool

logicalSize() → uint64

next() → int64

rewind()

setAutoScaleInfo(info)

store(os)

toBlob() → std::string

toCSV(os)

toFile(filename)

toSQL(os)

toSet(uids)

toUIDS()

schrodinger.infra.canvas.ChmColumnUIDFilter_fromFile(filename) → ChmColumnUIDFilter

class schrodinger.infra.canvas.ChmCombinationOut32

::ChmCombinationOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addDefaultSources()

addSource(source)

addZeros(toAdd)

append()

appends another ‘this’ object

clearAllSources()

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone)

open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmCombinationOut64

::ChmCombinationOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addDefaultSources()

addSource(source)

addZeros(toAdd)

append()

appends another ‘this’ object

clearAllSources()

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone)

open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmCompressedBitset

::ChmCompressedBitset

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

bitwiseAnd(rhs, wantPopulationCount) → ChmCompressedBitset

bitwiseNot() → ChmCompressedBitset

bitwiseOr(rhs, wantPopulationCount) → ChmCompressedBitset

bitwiseXor(rhs, wantPopulationCount) → ChmCompressedBitset

chmtostring() → std::string

count() → uint64

countCommonOff(rhs) → uint64

countCommonOff(rhs) -> uint64

countCommonOn(rhs) → uint64

countCommonOn(rhs) -> uint64

countDifference(rhs) → uint64

countDifference(rhs) -> uint64

defaultLogicalSize = -1

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

static fromString(idstring) → ChmCompressedBitset

getCompressionRatio() → float

getCompressionWithHeader() → float

getHash() → uint

getHash64() → uint64

getStorage() → size_t

getType() → int

getUncompressedStorage() → uint64

isWordAligned() → bool

next()

returns the next ‘this’ object

redoCount() → uint

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

store(sdata)

store(outputStream, extra=True) store(outputStream) store(os)

swap(rhs)

toBitString() → std::string

toBitset() → ChmBitset

toSet(hits)

toString() → std::string

toString(outputStream)

toVector() → std::vector< uint,std::allocator< uint > >

toVector(hits)

class schrodinger.infra.canvas.ChmCompressedBitset64

::ChmCompressedBitset64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

bitwiseAnd(rhs, wantPopulationCount) → ChmCompressedBitset64

bitwiseNot() → ChmCompressedBitset64

bitwiseOr(rhs, wantPopulationCount) → ChmCompressedBitset64

bitwiseXor(rhs, wantPopulationCount) → ChmCompressedBitset64

chmtostring() → std::string

count() → uint64

countCommonOff(rhs) → uint64

countCommonOff(rhs) -> uint64

countCommonOn(rhs) → uint64

countCommonOn(rhs) -> uint64

countDifference(rhs) → uint64

countDifference(rhs) -> uint64

defaultLogicalSize = -66

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

static fromString(idstring) → ChmCompressedBitset64

getCompressionRatio() → float

getCompressionWithHeader() → float

getHash() → uint

getHash64() → uint64

getStorage() → uint64

getType() → int

getUncompressedStorage() → uint64

isWordAligned() → bool

next()

returns the next ‘this’ object

redoCount() → uint64

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

store(sdata)

store(outputStream, extra=True) store(outputStream) store(os)

swap(rhs)

toBitString() → std::string

toSet(hits)

toString() → std::string

toString(outputStream)

toVector() → std::vector< uint64,std::allocator< uint64 > >

toVector(hits)

schrodinger.infra.canvas.ChmCompressedBitset64_fromString(idstring) → ChmCompressedBitset64

class schrodinger.infra.canvas.ChmCompressedBitsetIterator

::ChmCompressedBitsetIterator

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

hasNext() → bool

next() → uint

rewind()

class schrodinger.infra.canvas.ChmCompressedBitsetIterator64

::ChmCompressedBitsetIterator64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

hasNext() → bool

next() → uint64

rewind()

class schrodinger.infra.canvas.ChmCompressedBitsetWordIterator

::ChmCompressedBitsetWordIterator

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

finishWord()

getRepeatLength() → uint

hasNext() → bool

isFill() → bool

isOneFill() → bool

isZeroFill() → bool

next() → uint

rewind()

skip(n)

class schrodinger.infra.canvas.ChmCompressedBitsetWordIterator64

::ChmCompressedBitsetWordIterator64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

finishWord()

getRepeatLength() → uint64

hasNext() → bool

isFill() → bool

isOneFill() → bool

isZeroFill() → bool

next() → uint64

rewind()

skip(n)

schrodinger.infra.canvas.ChmCompressedBitset_fromString(idstring) → ChmCompressedBitset

class schrodinger.infra.canvas.ChmCoordGenOption

::ChmCoordGenOption

Default = 1

NoScaling = 0

Physical = 1

Rendering = 2

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmCouldFileExist(filename) → bool

class schrodinger.infra.canvas.ChmCustomMetric

::ChmCustomMetric

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateMetric(arg2, arg3, arg4, arg5) → double

isSimilarity() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmCustomOut32

::ChmCustomOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(bs, id)

write(bs, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmCustomOut64

::ChmCustomOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(bs, id)

write(bs, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmDbcs

::ChmDbcs

DBCSInit_DISE = 4

DBCSInit_DISE_FAST = 5

DBCSInit_Dissimilar = 2

DBCSInit_First = 3

DBCSInit_PredeterminedSet = 6

DBCSInit_Random = 0

DBCSInit_Representative = 1

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getSubset() → std::vector< std::pair< std::string,float >,std::allocator< std::pair< std::string,float > > > const &

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmDbcsScore

::ChmDbcsScore

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

execute(a_subset, a_pool, score) → uint

next()

returns the next ‘this’ object

source(pwm)

class schrodinger.infra.canvas.ChmDbcsScoreMaxMin

::ChmDbcsScoreMaxMin

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

execute(a_subset, a_pool, score) → uint

next()

returns the next ‘this’ object

source(pwm)

class schrodinger.infra.canvas.ChmDbcsScoreMaxSum

::ChmDbcsScoreMaxSum

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

execute(a_subset, a_pool, score) → uint

next()

returns the next ‘this’ object

source(pwm)

class schrodinger.infra.canvas.ChmDelimitedPatterns

::ChmDelimitedPatterns

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateBitCount() → uint

calculateColumnCount() → uint

calculateRowCount() → uint

close()

getAllColNames() → std::vector< std::string,std::allocator< std::string > >

getBitMask() → ChmBitset

getColMask() → ChmBitset

getColumnName(index) → std::string

static getDelimiter(filename) → char

static getDelimiterAndQualifier(filename) → std::pair< char,char >

getFilename() → std::string const &

getHeaderLine() → std::string

getIncludedColIndexes() → std::vector< size_t,std::allocator< size_t > >

getIncludedColNames() → std::vector< std::string,std::allocator< std::string > >

getIncludedCols() → int

getIndex(field) → int

getIndexWithinSelection(field) → int

getLastLine() → std::string

getNumericalColNames() → std::vector< std::string,std::allocator< std::string > >

getObsColumnAsDoubles() → std::vector< double,std::allocator< double > >

getObservationIncludedIndex() → size_t

getObservationIndex() → size_t

getObservationName() → std::string

getRowMask() → ChmBitset

getTotalCols() → int

getValuesOfColumn(index, values)

hasHeader() → bool

hasNext() → bool

isBinaryColumn(index, onBits) → bool

isNumericalCol(index) → bool

next()

returns the next ‘this’ object

nextPattern() → ChmPattern

numericalCols() → size_t

rewind()

setBitMask(mask)

setColMask(mask)

setObservationName(name)

setRowMask(mask)

skip()

schrodinger.infra.canvas.ChmDelimitedPatterns_getDelimiter(filename) → char

schrodinger.infra.canvas.ChmDelimitedPatterns_getDelimiterAndQualifier(filename) → std::pair< char,char >

class schrodinger.infra.canvas.ChmDendriticOut32

::ChmDendriticOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getMaxPath() → int

getMaxSpan() → int

getMinPath() → int

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

setMaxPath(maxPath_)

setMaxSpan(maxSpan_)

setMinPath(minPath_)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmDendriticOut64

::ChmDendriticOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getMaxPath() → int

getMaxSpan() → int

getMinPath() → int

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

setMaxPath(maxPath_)

setMaxSpan(maxSpan_)

setMinPath(minPath_)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmDenseFPIn

::ChmDenseFPIn

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getPos() → ChmDenseFPIn::OFFSET_TYPE

getTypeInfo() → std::string const &

hasNext() → bool

next() → ChmBitset

rewind()

setPos(pos)

class schrodinger.infra.canvas.ChmDenseFPOut

::ChmDenseFPOut

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

close()

getCurrentRowCount() → uint

next()

returns the next ‘this’ object

open(filename, logicalSize, params)

write(bs)

write(bs, id)

class schrodinger.infra.canvas.ChmDescriptorInfo

::ChmDescriptorInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

getDriver() → std::string

getRole() → std::string

m_longname

m_role

m_shortname

m_source

next()

returns the next ‘this’ object

roleFP = 3

roleUnknown = 0

roleX = 2

roleY = 1

class schrodinger.infra.canvas.ChmDescriptorMarshaler

::ChmDescriptorMarshaler

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getCanvasDescriptorsSwitch() → std::string

marshal(testMode=False) → std::string

marshal() -> std::string

next()

returns the next ‘this’ object

writeCfgFile(file) → bool

class schrodinger.infra.canvas.ChmDescriptorSourceMapper

::ChmDescriptorSourceMapper

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

canvasFPGen = 3

canvasMolDescriptors = 1

static getInfo(name) → ChmDescriptorInfo

static getInfoAll(names) → std::vector< ChmDescriptorInfo,std::allocator< ChmDescriptorInfo > >

mopac = 5

next()

returns the next ‘this’ object

qikprop = 4

static sourceToString(arg1) → std::string

sourceUnknown = 0

topo = 2

schrodinger.infra.canvas.ChmDescriptorSourceMapper_getInfo(name) → ChmDescriptorInfo

schrodinger.infra.canvas.ChmDescriptorSourceMapper_getInfoAll(names) → std::vector< ChmDescriptorInfo,std::allocator< ChmDescriptorInfo > >

schrodinger.infra.canvas.ChmDescriptorSourceMapper_sourceToString(arg2) → std::string

schrodinger.infra.canvas.ChmDirIsWriteable(dir) → bool

class schrodinger.infra.canvas.ChmEmptyFileMonitor

::ChmEmptyFileMonitor

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addFile(fileToMonitor)

append()

appends another ‘this’ object

clear()

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmEmptyFileMonitorRecord

::ChmEmptyFileMonitorRecord

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmEstateDescriptors

::ChmEstateDescriptors

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllEstates() → std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

getAllKeys() → std::vector< std::string,std::allocator< std::string > >

getAllKeysSortedByValue() → std::vector< std::string,std::allocator< std::string > >

getAllPossibleAssignments() → ChmValueAssignmentIterator

getAverage(mol, maxPath, fallOffPower, wantImpH=False) → std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

getAverage(mol, maxPath, fallOffPower) -> std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

getFallOffPower() → int

getKeyBool(mol, wantImplicitH=False) → std::map< std::string,bool,std::less< std::string >,std::allocator< std::pair< std::string const,bool > > >

getKeyBool(mol) -> std::map< std::string,bool,std::less< std::string >,std::allocator< std::pair< std::string const,bool > > >

getKeyCount(mol, wantImpH=False) → std::map< std::string,uint,std::less< std::string >,std::allocator< std::pair< std::string const,uint > > >

getKeyCount(mol) -> std::map< std::string,uint,std::less< std::string >,std::allocator< std::pair< std::string const,uint > > >

getMaxPath() → int

getSum(mol, maxPath, fallOffPower, wantImpH=False) → std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

getSum(mol, maxPath, fallOffPower) -> std::map< std::string,double,std::less< std::string >,std::allocator< std::pair< std::string const,double > > >

getUID() → size_t

getWeights() → std::vector< double,std::allocator< double > > const &

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setParam(maxPath, fallOffPower)

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmEstateKey

::ChmEstateKey

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

refNum

style

value

class schrodinger.infra.canvas.ChmEstateKeyGenerator

::ChmEstateKeyGenerator

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getFallOffPower() → int

getKeys(mol, wantImplicitHydrogens=False) → std::vector< ChmEstateKey,std::allocator< ChmEstateKey > >

getKeys(mol) -> std::vector< ChmEstateKey,std::allocator< ChmEstateKey > >

getMaxPath() → int

getUID() → size_t

getWeights() → std::vector< double,std::allocator< double > > const &

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setParam(maxPath, fallOffPower)

setRules(rulesString)

setRulesFile(rulesFile)

type(mol, wantImplicitHydrogens=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

exception schrodinger.infra.canvas.ChmException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.infra.canvas.ChmFPCombiner

::ChmFPCombiner

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addFile(fileName)

append()

appends another ‘this’ object

clearFiles()

combine(outputFileName, compress=False, cat=False)

combine(outputFileName, compress=False) combine(outputFileName)

combineInOrder(outputFileName, endToEnd=False, compress=False)

combineInOrder(outputFileName, endToEnd=False) combineInOrder(outputFileName)

deleteFiles()

isUnfiltered() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmFPCombiner64

::ChmFPCombiner64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addFile(fileName)

append()

appends another ‘this’ object

clearFiles()

combine(outputFileName, compress=False, cat=False)

combine(outputFileName, compress=False) combine(outputFileName)

combineInOrder(outputFileName, endToEnd=False, compress=False)

combineInOrder(outputFileName, endToEnd=False) combineInOrder(outputFileName)

deleteFiles()

isUnfiltered() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmFPIn32

::ChmFPIn< ChmSparseBitset >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

copyTo(dest)

decoder() → ChmFPDecode const &

filter(minFreq, maxFreq, maxBits, reduceBits)

getCounts() → std::vector< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,ChmFPIn< ChmSparseBitset >::POS_TYPE >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,ChmFPIn< ChmSparseBitset >::POS_TYPE > > > const &

getCovariance(covar, means)

getCovarianceofTranspose(covar, means)

getDisplayTypeInfo() → std::string

getExtraColumnNames() → std::vector< std::string,std::allocator< std::string > > const &

getFilename() → std::string

getFrequencyHash() → uint64

getInvariantBits() → ChmSparseBitset

getMapping(key) → ChmFPIn< ChmSparseBitset >::KEY_TYPE

getMatrix(unionData)

getOnBits() → ChmSparseBitset

getPos() → ChmFPIn< ChmSparseBitset >::OFFSET_TYPE

getPositionsByBitCount(posCount)

getRequired() → ChmSparseBitset

getRowCount() → ChmFPIn< ChmSparseBitset >::COUNT_TYPE

getRowNames() → std::vector< std::string,std::allocator< std::string > >

getScaledCovariance(covar, means, scalingFactors, tolerance)

getScaledCovarianceofTranspose(covar, means, scalingFactors, tolerance)

getTypeInfo() → std::string

getTypeInfoEx() → ChmFPTypeInfo

getUnionCount() → ChmFPIn< ChmSparseBitset >::COUNT_TYPE

getValues() → std::vector< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double > > > const &

getVariances() → std::vector< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset >::KEY_TYPE,double > > >

hasNext() → bool

static isCorrectPrecision(filename) → bool

next() → ChmSparseBitset

nextExtra() → ChmSparseBitset

nextReduced() → ChmBitset

nextReducedExtra() → ChmBitset

nextReducedValues() → std::vector< float,std::allocator< float > >

nextReducedValuesExtra() → std::vector< float,std::allocator< float > >

rewind()

setPos(pos)

shannonEntropy() → double

schrodinger.infra.canvas.ChmFPIn32_isCorrectPrecision(filename) → bool

class schrodinger.infra.canvas.ChmFPIn64

::ChmFPIn< ChmSparseBitset64 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

copyTo(dest)

decoder() → ChmFPDecode const &

filter(minFreq, maxFreq, maxBits, reduceBits)

getCounts() → std::vector< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,ChmFPIn< ChmSparseBitset64 >::POS_TYPE >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,ChmFPIn< ChmSparseBitset64 >::POS_TYPE > > > const &

getCovariance(covar, means)

getCovarianceofTranspose(covar, means)

getDisplayTypeInfo() → std::string

getExtraColumnNames() → std::vector< std::string,std::allocator< std::string > > const &

getFilename() → std::string

getFrequencyHash() → uint64

getInvariantBits() → ChmSparseBitset64

getMapping(key) → ChmFPIn< ChmSparseBitset64 >::KEY_TYPE

getMatrix(unionData)

getOnBits() → ChmSparseBitset64

getPos() → ChmFPIn< ChmSparseBitset64 >::OFFSET_TYPE

getPositionsByBitCount(posCount)

getRequired() → ChmSparseBitset64

getRowCount() → ChmFPIn< ChmSparseBitset64 >::COUNT_TYPE

getRowNames() → std::vector< std::string,std::allocator< std::string > >

getScaledCovariance(covar, means, scalingFactors, tolerance)

getScaledCovarianceofTranspose(covar, means, scalingFactors, tolerance)

getTypeInfo() → std::string

getTypeInfoEx() → ChmFPTypeInfo

getUnionCount() → ChmFPIn< ChmSparseBitset64 >::COUNT_TYPE

getValues() → std::vector< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double > > > const &

getVariances() → std::vector< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double >,std::allocator< std::pair< ChmFPIn< ChmSparseBitset64 >::KEY_TYPE,double > > >

hasNext() → bool

static isCorrectPrecision(filename) → bool

next() → ChmSparseBitset64

nextExtra() → ChmSparseBitset64

nextReduced() → ChmBitset

nextReducedExtra() → ChmBitset

nextReducedValues() → std::vector< float,std::allocator< float > >

nextReducedValuesExtra() → std::vector< float,std::allocator< float > >

rewind()

setPos(pos)

shannonEntropy() → double

schrodinger.infra.canvas.ChmFPIn64_isCorrectPrecision(filename) → bool

class schrodinger.infra.canvas.ChmFPMap32

::ChmFPMap< ChmSparseBitset >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

customize()

filter(requiredAtoms, requiredCnt=1) → ChmSparseBitset

filter(requiredAtoms) -> ChmSparseBitset

getAtomsMaskForCode(hashCode) → ChmBitsetVector

getBondsMaskForCode(hashCode) → ChmBitsetVector

getCode(index) → ChmFPMap< ChmSparseBitset >::key_type

getCodeCount() → uint

getCodeForAtom(atomIndex) → ChmFPMap< ChmSparseBitset >::key_type

getItem(index) → ChmFPMapItem32

getItemCount() → uint

getItemsForAtom(atomIndex) → std::vector< ChmFPMapItem< ChmFPMap< ChmSparseBitset >::key_type >,std::allocator< ChmFPMapItem< ChmFPMap< ChmSparseBitset >::key_type > > >

getOnBits() → ChmSparseBitset

getOnBitsCopy() → ChmSparseBitset

getOnBitsCount() → uint

getUniqueItems(uniqueItems)

hasCode(hashCode) → bool

m_atomCount

ChmFPMap<(ChmSparseBitset)>.m_atomCount

m_atomTypingStyle

ChmFPMap<(ChmSparseBitset)>.m_atomTypingStyle

m_bondCount

ChmFPMap<(ChmSparseBitset)>.m_bondCount

m_isSubStructural

ChmFPMap<(ChmSparseBitset)>.m_isSubStructural

m_onBits

ChmFPMap<(ChmSparseBitset)>.m_onBits

m_scaleType

ChmFPMap<(ChmSparseBitset)>.m_scaleType

m_sortedItems

ChmFPMap<(ChmSparseBitset)>.m_sortedItems

makeUniqueCode() → uint64

next()

returns the next ‘this’ object

removeByAtomMask(atoms) → ChmFPMap32

store(arg2)

class schrodinger.infra.canvas.ChmFPMap64

::ChmFPMap< ChmSparseBitset64 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

customize()

filter(requiredAtoms, requiredCnt=1) → ChmSparseBitset64

filter(requiredAtoms) -> ChmSparseBitset64

getAtomsMaskForCode(hashCode) → ChmBitsetVector

getBondsMaskForCode(hashCode) → ChmBitsetVector

getCode(index) → ChmFPMap< ChmSparseBitset64 >::key_type

getCodeCount() → uint

getCodeForAtom(atomIndex) → ChmFPMap< ChmSparseBitset64 >::key_type

getItem(index) → ChmFPMapItem64

getItemCount() → uint

getItemsForAtom(atomIndex) → std::vector< ChmFPMapItem< ChmFPMap< ChmSparseBitset64 >::key_type >,std::allocator< ChmFPMapItem< ChmFPMap< ChmSparseBitset64 >::key_type > > >

getOnBits() → ChmSparseBitset64

getOnBitsCopy() → ChmSparseBitset64

getOnBitsCount() → uint

getUniqueItems(uniqueItems)

hasCode(hashCode) → bool

m_atomCount

ChmFPMap<(ChmSparseBitset64)>.m_atomCount

m_atomTypingStyle

ChmFPMap<(ChmSparseBitset64)>.m_atomTypingStyle

m_bondCount

ChmFPMap<(ChmSparseBitset64)>.m_bondCount

m_isSubStructural

ChmFPMap<(ChmSparseBitset64)>.m_isSubStructural

m_onBits

ChmFPMap<(ChmSparseBitset64)>.m_onBits

m_scaleType

ChmFPMap<(ChmSparseBitset64)>.m_scaleType

m_sortedItems

ChmFPMap<(ChmSparseBitset64)>.m_sortedItems

makeUniqueCode() → uint64

next()

returns the next ‘this’ object

removeByAtomMask(atoms) → ChmFPMap64

store(arg2)

class schrodinger.infra.canvas.ChmFPMapItem32

::ChmFPMapItem< uint >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addItem(atoms, bonds, _atomIndices)

append()

appends another ‘this’ object

chmtostring() → std::string

getAtomAndBondCount() → uint

getAtomCount() → uint

getBondCount() → uint

getItemCount() → uint

getMatchCount() → uint

m_atomCount

ChmFPMapItem<(uint)>.m_atomCount

m_atomIndices

ChmFPMapItem<(uint)>.m_atomIndices

m_atomSize

ChmFPMapItem<(uint)>.m_atomSize

m_atomsThatMatch

ChmFPMapItem<(uint)>.m_atomsThatMatch

m_bondCount

ChmFPMapItem<(uint)>.m_bondCount

m_bondSize

ChmFPMapItem<(uint)>.m_bondSize

m_bondsThatMatch

ChmFPMapItem<(uint)>.m_bondsThatMatch

m_hashCode

ChmFPMapItem<(uint)>.m_hashCode

next()

returns the next ‘this’ object

store(os)

class schrodinger.infra.canvas.ChmFPMapItem64

::ChmFPMapItem< uint64 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addItem(atoms, bonds, _atomIndices)

append()

appends another ‘this’ object

chmtostring() → std::string

getAtomAndBondCount() → uint

getAtomCount() → uint

getBondCount() → uint

getItemCount() → uint

getMatchCount() → uint

m_atomCount

ChmFPMapItem<(uint64)>.m_atomCount

m_atomIndices

ChmFPMapItem<(uint64)>.m_atomIndices

m_atomSize

ChmFPMapItem<(uint64)>.m_atomSize

m_atomsThatMatch

ChmFPMapItem<(uint64)>.m_atomsThatMatch

m_bondCount

ChmFPMapItem<(uint64)>.m_bondCount

m_bondSize

ChmFPMapItem<(uint64)>.m_bondSize

m_bondsThatMatch

ChmFPMapItem<(uint64)>.m_bondsThatMatch

m_hashCode

ChmFPMapItem<(uint64)>.m_hashCode

next()

returns the next ‘this’ object

store(os)

class schrodinger.infra.canvas.ChmFPMapUniqueItem

::ChmFPMapUniqueItem

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

atomAndBondCount() → uint

atomAndBondCount2() → uint

check(rhs) → bool

chmtostring() → std::string

combine(rhs, hits, heavyAtoms, heavyBonds, bonds2atoms) → ChmFPMapUniqueItem

compare(rhs, arg3) → int

static getPercentCommitted() → double

static getTotalMem() → uint64

isRing() → bool

m_atomCount

m_atoms

m_automorphicGroups

m_bondCount

m_bonds

m_code

next()

returns the next ‘this’ object

store(os)

schrodinger.infra.canvas.ChmFPMapUniqueItem_getPercentCommitted() → double

schrodinger.infra.canvas.ChmFPMapUniqueItem_getTotalMem() → uint64

class schrodinger.infra.canvas.ChmFPOut32

::ChmFPOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmFPOut64

::ChmFPOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmFPTypeInfo

::ChmFPTypeInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static areCompatible(fp1, fp2) → bool

static fromFile(fpInfoFile) → ChmFPTypeInfo

getBool(key) → bool

getDalkeHeader() → std::string

getDisplayInfo() → std::string

getDisplayInfoEx() → std::string

getFloat(key) → float

getInt(key) → int

getMaxBits() → uint64

getMaxFreq() → float

getMinFreq() → float

getProp(key, missingOk=False) → std::string

getProp(key) -> std::string

getProps() → std::map< std::string,std::string,std::less< std::string >,std::allocator< std::pair< std::string const,std::string > > > const &

getRightShift() → uint

getScaleType() → FingerprintScaleType

getUID() → int64

hasProp(key) → bool

hasValues() → bool

is32Bit() → bool

is64Bit() → bool

isCompatible(rhs) → bool

isConsistentWith(rhs, ignoreFiltering, ignoreScale) → bool

isCustom() → bool

isCustomType() → bool

isFiltered() → bool

isFilteredOrReduced() → bool

isReduced() → bool

isSupersetOf(rhs) → bool

isValid() → bool

makeTableName() → std::string

makeXORTableName() → std::string

next()

returns the next ‘this’ object

testProp(key, value) → bool

toFPOut() → ChmFPOut32

toFPOut64() → ChmFPOut64

toString() → std::string

schrodinger.infra.canvas.ChmFPTypeInfo_areCompatible(fp1, fp2) → bool

schrodinger.infra.canvas.ChmFPTypeInfo_fromFile(fpInfoFile) → ChmFPTypeInfo

class schrodinger.infra.canvas.ChmFPWrapper

::ChmFPWrapper

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmFastString

::ChmFastString

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

matches(target) → bool

matches(target, positions)

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmFileExists(filename) → bool

schrodinger.infra.canvas.ChmFileIsWriteable(filename) → bool

class schrodinger.infra.canvas.ChmFileLineReader

::ChmFileLineReader

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

close()

directorySeparator = '/'

getCumulativeLinesRead() → uint64

getFilename() → std::string const &

getLastPos() → uint64

getLineNumber() → uint64

getPos() → uint64

getStream() → std::istream &

hasNextLine() → bool

static isCompressedFileName(filename) → bool

static isZipped(filename) → bool

next()

returns the next ‘this’ object

nextLine() → std::string

nextLine(line)

open(filename, isZipped=False)

open(filename)

peekNextLine(line) → bool

reset()

rewind()

seekg(pos)

setPos(pos)

tellg() → uint64

totalBytes() → uint64

schrodinger.infra.canvas.ChmFileLineReader_isCompressedFileName(filename) → bool

schrodinger.infra.canvas.ChmFileLineReader_isZipped(filename) → bool

schrodinger.infra.canvas.ChmFileTruncate(filename) → bool

class schrodinger.infra.canvas.ChmFingerprints

::ChmFingerprints

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static getRGACodes(mol) → ChmSparseBitset

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmFingerprints_getRGACodes(mol) → ChmSparseBitset

class schrodinger.infra.canvas.ChmGasteigerCharge

::ChmGasteigerCharge

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calcGasteigerCharges(arg2, maxIter=7, delta=0.001) → bool

calcGasteigerCharges(arg2, maxIter=7) -> bool calcGasteigerCharges(arg2) -> bool

getAtomTypes() → std::vector< int64,std::allocator< int64 > >

getCharges(includeImplicitH=True) → std::vector< double,std::allocator< double > >

getCharges() -> std::vector< double,std::allocator< double > >

getStepAtomicCharge(atom, iter) → double

getStepAtomicEneg(atom, iter) → double

getTotalIteration() → size_t

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmGenericMolSource

::ChmGenericMolSource

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

advance() → ChmMol

append()

appends another ‘this’ object

getCurrentRecord() → std::string

getLogicalIndex() → uint

goTop()

isDone() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmGetLine(inputstream, line, delimiterFound) → std::istream

ChmGetLine(inputstream, line) -> std::istream &

class schrodinger.infra.canvas.ChmHbond

::ChmHbond

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

assignAcceptors(mol)

assignDonors(mol)

isAcceptor(atomIndex) → bool

isDonor(atomIndex) → bool

isUsingDefaultAcceptorFile() → bool

isUsingDefaultDonorFile() → bool

next()

returns the next ‘this’ object

overrideAcceptorFile(acceptorFile)

overrideDonorFile(donorFile)

printHBADef()

printHBDDef()

class schrodinger.infra.canvas.ChmHierarchicalClustering

::ChmHierarchicalClustering

CompleteLinkage = 2

FlexibleBetaLinkage = 8

GroupAverageLinkage = 3

SchrodingerLinkage = 9

SingleLinkage = 1

UnweightedCentroidLinkage = 4

UseEither = 0

UseLower = 4

UseMaxAB = 2

UseMinAB = 1

UseUpper = 3

WardsMinimumVarianceLinkage = 6

WeightedAverageLinkage = 5

WeightedCentroidLinkage = 7

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

cluster(source, dendrogram_filename, intermediate_info_filename, statistics_filename, arg6, collectDuplicates) → double

cluster(source, dendrogram_filename, grouping_detail_filename, threshold, arg6, collectDuplicates) -> double

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmIndexedFPIn32

::ChmIndexedFPIn< ChmSparseBitset >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

collectKeys(keys)

collectKeysByCount(keysByCount)

getBS(key, bs) → bool

getExtraColumnNames() → std::vector< std::string,std::allocator< std::string > >

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmIndexedFPIn64

::ChmIndexedFPIn< ChmSparseBitset64 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

collectKeys(keys)

collectKeysByCount(keysByCount)

getBS(key, bs) → bool

getExtraColumnNames() → std::vector< std::string,std::allocator< std::string > >

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmKPLSParser

::ChmKPLSParser

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clear()

getAUC(numFactor) → std::string

getCISDAll(numFactor) → std::vector< std::string,std::allocator< std::string > >

getCISDs(numFactor) → std::vector< std::string,std::allocator< std::string > >

getConfidenceIntervals(numFactor) → std::vector< std::string,std::allocator< std::string > >

getFPTypeInfo() → std::string

getMaxFactor() → size_t

getMinFactor() → size_t

getNamesAll() → std::vector< std::string,std::allocator< std::string > >

getNumObsInTrainingTestTotal() → std::vector< int,std::allocator< int > >

getObsAll() → std::vector< std::string,std::allocator< std::string > >

getPredAll(numFactor) → std::vector< std::string,std::allocator< std::string > >

getQsqr(numFactor) → std::string

static getResultsParser(file) → ChmModelParser

getRsqr(numFactor) → std::string

getSD(numFactor) → std::string

getSigma() → double

getTestSetNames() → std::vector< std::string,std::allocator< std::string > >

getTestSetObs() → std::vector< std::string,std::allocator< std::string > >

getTestSetPred(numFactor) → std::vector< std::string,std::allocator< std::string > >

getTestSetRMSE(numFactor) → std::string

getTrainingSetNames() → std::vector< std::string,std::allocator< std::string > >

getTrainingSetObs() → std::vector< std::string,std::allocator< std::string > >

getTrainingSetPred(numFactor) → std::vector< std::string,std::allocator< std::string > >

getVariableNames() → std::vector< std::string,std::allocator< std::string > >

getYvar() → std::string

haveConfidenceInterval() → bool

haveTestSet() → bool

haveTrainingSet() → bool

next()

returns the next ‘this’ object

read(arg2, arg3)

writePredictions(filename, namefield, delim, extraParameter=- 1)

writePredictions(filename, namefield, delim) writePredictions(filename, namefield) writePredictions(filename)

class schrodinger.infra.canvas.ChmLU

::ChmLU

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

det() → double

getL() → ChmMatrix< double >

getPivot() → std::vector< int,std::allocator< int > > const &

getU() → ChmMatrix< double >

isSingular() → bool

next()

returns the next ‘this’ object

solve(B) → ChmMatrix< double >

solve(b) -> std::vector< double,std::allocator< double > >

class schrodinger.infra.canvas.ChmLicenseAutoQsar

::ChmLicenseAutoQsar

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmLicenseAutoQsar_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseElements

::ChmLicenseElements

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmLicenseElementsOrFull

::ChmLicenseElementsOrFull

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmLicenseElements_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseFull

::ChmLicenseFull

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmLicenseFullOrMain

::ChmLicenseFullOrMain

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmLicenseFull_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseMain

::ChmLicenseMain

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

reset()

schrodinger.infra.canvas.ChmLicenseMain_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseMatSci

::ChmLicenseMatSci

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmLicenseMatSci_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseShared

::ChmLicenseShared

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmLicenseShared_isValid() → bool

class schrodinger.infra.canvas.ChmLicenseXCluster

::ChmLicenseXCluster

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getType() → canvasLicenseType

static isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmLicenseXCluster_isValid() → bool

class schrodinger.infra.canvas.ChmLinearOut32

::ChmLinearOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getHalfStep() → bool

getMaxPath() → int

getMaxRingPath() → int

getMinPath() → int

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

setHalfStep(halfstep)

setMaxPath(maxPath_)

setMaxRingPath(maxRingPath_)

setMinPath(minPath_)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmLinearOut64

::ChmLinearOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getHalfStep() → bool

getMaxPath() → int

getMaxRingPath() → int

getMinPath() → int

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

setHalfStep(halfstep)

setMaxPath(maxPath_)

setMaxRingPath(maxRingPath_)

setMinPath(minPath_)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmMCSLicense

::ChmMCSLicense

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmMCSRecord

::ChmMCSRecord

DetailBitset = 1

DetailMapping = 2

DetailNone = 0

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

abCount

append()

appends another ‘this’ object

atomCount

atoms

bondCount

bonds

code

containmentGroup

fepNoRingBreak = 1

fepNone = 0

fepRingBreak = 2

findInvalidAtomsAndBonds(mol) → std::pair< ChmBitset,ChmBitset >

fixInvalidAtomsAndBonds(mol, atomPositionsToRemove, bondPositionsToRemove)

m_score

mapAtoms

mapBonds

markMappedAtomsAndBonds(mol)

mcsSmarts

molCount

molID

molSMILES

next()

returns the next ‘this’ object

page

policy

printCSVHeader(os, outputDelim)

printCSVProperties(os, mol, outputDelim, oneBased, wantUniqueSMILES)

printPWHeader(os, outputDelim)

score() → double

setAsMaeProperties(ctHandle, molTitle, colorInt)

setAsSDProperties(mol)

weight() → double

wscore() → double

class schrodinger.infra.canvas.ChmMLRModelReporter

::ChmMLRModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getPearsonCorr() → double

getQSQR() → double

getRSQR() → double

getRegB() → std::vector< double,std::allocator< double > >

getRegBSE() → std::vector< double,std::allocator< double > >

getRegF() → double

getRegP() → double

getRegSD() → double

getRegVarNames() → std::vector< std::string,std::allocator< std::string > >

getStatus() → ChmModelStatus

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTestRMSE() → double

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

getTrainingRMSE() → double

getYobsTest() → std::vector< double,std::allocator< double > >

getYobsTestOK() → std::vector< bool,std::allocator< bool > >

getYobsTraining() → std::vector< double,std::allocator< double > >

getYpredTaining() → std::vector< double,std::allocator< double > >

getYpredTest() → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setPearsonCorr(r)

setQSQR(q)

setRSQR(r)

setRegB(b)

setRegBSE(bse)

setRegF(f)

setRegP(p)

setRegSD(s)

setRegVarNames(names)

setStatus(s)

setTestRMSE(r)

setTrainingRMSE(r)

setYobsTest(obs)

setYobsTestOK(t)

setYobsTraining(obs)

setYpredTaining(pred)

setYpredTest(pred)

success() → bool

static translateCode(st) → std::string

class schrodinger.infra.canvas.ChmMaccsOut32

::ChmMaccsOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmMaccsOut64

::ChmMaccsOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmMatch

::ChmMatch

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getMatchedAtoms() → ChmAtoms

getMatchedAtomsInfo() → SwigChmAtomIntPairVector

getMatchedHeavyAtoms() → ChmAtoms

getReactionIndices() → std::vector< int,std::allocator< int > >

isRelativeStereoMatch() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmMatchEx

::ChmMatchEx

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getMatchedAtomIndices(base=0) → std::vector< int,std::allocator< int > >

getMatchedAtomIndices() -> std::vector< int,std::allocator< int > >

getMatchedAtoms() → ChmAtoms

getMatchedAtomsInfo() → SwigChmAtomIntPairVector

getMatchedBondIndices(base=0) → std::vector< int,std::allocator< int > >

getMatchedBondIndices() -> std::vector< int,std::allocator< int > >

getMatchedBonds() → ChmBonds

getMatchedHeavyAtoms() → ChmAtoms

getMatchedHeavyBonds() → ChmBonds

getReactionIndices() → std::vector< int,std::allocator< int > >

isRelativeStereoMatch() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmMatchExIterator

::ChmIterator< ChmMatchEx >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmMatchEx,std::allocator< ChmMatchEx > > const &

asVector() -> std::vector< ChmMatchEx,std::allocator< ChmMatchEx > >

at(index) → ChmMatchEx

at(index) -> ChmMatchEx

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmMatchEx

prev() → ChmMatchEx

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmMatchIterator

::ChmIterator< ChmMatch >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmMatch,std::allocator< ChmMatch > > const &

asVector() -> std::vector< ChmMatch,std::allocator< ChmMatch > >

at(index) → ChmMatch

at(index) -> ChmMatch

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmMatch

prev() → ChmMatch

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmMatcherData

::ChmMatcherData

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

allowRelative

append()

appends another ‘this’ object

hydrogensInterchangeable

ignoreImplicitHydrogens

limit

mol

next()

returns the next ‘this’ object

query

rigorousValidationOfSource

unique

class schrodinger.infra.canvas.ChmMatches

::ChmMatches

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmMatch,std::allocator< ChmMatch > > const &

asVector() -> std::vector< ChmMatch,std::allocator< ChmMatch > >

at(index) → ChmMatch

at(index) -> ChmMatch

chmtostring() → std::string

filter(atoms) → ChmMatches

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmMatch

prev() → ChmMatch

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmMatchesEx

::ChmMatchesEx

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmMatchEx,std::allocator< ChmMatchEx > > const &

asVector() -> std::vector< ChmMatchEx,std::allocator< ChmMatchEx > >

at(index) → ChmMatchEx

at(index) -> ChmMatchEx

chmtostring() → std::string

filter(atoms) → ChmMatchesEx

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmMatchEx

prev() → ChmMatchEx

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ChmMatrixUnsignedInt

::ChmMatrix< uint >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

autoScale(tolerance=1.0e-24)

autoScale()

base() → unsigned int const *

center()

chmtostring() → std::string

clear()

cols() → uint

doubleCenter()

fastItem(i, j) → unsigned int &

fastReadItem(i, j) → unsigned int const &

fill(value)

getColumnMeans(means)

getColumnMeansAndDeviations(means, stdDeviations)

getCovariance(covariance)

getCovariance(rhs, covariance) getCovariance(covariance, means) getCovariance(covariance, means, scalingFactors, tolerance=1.0e-24) getCovariance(covariance, means, scalingFactors)

getDM(distanceMatrix, lambda1=2, lambda2=0.5)

getDM(distanceMatrix, lambda1=2) getDM(distanceMatrix)

getLaplacian(laplacian)

getLaplacian(laplacian)

getMahalanobisDM(distanceMatrix, lambda1=2, lambda2=0.5) → int

getMahalanobisDM(distanceMatrix, lambda1=2) -> int getMahalanobisDM(distanceMatrix) -> int

getRMSD(rmsd)

getRMSD(rhs, rmsd)

getScaledCovariance(covariance, tolerance=1.0e-24)

getScaledCovariance(covariance) getScaledCovariance(rhs, covariance, tolerance=1.0e-24) getScaledCovariance(rhs, covariance)

getScaledMahalanobisDM(distanceMatrix, lambda1=2, lambda2=0.5, tolerance=1.0e-24) → int

getScaledMahalanobisDM(distanceMatrix, lambda1=2, lambda2=0.5) -> int getScaledMahalanobisDM(distanceMatrix, lambda1=2) -> int getScaledMahalanobisDM(distanceMatrix) -> int

invert()

isSquare() → bool

item(i, j) → unsigned int &

next()

returns the next ‘this’ object

pivot(piv) → ChmMatrixUnsignedInt

pivot(piv, fromIndex, toIndex) -> ChmMatrixUnsignedInt

readItem(i, j) → unsigned int const &

resize(dim)

resize(rows, cols)

rows() → uint

swap(rhs)

transpose() → ChmMatrixUnsignedInt

type() → bool

class schrodinger.infra.canvas.ChmMdlReader

::ChmMdlReader

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

hasNext() → bool

next() → ChmMol

class schrodinger.infra.canvas.ChmMdlWriter

::ChmMdlWriter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

write(mol)

static writeV3(os, mol, echoMaeType)

schrodinger.infra.canvas.ChmMdlWriter_writeV3(os, mol, echoMaeType)

class schrodinger.infra.canvas.ChmMinimalRPParser

::ChmMinimalRPParser

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clear()

static getResultsParser(file) → ChmModelParser

getTestSetNames() → std::vector< std::string,std::allocator< std::string > >

getTrainingSetNames() → std::vector< std::string,std::allocator< std::string > >

m_xvarNames

m_yvarNames

next()

returns the next ‘this’ object

read(arg2, arg3)

writePredictions(filename, namefield, delim, extraParameter=- 1)

writePredictions(filename, namefield, delim) writePredictions(filename, namefield) writePredictions(filename)

class schrodinger.infra.canvas.ChmMmctAdaptor

::ChmMmctAdaptor

NoStereo = 0

StereoFromAnnotation = 3

StereoFromAnnotationAndGeometry = 5

StereoFromAnnotationAndGeometry_Safe = 6

StereoFromAnnotation_Safe = 4

StereoFromGeometry = 1

StereoFromGeometry_Safe = 2

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static applyBondOrdersAndCharges(source, dest)

static calculateSASA(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True, divideByTotalAtomSurfaceArea=False) → double

calculateSASA(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True) -> double calculateSASA(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2) -> double calculateSASA(ctHandle, probeRadiusAngstroms=1.4) -> double calculateSASA(ctHandle) -> double calculateSASA(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False) -> double calculateSASA(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2) -> double calculateSASA(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4) -> double calculateSASA(ctHandle, mmbsSubsetAtoms) -> double calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False) -> double calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2) -> double calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4) -> double calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider) -> double

static calculateSASAByAtom(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True, divideByTotalAtomSurfaceArea=False) → std::vector< double,std::allocator< double > >

calculateSASAByAtom(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, excludeH=True) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, probeRadiusAngstroms=1.4) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtoms, probeRadiusAngstroms=1.4) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtoms) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2, divideByTotalAtomSurfaceArea=False) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4, resolutionAngstroms=0.2) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider, probeRadiusAngstroms=1.4) -> std::vector< double,std::allocator< double > > calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider) -> std::vector< double,std::allocator< double > >

static calculateVolume(ctHandle, gridAngstroms=1.0, excludeH=True) → double

calculateVolume(ctHandle, gridAngstroms=1.0) -> double calculateVolume(ctHandle) -> double

static collectMaeProperties(maefile, props, wantMMStereo, pf)

create(a_ctHandle, a_mol, stereo, hydrogenTreatment, wantProperties=True, wantMMStereoProps=False, readAtomBondProperties=True, allowRadicals=False)

create(a_ctHandle, a_mol, stereo, hydrogenTreatment, wantProperties=True, wantMMStereoProps=False, readAtomBondProperties=True) create(a_ctHandle, a_mol, stereo, hydrogenTreatment, wantProperties=True, wantMMStereoProps=False) create(a_ctHandle, a_mol, stereo, hydrogenTreatment, wantProperties=True) create(a_ctHandle, a_mol, stereo, hydrogenTreatment) create(a_ctHandle, a_mol, stereo) create(a_ctHandle, a_mol) create(a_ctHandle, stereo, hydrogenTreatment, wantProperties=True, wantMMStereoProps=False, readAtomBondProperties=True, allowRadicals=False) -> ChmMol create(a_ctHandle, stereo, hydrogenTreatment, wantProperties=True, wantMMStereoProps=False, readAtomBondProperties=True) -> ChmMol create(a_ctHandle, stereo, hydrogenTreatment, wantProperties=True, wantMMStereoProps=False) -> ChmMol create(a_ctHandle, stereo, hydrogenTreatment, wantProperties=True) -> ChmMol create(a_ctHandle, stereo, hydrogenTreatment) -> ChmMol create(a_ctHandle, stereo) -> ChmMol create(a_ctHandle) -> ChmMol create(a_mol, wantProperties=True, hydrogenTreatment) -> MM_Index create(a_mol, wantProperties=True) -> MM_Index create(a_mol) -> MM_Index

static estimateRecordCount(maefile, scanDepth, isExact) → uint64

getAcyclicBonds(a_ctHandle) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

getAromaticityInfo(a_ctHandle) → std::vector< bool,std::allocator< bool > >

static getComponents(source, mappings) → std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

getComponents(source) -> std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

getRingBonds(a_ctHandle) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

getTitle(maestring) → std::string

kekulize(target) → bool

load(maesource, rf, mols, positions, offset, blockSize, stereo, hydrogenTreatment, wantProperties, wantMMStereoProps, readPartial, fieldAsName, textOnly, decode, wantMolData) → bool

next()

returns the next ‘this’ object

readProperties(a_ctHandle, properties, wantMMStereoProps, decode)

readProperties(maestring, properties, wantMMStereoProps, stripOutProp, decode) -> bool

static safeDelete(ctHandle, warn=False)

safeDelete(ctHandle)

simpleLoad(maefile, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoad(maefile, decode=False) -> std::vector< ChmMol,std::allocator< ChmMol > > simpleLoad(maefile) -> std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilter(maefile, logicalRowFilter, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilter(maefile, logicalRowFilter, decode=False) -> std::vector< ChmMol,std::allocator< ChmMol > > simpleLoadWithFilter(maefile, logicalRowFilter) -> std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilterRegEx(maefile, filter, regularExpressionToMatch, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilterRegEx(maefile, filter, regularExpressionToMatch, decode=False) -> std::vector< ChmMol,std::allocator< ChmMol > > simpleLoadWithFilterRegEx(maefile, filter, regularExpressionToMatch) -> std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilterRegExs(maefile, filter, regularExpressionsToMatch, decode=False, wantEmpty=True) → std::vector< ChmMol,std::allocator< ChmMol > >

simpleLoadWithFilterRegExs(maefile, filter, regularExpressionsToMatch, decode=False) -> std::vector< ChmMol,std::allocator< ChmMol > > simpleLoadWithFilterRegExs(maefile, filter, regularExpressionsToMatch) -> std::vector< ChmMol,std::allocator< ChmMol > >

schrodinger.infra.canvas.ChmMmctAdaptor_applyBondOrdersAndCharges(source, dest)

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASA(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider) → double

schrodinger.infra.canvas.ChmMmctAdaptor_calculateSASAByAtom(ctHandle, mmbsSubsetAtomsCount, mmbsSubsetAtomsConsider) → std::vector< double,std::allocator< double > >

schrodinger.infra.canvas.ChmMmctAdaptor_calculateVolume(ctHandle) → double

schrodinger.infra.canvas.ChmMmctAdaptor_collectMaeProperties(maefile, props, wantMMStereo, pf)

schrodinger.infra.canvas.ChmMmctAdaptor_estimateRecordCount(maefile, scanDepth, isExact) → uint64

schrodinger.infra.canvas.ChmMmctAdaptor_getComponents(source) → std::vector< ChmMMIndex,std::allocator< ChmMMIndex > >

schrodinger.infra.canvas.ChmMmctAdaptor_safeDelete(ctHandle)

class schrodinger.infra.canvas.ChmMmctSmartsMatcher

::ChmMmctSmartsMatcher

MATCH_BUT_EXCLUDE_FROM_ATOM_LIST = 1

NO_MATCH = 0

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getMatchCountLimit() → int

getUniqueFilter() → bool

hasMatch(a_pattern) → bool

hasMatch(query_ctHandle) -> bool

hydrogensInterchangeable_NO = 0

hydrogensInterchangeable_YES = 1

matches(a_pattern) → std::vector< std::vector< uint,std::allocator< uint > >,std::allocator< std::vector< uint,std::allocator< uint > > > >

next()

returns the next ‘this’ object

numMatches(a_pattern) → int

numMatches(query_ctHandle) -> int

setMatchCountLimit(limit)

setUniqueFilter(a_isUnique)

class schrodinger.infra.canvas.ChmMmctSmilesGenerator

::ChmMmctSmilesGenerator

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

canonicalize(smiles) → std::string

getHashCode(a_ctHandle, arg3) → uint

getHashCode(a_ctHandle) -> uint

getHashCode64(a_ctHandle, arg3) → uint64

getHashCode64(a_ctHandle) -> uint64

getSMARTS(a_ctHandle, arg3, arg4, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, wantCharge=True) → std::string

getSMARTS(a_ctHandle, arg3, arg4, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False) -> std::string getSMARTS(a_ctHandle, arg3, arg4, wantStereo=False, wantMapping=False, atomMappings=None) -> std::string getSMARTS(a_ctHandle, arg3, arg4, wantStereo=False, wantMapping=False) -> std::string getSMARTS(a_ctHandle, arg3, arg4, wantStereo=False) -> std::string getSMARTS(a_ctHandle, arg3, arg4) -> std::string getSMARTS(a_ctHandle, arg3) -> std::string getSMARTS(a_ctHandle) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, atomMappings=None) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5, arg6, wantStereo=False) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5, arg6) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5) -> std::string getSMARTS(a_ctHandle, atomInclusionMask, markRings=False) -> std::string

getSmiles(a_ctHandle, arg3, wildCardHeavyAtoms=False) → std::string

getSmiles(a_ctHandle, arg3) -> std::string getSmiles(a_ctHandle) -> std::string

getSmilesAndMap(a_ctHandle, arg4) → std::string

getSmilesAndMap(a_ctHandle) -> std::string

getSubsetSMARTS(a_ctHandle, atomInclusionMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, wantCharge=True) → std::string

getSubsetSMARTS(a_ctHandle, atomInclusionMask) -> std::string

getTautomerCode(a_ctHandle, arg3) → uint

getTautomerCode(a_ctHandle) -> uint

getTautomerCode64(a_ctHandle, arg3) → uint64

getTautomerCode64(a_ctHandle) -> uint64

getUniqueOrder(a_ctHandle) → std::vector< int,std::allocator< int > >

getUniqueSmiles(a_ctHandle, arg3, wildCardHeavyAtoms=False) → std::string

getUniqueSmiles(a_ctHandle, arg3) -> std::string getUniqueSmiles(a_ctHandle) -> std::string

getUniqueSmilesAndMap(a_ctHandle, arg4) → std::string

getUniqueSmilesAndMap(a_ctHandle) -> std::string

neutralize(smiles) → std::string

neutralize2(smiles) → std::string

next()

returns the next ‘this’ object

setCharge(a_val)

setChiral(a_val)

setForceAllBondOrders(a_val)

setForceHydrogens(a_val)

validateSmilesString(smiles) → bool

validateSmilesString(smiles, errorString) -> bool

class schrodinger.infra.canvas.ChmModelParser

::ChmModelParser

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clear()

static getResultsParser(file) → ChmModelParser

getTestSetNames() → std::vector< std::string,std::allocator< std::string > >

getTrainingSetNames() → std::vector< std::string,std::allocator< std::string > >

next()

returns the next ‘this’ object

read(arg2, arg3)

writePredictions(filename, namefield, delim, extraParameter=- 1)

writePredictions(filename, namefield, delim) writePredictions(filename, namefield) writePredictions(filename)

schrodinger.infra.canvas.ChmModelParser_getResultsParser(file) → ChmModelParser

class schrodinger.infra.canvas.ChmModelReporter

::ChmModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getStatus() → ChmModelStatus

m_maxFactor

m_method

m_qsqr

m_rcorr

m_regB

m_regBSE

m_regF

m_regP

m_regSD

m_regStability

m_regVarNames

m_regrsqr

m_regrsqrCv

m_rmsErr_test

m_rmsErr_train

m_testList

m_trainList

m_yobsBinTestBayes

m_yobsBinTrainBayes

m_yobsLabelTestBayes

m_yobsLabelTrainBayes

m_yobsTest

m_yobsTestNnet

m_yobsTestOK

m_yobsTestOKNnet

m_yobsTrain

m_yobsTrainNnet

m_ypredBinTestBayes

m_ypredBinTrainBayes

m_ypredLabelTestBayes

m_ypredLabelTrainBayes

m_ypredTestNnetVec

m_ypredTestVec

m_ypredTrainNnetVec

m_ypredTrainVec

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setStatus(s)

success() → bool

static translateCode(st) → std::string

schrodinger.infra.canvas.ChmModelReporter_translateCode(st) → std::string

class schrodinger.infra.canvas.ChmModelTypeInfo

::ChmModelTypeInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

getChmDescriptorInfo() → std::vector< ChmDescriptorInfo,std::allocator< ChmDescriptorInfo > >

getFP() → std::vector< std::string,std::allocator< std::string > >

getModelType() → ChmModelTypeInfo::modelType

getSource() → std::string

getX() → std::vector< std::string,std::allocator< std::string > >

getY() → std::vector< std::string,std::allocator< std::string > >

modelBayes = 11

modelKPLS = 14

modelMLR = 16

modelMultiKPLS = 15

modelNnet = 13

modelPCAReg = 17

modelPLS = 18

modelRP = 12

modelUnknown = 0

next()

returns the next ‘this’ object

show(testMode=False) → std::string

show() -> std::string

class schrodinger.infra.canvas.ChmMol

::ChmMol

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addAromaticBond(a1, a2)

addAtom(arg2)

addBond(a1, a2, order=Single) → ChmBond

addBond(a1, a2) -> ChmBond

addConformation(arg2)

addDoubleBond(a1, a2, cisTrans=BondNotApplicable)

addDoubleBond(a1, a2)

addMolecule(arg2)

addMoleculeRaw(arg2, arg3)

addSingleBond(a1, a2)

addTripleBond(a1, a2)

addZeroOrderBond(a1, a2)

append()

appends another ‘this’ object

areBonded(atomIndex1, atomIndex2) → bool

atomsAtOrigin() → uint

checkCoords()

checkStereo()

chiralCenters(includeUndefined=False) → int

chiralCenters() -> int

chmtostring() → std::string

cisTransBonds() → int

clear()

clearAllUserData()

clearAtomBondProperties()

clearAtomProperty(atom, key)

clearBondFlags()

clearBondProperty(bond, key)

clearConfs()

clearCoords()

clearProperties()

clone(randomizeNumbering=False, atomsToDiscard=None, raw=False) → ChmMol

clone(randomizeNumbering=False, atomsToDiscard=None) -> ChmMol clone(randomizeNumbering=False) -> ChmMol clone() -> ChmMol

cloneProperties(mol)

deleteProperty(key)

destroyAtom(arg2, packIndices=True)

destroyAtom(arg2) destroyAtom(index, packIndices=True) destroyAtom(index)

destroyBond(bond)

destroyBond(index)

flipBondFlags()

static fromMAE(maeString) → ChmMol

static fromMDL(arg1, autoName=False, validateCisTrans=False, perceiveHybridization=True, rigorousAromaticity=True) → ChmMol

fromMDL(arg1, autoName=False, validateCisTrans=False, perceiveHybridization=True) -> ChmMol fromMDL(arg1, autoName=False, validateCisTrans=False) -> ChmMol fromMDL(arg1, autoName=False) -> ChmMol fromMDL(arg1) -> ChmMol fromMDL(inputstream, autoName=False, validateCisTrans=False, perceiveHybridization=True) -> ChmMol fromMDL(inputstream, autoName=False, validateCisTrans=False) -> ChmMol fromMDL(inputstream, autoName=False) -> ChmMol fromMDL(inputstream) -> ChmMol

static fromSMILES(arg1, autoName=False, validateCisTrans=False, perceiveHybridization=True) → ChmMol

fromSMILES(arg1, autoName=False, validateCisTrans=False) -> ChmMol fromSMILES(arg1, autoName=False) -> ChmMol fromSMILES(arg1) -> ChmMol fromSMILES(inputstream, autoName=False, validateCisTrans=False, perceiveHybridization=True) -> ChmMol fromSMILES(inputstream, autoName=False, validateCisTrans=False) -> ChmMol fromSMILES(inputstream, autoName=False) -> ChmMol fromSMILES(inputstream) -> ChmMol

genCoords()

getAbsoluteChiralityFlag() → bool

getAtom(arg2) → ChmAtom

getAtomCount(wantImplicitHydrogens=False) → int

getAtomCount() -> int

getAtoms(wantImplicitHydrogens=False) → ChmAtoms

getAtoms() -> ChmAtoms

getAtomsByMask(mask) → ChmAtoms

getAtomsForBonds(bonds) → ChmAtoms

getBond(arg2) → ChmBond

getBond(a1, a2) -> ChmBond

getBondCount(wantImplicitHydrogens=False) → int

getBondCount() -> int

getBondFlags(flags, explicitH)

getBondMaskForAtomMask(atomMask) → ChmBitset

getBonds(wantImplicitHydrogens=False) → ChmBonds

getBonds() -> ChmBonds

getBondsByMask(mask) → ChmBonds

getBondsForAtomMask(atomMask) → ChmBonds

getBondsForAtoms(atoms) → ChmBonds

getComponentCount() → uint

getConformation(arg2) → ChmConformation

getConformationCount() → int

getConformations() → ChmConformations

getConnectionTable(wantImplicitHydrogens=False) → ChmSymmetricMatrixUnsignedInt

getConnectionTable() -> ChmSymmetricMatrixUnsignedInt

getConnectionTableWithBondOrders(wantImplicitHydrogens=False, wantMaeOrder=False) → ChmSymmetricMatrixUnsignedInt

getConnectionTableWithBondOrders(wantImplicitHydrogens=False) -> ChmSymmetricMatrixUnsignedInt getConnectionTableWithBondOrders() -> ChmSymmetricMatrixUnsignedInt

getCoordinates(coords)

getDistanceMatrix(wantImplicitHydrogens=False, storeInfiniteDistancesAsZero=True, throwExceptionIfMultipleFragments=False) → ChmSymmetricMatrixUnsignedInt

getDistanceMatrix(wantImplicitHydrogens=False, storeInfiniteDistancesAsZero=True) -> ChmSymmetricMatrixUnsignedInt getDistanceMatrix(wantImplicitHydrogens=False) -> ChmSymmetricMatrixUnsignedInt getDistanceMatrix() -> ChmSymmetricMatrixUnsignedInt

getDistanceMatrix3D(wantImplicitHydrogens=False, wantRoot=True) → ChmSymmetricMatrix< float >

getDistanceMatrix3D(wantImplicitHydrogens=False) -> ChmSymmetricMatrix< float > getDistanceMatrix3D() -> ChmSymmetricMatrix< float >

getDistanceMatrix3D2(wantImplicitHydrogens=False, wantRoot=True) → ChmSymmetricMatrix< double >

getDistanceMatrix3D2(wantImplicitHydrogens=False) -> ChmSymmetricMatrix< double > getDistanceMatrix3D2() -> ChmSymmetricMatrix< double >

getFirstImplicitHydrogenIndex() → int

getHash() → uint

getHash64() → uint64

getHeavyAtomCount() → int

getHeavyAtoms() → ChmAtoms

getHeavyBondCount() → int

getHeavyBonds() → ChmBonds

getHydrogens() → ChmAtoms

getMW() → double

getName() → std::string

getNetCharge() → int

getProperties() → PROPDATA

getPropertiesBegin() → CHMMOLPROPINFO::const_iterator

getPropertiesEnd() → CHMMOLPROPINFO::const_iterator

getPropertiesFor(atom) → std::vector< PROPPAIR,std::allocator< PROPPAIR > >

getPropertiesFor(bond) -> std::vector< PROPPAIR,std::allocator< PROPPAIR > >

getPropertiesForAtom(atomIndex) → std::vector< PROPPAIR,std::allocator< PROPPAIR > >

getPropertiesForBond(bondIndex) → std::vector< PROPPAIR,std::allocator< PROPPAIR > >

getProperty(arg2) → std::string

getPropertyCount() → size_t

getPropertyForAtom(arg2, arg3) → std::string

getPropertyForBond(arg2, arg3) → std::string

getRingCount(deterministic=False) → int

getRingCount() -> int

getRotatableBonds() → ChmBonds

getSMARTS(arg2, arg3, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) → std::string

getSMARTS(arg2, arg3, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False) -> std::string getSMARTS(arg2, arg3, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False) -> std::string getSMARTS(arg2, arg3, wantStereo=False, wantMapping=False, atomMappings=None) -> std::string getSMARTS(arg2, arg3, wantStereo=False, wantMapping=False) -> std::string getSMARTS(arg2, arg3, wantStereo=False) -> std::string getSMARTS(arg2, arg3) -> std::string getSMARTS(arg2) -> std::string getSMARTS() -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, overrideAtomLabels=None, overrideBondLabels=None, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, overrideAtomLabels=None, overrideBondLabels=None, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, overrideAtomLabels=None, overrideBondLabels=None, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, overrideAtomLabels=None, overrideBondLabels=None, atomMappings=None) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, overrideAtomLabels=None, overrideBondLabels=None) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False, overrideAtomLabels=None) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False, wantMapping=False) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6, wantStereo=False) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5, arg6) -> std::string getSMARTS(atomMask, bondMask, markRings=False, arg5) -> std::string getSMARTS(atomMask, bondMask, markRings=False) -> std::string getSMARTS(atomMask, bondMask) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5, wantStereo=False, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5, wantStereo=False, wantMapping=False, atomMappings=None) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5, wantStereo=False, wantMapping=False) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5, wantStereo=False) -> std::string getSMARTS(atomMask, markRings=False, arg4, arg5) -> std::string getSMARTS(atomMask, markRings=False, arg4) -> std::string getSMARTS(atomMask, markRings=False) -> std::string getSMARTS(atomMask) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5, wantStereo=True, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False, wantCharge=True) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5, wantStereo=True, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False, useBaseOne=False) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5, wantStereo=True, wantMapping=False, atomMappings=None, useAtomicNumberOnAcyclicAtoms=False) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5, wantStereo=True, wantMapping=False, atomMappings=None) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5, wantStereo=True, wantMapping=False) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5, wantStereo=True) -> std::string getSMARTS(atomInfo, bondInfo, arg4, arg5) -> std::string getSMARTS(atomInfo, bondInfo, arg4) -> std::string getSMARTS(atomInfo, bondInfo) -> std::string

getTautomerCode(considerEZStereo=True, considerRSStereo=True) → uint

getTautomerCode(considerEZStereo=True) -> uint getTautomerCode() -> uint

getTautomerCode64(considerEZStereo=True, considerRSStereo=True) → uint64

getTautomerCode64(considerEZStereo=True) -> uint64 getTautomerCode64() -> uint64

getTerminalAtoms() → ChmAtoms

getUnrotatableBonds() → ChmBonds

getUserData() → uint

getZeroOrderBonds() → std::vector< CHMZOBITEM,std::allocator< CHMZOBITEM > >

has2DCoords(duplicateOK=False, implicitToo=True) → bool

has2DCoords(duplicateOK=False) -> bool has2DCoords() -> bool

has3DCoords(duplicateOK=False, implicitToo=True) → bool

has3DCoords(duplicateOK=False) -> bool has3DCoords() -> bool

hasAllHydrogens() → bool

hasBondDirectionHint() → bool

hasCoords() → bool

hasDistinctCoords(arg2) → bool

hasDistinctCoords() -> bool

hasImplicitHydrogens() → bool

hasIsotope() → bool

hasProperty(arg2) → bool

isEmpty() → bool

isKekulized() → bool

kekulize()

makeWildcard()

mapToSMILES(atomMapping, wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False, forceOrder=False, rigorousAromaticity=True) → std::string

mapToSMILES(atomMapping, wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False, forceOrder=False) -> std::string mapToSMILES(atomMapping, wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False) -> std::string mapToSMILES(atomMapping, wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True) -> std::string mapToSMILES(atomMapping, wantKekulized=False, wantAllH=False, wantStereo=True) -> std::string mapToSMILES(atomMapping, wantKekulized=False, wantAllH=False) -> std::string mapToSMILES(atomMapping, wantKekulized=False) -> std::string mapToSMILES(atomMapping) -> std::string

markHydrogens(arg2) → int

markProchiral(onlyTerminal=False)

markProchiral()

needsBondDirectionHint() → bool

neutralize()

next()

returns the next ‘this’ object

packIndices() → bool

perceiveHybridization()

perceiveHydrogens(wantRadicals=False)

perceiveHydrogens()

perceiveRings(rigorousAromaticity=False, force=False)

perceiveRings(rigorousAromaticity=False) perceiveRings()

placeHydrogens()

randomizeOrientation()

reflectX0()

reflectY0()

removeAChiralHydrogens()

removeAtom(atom, packIndices=True)

removeAtom(atom)

removeAtomByIndex(index, packIndices=True)

removeAtomByIndex(index)

removeAtoms(atoms, packIndices=True)

removeAtoms(atoms)

removeConformation(arg2)

removeFormalCharges()

removeHydrogens(hydrogenTreatment)

removeHydrogens()

removeHydrogensAtOrigin()

removeImplicitHydrogens()

removeNonPolarHydrogens()

setAbsoluteChiralityFlag(on)

setAtomProperty(atom, key, value)

setBondProperty(bond, key, value)

setCoordinates(newCoords)

setMaeProperty(key, value)

setMaeProperty(key, value) setMaeProperty(key, value, precision) setMaeProperty(key, value) setMaeProperty(key, value)

setName(arg2)

setProperty(key, value)

setPropertyForAtom(atomIndex, key, value)

setPropertyforBond(bondIndex, key, value)

setUserData(data)

store(os, wantCoordinates=True, overrideName=None)

store(os, wantCoordinates=True) store(os)

subset(desiredAtoms, breakAliphaticRings=True, breakAromaticRings=False) → ChmMol

subset(desiredAtoms, breakAliphaticRings=True) -> ChmMol subset(desiredAtoms) -> ChmMol

subsetByBonds(desiredBonds) → ChmMol

toCanonicalSMILES(wantAllH=False, test=False) → std::string

toCanonicalSMILES(wantAllH=False) -> std::string toCanonicalSMILES() -> std::string

toChmQuery(allH=False, wantX=False) → ChmQuery

toChmQuery(allH=False) -> ChmQuery toChmQuery() -> ChmQuery toChmQuery(atomInfo, bondInfo) -> ChmQuery

toGenericSMARTS(wantBondOrder=False, wantCharge=False, wantAromaticity=False, genericAtomToo=False, wantStereo=False, wantAllHydrogens=False, wantAllClosureBonds=False) → std::string

toGenericSMARTS(wantBondOrder=False, wantCharge=False, wantAromaticity=False, genericAtomToo=False, wantStereo=False, wantAllHydrogens=False) -> std::string toGenericSMARTS(wantBondOrder=False, wantCharge=False, wantAromaticity=False, genericAtomToo=False, wantStereo=False) -> std::string toGenericSMARTS(wantBondOrder=False, wantCharge=False, wantAromaticity=False, genericAtomToo=False) -> std::string toGenericSMARTS(wantBondOrder=False, wantCharge=False, wantAromaticity=False) -> std::string toGenericSMARTS(wantBondOrder=False, wantCharge=False) -> std::string toGenericSMARTS(wantBondOrder=False) -> std::string toGenericSMARTS() -> std::string

toMAE(wantProperties, addH) → std::string

toMDL(arg2, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True, echoMaeType=False, check=False) → std::string

toMDL(arg2, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True, echoMaeType=False) -> std::string toMDL(arg2, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True) -> std::string toMDL(arg2, withprops=True, withCoords=True, overrideName=None, v3format=0) -> std::string toMDL(arg2, withprops=True, withCoords=True, overrideName=None) -> std::string toMDL(arg2, withprops=True, withCoords=True) -> std::string toMDL(arg2, withprops=True) -> std::string toMDL(arg2) -> std::string toMDL() -> std::string toMDL(os, arg3, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True, echoMaeType=False, check=False) toMDL(os, arg3, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True, echoMaeType=False) toMDL(os, arg3, withprops=True, withCoords=True, overrideName=None, v3format=0, wantDollarSigns=True) toMDL(os, arg3, withprops=True, withCoords=True, overrideName=None, v3format=0) toMDL(os, arg3, withprops=True, withCoords=True, overrideName=None) toMDL(os, arg3, withprops=True, withCoords=True) toMDL(os, arg3, withprops=True) toMDL(os, arg3) toMDL(os)

toSMILES(wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False, forceOrder=False, rigorousAromaticity=True) → std::string

toSMILES(wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False, forceOrder=False) -> std::string toSMILES(wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True, test=False) -> std::string toSMILES(wantKekulized=False, wantAllH=False, wantStereo=True, wantCharge=True) -> std::string toSMILES(wantKekulized=False, wantAllH=False, wantStereo=True) -> std::string toSMILES(wantKekulized=False, wantAllH=False) -> std::string toSMILES(wantKekulized=False) -> std::string toSMILES() -> std::string

toString() → std::string

toUniqueSMILES(wantAllH=False, test=False) → std::string

toUniqueSMILES(wantAllH=False) -> std::string toUniqueSMILES() -> std::string

topoCentroid(radius=3.0) → ChmMol

topoCentroid() -> ChmMol

topoCentroidByCount(desiredHeavyAtomCount, binWidth=0.5) → ChmMol

topoCentroidByCount(desiredHeavyAtomCount) -> ChmMol

translateAlleneStereo(atomChain, MorP)

translateCisTransStereo(atomChain, CisTrans, permissive=0)

translateCisTransStereo(atomChain, CisTrans)

translateTetrahedralStereo(central, priorities, RorS, permissive=0)

translateTetrahedralStereo(central, priorities, RorS)

undefinedChiralCenters() → int

unkekulize()

unmarkProchiral()

validateCisTrans()

zeroCoords()

class schrodinger.infra.canvas.ChmMolNameGT

::ChmMolNameGT

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmMolNameLT

::ChmMolNameLT

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmMol_fromMAE(maeString) → ChmMol

schrodinger.infra.canvas.ChmMol_fromMDL(inputstream) → ChmMol

schrodinger.infra.canvas.ChmMol_fromSMILES(inputstream) → ChmMol

class schrodinger.infra.canvas.ChmMolprint2D32

::ChmMolprint2D32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmMolprint2D64

::ChmMolprint2D64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmMultiYDelimitedPatterns

::ChmMultiYDelimitedPatterns

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateBitCount() → uint

calculateColumnCount() → uint

calculateRowCount() → uint

close()

getAllColNames() → std::vector< std::string,std::allocator< std::string > >

getBitMask() → ChmBitset

getColMask() → ChmBitset

getColumnName(index) → std::string

getDelimiter() → char

getFirstObsColumnAsDoubles() → std::vector< double,std::allocator< double > >

getIncludedColIndexes() → std::vector< size_t,std::allocator< size_t > >

getIncludedColNames() → std::vector< std::string,std::allocator< std::string > >

getIncludedCols() → size_t

getIncludedXvarNames(indexes) → std::vector< std::string,std::allocator< std::string > >

getLastLine() → std::string

getNumericalColNames() → std::vector< std::string,std::allocator< std::string > >

getObservationIncludedIndexes() → std::vector< size_t,std::allocator< size_t > >

getObservationIndexes() → std::vector< size_t,std::allocator< size_t > >

getObservationNames() → std::vector< std::string,std::allocator< std::string > >

getRowMask() → ChmBitset

getTotalCols() → size_t

getValuesOfColumn(index, values)

hasHeader() → bool

hasNext() → bool

isNumericalCol(index) → bool

next()

returns the next ‘this’ object

nextPattern() → ChmPattern

numericalCols() → size_t

rewind()

setBitMask(mask)

setColMask(mask)

setObservationNames(names)

setRowMask(mask)

skip()

class schrodinger.infra.canvas.ChmNnetModelReporter

::ChmNnetModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getNumNets() → size_t

getNumYvars() → size_t

getStatus() → ChmModelStatus

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTestRMSE() → std::vector< double,std::allocator< double > >

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

getTrainingRMSE() → std::vector< double,std::allocator< double > >

getYobsTest() → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getYobsTestOK() → std::vector< std::vector< bool,std::allocator< bool > >,std::allocator< std::vector< bool,std::allocator< bool > > > >

getYobsTraining() → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getYpredTest() → std::vector< std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >,std::allocator< std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > > >

getYpredTraining() → std::vector< std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >,std::allocator< std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > > >

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setNumNets(nnet)

setNumYvars(ny)

setStatus(s)

setTestRMSE(q)

setTrainingRMSE(q)

setYobsTest(obs)

setYobsTestOK(obs)

setYobsTraining(obs)

setYpredTest(pred)

setYpredTraining(pred)

success() → bool

static translateCode(st) → std::string

class schrodinger.infra.canvas.ChmObjChmAtomImpl

::ChmObj< ChmAtomImpl >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

debug() → std::string

getUID() → size_t

isValid() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmObjChmAtomTyperImpl

::ChmObj< ChmAtomTyperImpl >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

debug() → std::string

getUID() → size_t

isValid() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmObjChmMatcherImpl

::ChmObj< ChmSmartsMatcherImpl >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

debug() → std::string

getUID() → size_t

isValid() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmObjChmQueryImpl

::ChmObj< ChmQueryImpl >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

debug() → std::string

getUID() → size_t

isValid() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmPCARegModelReporter

::ChmPCARegModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getMaxFactor() → size_t

getPearsonCorr() → std::vector< double,std::allocator< double > >

getQSQR() → std::vector< double,std::allocator< double > >

getRSQR() → std::vector< double,std::allocator< double > >

getRegF() → std::vector< double,std::allocator< double > >

getRegP() → std::vector< double,std::allocator< double > >

getRegSD() → std::vector< double,std::allocator< double > >

getRegVarNames() → std::vector< std::string,std::allocator< std::string > >

getStatus() → ChmModelStatus

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTestRMSE() → std::vector< double,std::allocator< double > >

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

getTrainingRMSE() → std::vector< double,std::allocator< double > >

getYobsTest() → std::vector< double,std::allocator< double > >

getYobsTestOK() → std::vector< bool,std::allocator< bool > >

getYobsTraining() → std::vector< double,std::allocator< double > >

getYpredTaining() → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getYpredTest() → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setMaxFactor(f)

setPearsonCorr(q)

setQSQR(q)

setRSQR(q)

setRegF(q)

setRegP(q)

setRegSD(q)

setRegVarNames(names)

setStatus(s)

setTestRMSE(q)

setTrainingRMSE(q)

setYobsTest(obs)

setYobsTestOK(t)

setYobsTraining(obs)

setYpredTaining(pred)

setYpredTest(pred)

success() → bool

static translateCode(st) → std::string

class schrodinger.infra.canvas.ChmPLSModelReporter

::ChmPLSModelReporter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

appendErr(str)

appendLog(str)

appendWarning(str)

getMaxFactor() → size_t

getPearsonCorr() → std::vector< double,std::allocator< double > >

getQSQR() → std::vector< double,std::allocator< double > >

getRSQR() → std::vector< double,std::allocator< double > >

getRSQRCV() → std::vector< double,std::allocator< double > >

getRegF() → std::vector< double,std::allocator< double > >

getRegP() → std::vector< double,std::allocator< double > >

getRegSD() → std::vector< double,std::allocator< double > >

getRegVarNames() → std::vector< std::string,std::allocator< std::string > >

getStability() → std::vector< double,std::allocator< double > >

getStatus() → ChmModelStatus

getTestList() → std::vector< size_t,std::allocator< size_t > >

getTestRMSE() → std::vector< double,std::allocator< double > >

getTrainingList() → std::vector< size_t,std::allocator< size_t > >

getTrainingRMSE() → std::vector< double,std::allocator< double > >

getYobsTest() → std::vector< double,std::allocator< double > >

getYobsTestOK() → std::vector< bool,std::allocator< bool > >

getYobsTraining() → std::vector< double,std::allocator< double > >

getYpredTaining() → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getYpredTest() → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

next()

returns the next ‘this’ object

printErr(os)

printLog(os)

printWarning(os)

setMaxFactor(f)

setPearsonCorr(q)

setQSQR(q)

setRSQR(q)

setRSQRCV(q)

setRegF(q)

setRegP(q)

setRegSD(q)

setRegVarNames(names)

setStability(q)

setStatus(s)

setTestRMSE(q)

setTrainingRMSE(q)

setYobsTest(obs)

setYobsTestOK(t)

setYobsTraining(obs)

setYpredTaining(pred)

setYpredTest(pred)

success() → bool

static translateCode(st) → std::string

class schrodinger.infra.canvas.ChmPLSParser

::ChmPLSParser

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clear()

getLoading(var, pcIndex) → std::string

getMaxFactor() → size_t

getMinFactor() → size_t

getNumObsInTrainingTestTotal() → std::vector< int,std::allocator< int > >

getNumOfXvarsWithLoading() → size_t

getPearsonR(numFactor) → std::string

getQsqr(numFactor) → std::string

getRegF(numFactor) → std::string

getRegP(numFactor) → std::string

static getResultsParser(file) → ChmModelParser

getRsqr(numFactor) → std::string

getRsqrCv(numFactor) → std::string

getSD(numFactor) → std::string

getStability(numFactor) → std::string

getTestSetNames() → std::vector< std::string,std::allocator< std::string > >

getTestSetObs() → std::vector< std::string,std::allocator< std::string > >

getTestSetPred(numFactor) → std::vector< std::string,std::allocator< std::string > >

getTestSetRMSE(numFactor) → std::string

getTrainingSetNames() → std::vector< std::string,std::allocator< std::string > >

getTrainingSetObs() → std::vector< std::string,std::allocator< std::string > >

getTrainingSetPred(numFactor) → std::vector< std::string,std::allocator< std::string > >

getVariableNames() → std::vector< std::string,std::allocator< std::string > >

getYvar() → std::string

hasLoading(var) → bool

haveTestSet() → bool

haveTrainingSet() → bool

next()

returns the next ‘this’ object

read(arg2, arg3)

writePredictions(filename, namefield, delim, extraParameter=- 1)

writePredictions(filename, namefield, delim) writePredictions(filename, namefield) writePredictions(filename)

class schrodinger.infra.canvas.ChmPairwiseFPIn

::ChmPairwiseFPIn

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

cols() → size_t

getColumn(column, columnData, castAsDistances=False)

getColumn(column, columnData) getColumn(column, columnData, castAsDistances=False) getColumn(column, columnData)

getColumnName(index) → std::string

getColumnNames() → std::vector< std::string,std::allocator< std::string > > const &

getData(castAsDistances=False) → std::vector< std::vector< float,std::allocator< float > >,std::allocator< std::vector< float,std::allocator< float > > > >

getData() -> std::vector< std::vector< float,std::allocator< float > >,std::allocator< std::vector< float,std::allocator< float > > > > getData(data, castAsDistances=False) getData(data) getData(data, rowIDs, castAsDistances=False) getData(data, rowIDs) getData(data, castAsDistances=False) getData(data) getData(data, rowIDs, castAsDistances=False) getData(data, rowIDs) getData(data, castAsDistances=False) getData(data) getData(data, rowIDs, castAsDistances=False) getData(data, rowIDs)

getRow(index, castAsDistances=False) → std::vector< float,std::allocator< float > >

getRow(index) -> std::vector< float,std::allocator< float > > getRow(index, row, castAsDistances=False) -> bool getRow(index, row) -> bool getRow(index, row, name, castAsDistances=False) -> bool getRow(index, row, name) -> bool

getRowName(index) → std::string

isDistanceMatrix() → bool

isSimilarityMatrix() → bool

isSquare() → bool

isSymmetric() → bool

isValid() → bool

next()

returns the next ‘this’ object

rows() → size_t

sortFilter(outputFileName, mode, topR=0, topC=0, outputFormat=0)

sortFilter(outputFileName, mode, topR=0, topC=0) sortFilter(outputFileName, mode, topR=0) sortFilter(outputFileName, mode)

class schrodinger.infra.canvas.ChmPairwiseFPOut

::ChmPairwiseFPOut

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

formatBinary = 0

formatCSV = 1

formatLong = 3

formatWide = 2

getFlattening() → double

getHumanReadable() → bool

getLowerBound() → double

getMaximumViolations() → int

getMetric() → ChmMetricStyle

getOutputType() → ChmPairwiseFPOut::outputType

getUpperBound() → double

hasLowerBound() → bool

hasUpperBound() → bool

next()

returns the next ‘this’ object

process(fpFileName, readBlockSize=1000)

process(fpFileName) process(fpFileName, start, end, readBlockSize=1000) process(fpFileName, start, end) process(fpFileName1, fpFileName2, readBlockSize=1000) process(fpFileName1, fpFileName2) process(fpFileName1, start1, end1, fpFileName2, start2, end2, readBlockSize=1000) process(fpFileName1, start1, end1, fpFileName2, start2, end2) process(fpFileName1, start1, end1, fpFileName2, readBlockSize=1000) process(fpFileName1, start1, end1, fpFileName2) process(fpFileName1, fpFileName2, start2, end2, readBlockSize=1000) process(fpFileName1, fpFileName2, start2, end2)

setCustomMetric(metric)

setFlattening(value=25)

setFlattening()

setHumanReadable(on)

setLowerBound(value)

setMaximumViolations(value)

setMetric(style)

setOutputType(on)

setTverskyMetric(alpha, beta)

setUpperBound(value)

class schrodinger.infra.canvas.ChmPairwiseFPOut32

::ChmPairwiseFPOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getFlattening() → double

getHumanReadable() → bool

getLowerBound() → double

getMaximumViolations() → int

getMetric() → ChmMetricStyle

getOutputType() → ChmPairwiseFPOut::outputType

getUpperBound() → double

hasLowerBound() → bool

hasUpperBound() → bool

next()

returns the next ‘this’ object

process(fpFileName, readBlockSize=1000)

process(fpFileName) process(fpFileName, start, end, readBlockSize=1000) process(fpFileName, start, end) process(fpFileName1, fpFileName2, readBlockSize=1000) process(fpFileName1, fpFileName2) process(fpFileName1, start1, end1, fpFileName2, start2, end2, readBlockSize=1000) process(fpFileName1, start1, end1, fpFileName2, start2, end2)

setCustomMetric(metric)

setFlattening(value=25)

setFlattening()

setHumanReadable(on)

setLowerBound(value)

setMaximumViolations(value)

setMetric(style)

setOutputType(on)

setUpperBound(value)

class schrodinger.infra.canvas.ChmPairwiseFPOut64

::ChmPairwiseFPOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getFlattening() → double

getHumanReadable() → bool

getLowerBound() → double

getMaximumViolations() → int

getMetric() → ChmMetricStyle

getOutputType() → ChmPairwiseFPOut::outputType

getUpperBound() → double

hasLowerBound() → bool

hasUpperBound() → bool

next()

returns the next ‘this’ object

process(fpFileName, readBlockSize=1000)

process(fpFileName) process(fpFileName, start, end, readBlockSize=1000) process(fpFileName, start, end) process(fpFileName1, fpFileName2, readBlockSize=1000) process(fpFileName1, fpFileName2) process(fpFileName1, start1, end1, fpFileName2, start2, end2, readBlockSize=1000) process(fpFileName1, start1, end1, fpFileName2, start2, end2)

setCustomMetric(metric)

setFlattening(value=25)

setFlattening()

setHumanReadable(on)

setLowerBound(value)

setMaximumViolations(value)

setMetric(style)

setOutputType(on)

setUpperBound(value)

class schrodinger.infra.canvas.ChmPairwiseOut32

::ChmPairwiseOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset generate(distanceMatrix) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32 generateMap(distanceMatrix) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

set3D(on)

setBinWidth(width)

setFuzzyDistance(fuzzy)

setMaxDistance(max)

setMinDistance(min)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmPairwiseOut64

::ChmPairwiseOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64 generate(distanceMatrix) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64 generateMap(distanceMatrix) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

set3D(on)

setBinWidth(width)

setFuzzyDistance(fuzzy)

setMaxDistance(max)

setMinDistance(min)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmPathTools

::ChmPathTools

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static classifyAtoms(mol, atomClasses)

static computeLaplacian(mol) → ChmSymmetricMatrix< int >

computeLaplacian(connectionTable, degrees) -> ChmSymmetricMatrix< int >

static computePathsUpToLength(mol, length) → ChmSymmetricMatrixUnsignedInt

static computeShortestPaths(connectionTable, zeroOutDisconnected=True, throwExceptionIfDisconnnected=True) → ChmSymmetricMatrixUnsignedInt

computeShortestPaths(connectionTable, zeroOutDisconnected=True) -> ChmSymmetricMatrixUnsignedInt computeShortestPaths(connectionTable) -> ChmSymmetricMatrixUnsignedInt

static deriveMapping(source, sourcemcs, reference, referencemcs, mapatoms, mapbonds, rmsd, flipY) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

deriveMapping(source, reference, alignBy, rmsd, flipY) -> std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

static fuseRings(n)

static getComponentCount(mol) → uint

static getComponents(mol) → std::vector< ChmMol,std::allocator< ChmMol > >

getComponents(mol, mappings) -> std::vector< ChmMol,std::allocator< ChmMol > >

static getComponentsMappings(mol) → std::vector< std::vector< uint,std::allocator< uint > >,std::allocator< std::vector< uint,std::allocator< uint > > > >

static getCoreAtoms(mol, desiredHeavyAtomCount=20, binWidth=0.5) → ChmBitset

getCoreAtoms(mol, desiredHeavyAtomCount=20) -> ChmBitset getCoreAtoms(mol) -> ChmBitset

static getDistancesToCentroid(data, distancesToCentroid)

static getFeaturePaths(mol, atomsFeature1, atomsFeature2)

static getSSSR(mol, deterministic=False)

getSSSR(mol)

static getSSSRAndAcyclicAtoms(mol, deterministic=False)

getSSSRAndAcyclicAtoms(mol)

static getShortestPathsBetweenAtoms(mol, startAtomIndex, endAtomIndex)

static getShortestPathsBetweenAtomsWithSideChains(mol, startAtomIndex, endAtomIndex)

static getSymmetryGroups(mol, groups, wantEZStereo=True, wantRSStereo=True, wantHydrogens=False, depth=10, atomTyping=7)

getSymmetryGroups(mol, groups, wantEZStereo=True, wantRSStereo=True, wantHydrogens=False, depth=10) getSymmetryGroups(mol, groups, wantEZStereo=True, wantRSStereo=True, wantHydrogens=False) getSymmetryGroups(mol, groups, wantEZStereo=True, wantRSStereo=True) getSymmetryGroups(mol, groups, wantEZStereo=True) getSymmetryGroups(mol, groups)

static getmmsymLikeGroup(mol, atomTyping) → std::vector< int,std::allocator< int > >

static isConnected(mol) → bool

next()

returns the next ‘this’ object

static scoreConnections(mol, atom, ignoreAtoms, wantRingLogic) → std::vector< connectInfo,std::allocator< connectInfo > >

scoreConnections(mol, bond, ignoreAtoms) -> std::vector< connectInfo,std::allocator< connectInfo > >

static strip(mol) → ChmMol

static stripToScaffold(mol) → ChmMol

schrodinger.infra.canvas.ChmPathTools_classifyAtoms(mol, atomClasses)

schrodinger.infra.canvas.ChmPathTools_computeLaplacian(connectionTable, degrees) → ChmSymmetricMatrix< int >

schrodinger.infra.canvas.ChmPathTools_computePathsUpToLength(mol, length) → ChmSymmetricMatrixUnsignedInt

schrodinger.infra.canvas.ChmPathTools_computeShortestPaths(connectionTable) → ChmSymmetricMatrixUnsignedInt

schrodinger.infra.canvas.ChmPathTools_deriveMapping(source, reference, alignBy, rmsd, flipY) → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > >

schrodinger.infra.canvas.ChmPathTools_fuseRings(n)

schrodinger.infra.canvas.ChmPathTools_getComponentCount(mol) → uint

schrodinger.infra.canvas.ChmPathTools_getComponents(mol, mappings) → std::vector< ChmMol,std::allocator< ChmMol > >

schrodinger.infra.canvas.ChmPathTools_getComponentsMappings(mol) → std::vector< std::vector< uint,std::allocator< uint > >,std::allocator< std::vector< uint,std::allocator< uint > > > >

schrodinger.infra.canvas.ChmPathTools_getCoreAtoms(mol) → ChmBitset

schrodinger.infra.canvas.ChmPathTools_getDistancesToCentroid(data, distancesToCentroid)

schrodinger.infra.canvas.ChmPathTools_getFeaturePaths(mol, atomsFeature1, atomsFeature2)

schrodinger.infra.canvas.ChmPathTools_getSSSR(mol)

schrodinger.infra.canvas.ChmPathTools_getSSSRAndAcyclicAtoms(mol)

schrodinger.infra.canvas.ChmPathTools_getShortestPathsBetweenAtoms(mol, startAtomIndex, endAtomIndex)

schrodinger.infra.canvas.ChmPathTools_getShortestPathsBetweenAtomsWithSideChains(mol, startAtomIndex, endAtomIndex)

schrodinger.infra.canvas.ChmPathTools_getSymmetryGroups(mol, groups)

schrodinger.infra.canvas.ChmPathTools_getmmsymLikeGroup(mol, atomTyping) → std::vector< int,std::allocator< int > >

schrodinger.infra.canvas.ChmPathTools_isConnected(mol) → bool

schrodinger.infra.canvas.ChmPathTools_scoreConnections(mol, bond, ignoreAtoms) → std::vector< connectInfo,std::allocator< connectInfo > >

schrodinger.infra.canvas.ChmPathTools_strip(mol) → ChmMol

schrodinger.infra.canvas.ChmPathTools_stripToScaffold(mol) → ChmMol

class schrodinger.infra.canvas.ChmPattern

::ChmPattern

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

allNumAsDouble() → std::vector< double,std::allocator< double > >

append()

appends another ‘this’ object

chmtostring() → std::string

empty() → bool

getDouble(index) → double

getID() → std::string

getString(index, wasQuoted=None) → std::string

getString(index) -> std::string

next()

returns the next ‘this’ object

size() → uint

class schrodinger.infra.canvas.ChmPatterns

::ChmPatterns

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateBitCount() → uint

calculateColumnCount() → uint

calculateRowCount() → uint

getBitMask() → ChmBitset

getColMask() → ChmBitset

getColumnName(index) → std::string

getRowMask() → ChmBitset

hasNext() → bool

isNumericalCol(index) → bool

next()

returns the next ‘this’ object

nextPattern() → ChmPattern

numericalCols() → size_t

rewind()

setBitMask(mask)

setColMask(mask)

setRowMask(mask)

skip(numberOfRows=1)

skip()

class schrodinger.infra.canvas.ChmQR

::ChmQR

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getH() → ChmMatrix< double >

getQ() → ChmMatrix< double >

getR() → ChmMatrix< double >

isFullRank() → int

next()

returns the next ‘this’ object

solve(b) → std::vector< double,std::allocator< double > >

solve(B) -> ChmMatrix< double >

class schrodinger.infra.canvas.ChmQuartetOut32

::ChmQuartetOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset generate(distanceMatrix) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32 generateMap(distanceMatrix) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

set3D(on)

setBinWidth(width)

setFuzzyDistance(fuzzy)

setMaxDistance(max)

setMinDistance(min)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmQuartetOut64

::ChmQuartetOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64 generate(distanceMatrix) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64 generateMap(distanceMatrix) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

set3D(on)

setBinWidth(width)

setFuzzyDistance(fuzzy)

setMaxDistance(max)

setMinDistance(min)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmQuery

::ChmQuery

MDL = 3

SMARTS = 2

SMILES = 1

UNKNOWN = 0

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

clear()

clone() → ChmQuery

debug(os, indent)

debug(os) debug()

static fromMDL(molData, v3, wantX) → ChmQuery

static fromMDLFile(source, v3, wantX) → ChmQuery

fromMDLFile(fileName, v3, wantX) -> ChmQuery

static fromSMARTS(smarts) → ChmQuery

static fromStream(inputstream) → ChmQuery

getABInfo(arg2, arg3, hydrogenOk) → ChmMol

getAtomCount() → int

getBondCount() → int

getFragmentCount() → int

getSearchKey() → ChmSearchKey

getSource() → std::string const &

getSourceType() → ChmQuery::sourceType

getUID() → size_t

involvesAromaticity() → bool

involvesCisTrans() → bool

involvesHybridization() → bool

isIndexable() → bool

isValid() → bool

mapToSource(pos) → int

next()

returns the next ‘this’ object

store(os)

toSMARTS() → std::string

static validateSMARTS(smarts) → std::pair< bool,std::string >

class schrodinger.infra.canvas.ChmQueryMatcher

::ChmQueryMatcher

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

clear()

clone() → ChmQueryMatcher

debug() → std::string

getAllowRelativeStereoMatches() → bool

getHydrogensInterchangeable() → bool

getImplicitHydrogensIgnored() → bool

getMatchCountLimit() → int

getUID() → size_t

getUniqueFilter() → bool

hasExactMatch(query, mol) → bool

hasMatch(query, mol) → bool

hasMatchStartingWith(query, mol, startingAtom) → bool

hideMatched(query, mol)

hideNonMatched(query, mol)

isValid() → bool

match(query, mol) → ChmMatches

matchCount(query, mol) → int

matchEx(query, mol) → ChmMatchesEx

matchMask(query, mol) → ChmBitsetIterator

matchMaskSubset(query, mol, subset) → ChmBitsetIterator

matchMasks(query, mol) → ChmAtomAndBondMasks

matchSubset(query, mol, subset) → ChmMatches

matchTo(query, mol, startingAtom) → ChmMatches

matchToEx(query, mol, startingAtom) → ChmMatchesEx

matchToMask(query, mol, startingAtom) → ChmBitsetIterator

next()

returns the next ‘this’ object

setAllowRelativeStereoMatches(on)

setHydrogensInterchangeable(on)

setImplicitHydrogensIgnored(on)

setMatchCountLimit(limit)

setUniqueFilter(on)

schrodinger.infra.canvas.ChmQuery_fromMDL(molData, v3, wantX) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromMDLFile(fileName, v3, wantX) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromSMARTS(smarts) → ChmQuery

schrodinger.infra.canvas.ChmQuery_fromStream(inputstream) → ChmQuery

schrodinger.infra.canvas.ChmQuery_validateSMARTS(smarts) → std::pair< bool,std::string >

class schrodinger.infra.canvas.ChmRadialOut32

::ChmRadialOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getConsiderHydrogens() → bool

getConsiderStereoEZ() → bool

getConsiderStereoRS() → bool

getCurrentRowCount() → uint

getFilename() → std::string

getIterations() → int

getMinSize() → uint

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

setConsiderHydrogens(on)

setConsiderStereoEZ(on)

setConsiderStereoRS(on)

setIterations(iterations_)

setMinSize(minSize_)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmRadialOut64

::ChmRadialOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getConsiderHydrogens() → bool

getConsiderStereoEZ() → bool

getConsiderStereoRS() → bool

getCurrentRowCount() → uint

getFilename() → std::string

getIterations() → int

getMinSize() → uint

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

setConsiderHydrogens(on)

setConsiderStereoEZ(on)

setConsiderStereoRS(on)

setIterations(iterations_)

setMinSize(minSize_)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmRandom

::ChmRandom

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

boundedNextInt(n) → uint

boundedNextInt64(n) → uint64

static fromFile(filename) → ChmRandom

static fromSeed(seed) → ChmRandom

getManualSeed() → uint

next()

returns the next ‘this’ object

nextAngle() → double

nextBitset(length, onBits) → ChmBitset

nextBitsetByFraction(length, density) → ChmBitset

nextBoolean() → bool

nextDouble() → double

nextGaussian(mean=0.0, stddev=1.0) → double

nextGaussian(mean=0.0) -> double nextGaussian() -> double

nextGaussianFast(mean=0.0, stddev=1.0) → double

nextGaussianFast(mean=0.0) -> double nextGaussianFast() -> double

nextInt() → uint

nextInt64() → uint64

nextPartition(length, numberOfBins, sortEachBin, memberships, binBase=0)

nextPartition(length, numberOfBins, sortEachBin, memberships)

nextRotation(cos, sin)

nextSelectWithReplacementSet(size, subset)

nextString(len) → std::string

nextSubset(length, numberToChoose, subset)

nextSubsetByFraction(length, density, subset)

toFile(filename)

schrodinger.infra.canvas.ChmRandom_fromFile(filename) → ChmRandom

schrodinger.infra.canvas.ChmRandom_fromSeed(seed) → ChmRandom

class schrodinger.infra.canvas.ChmRangeFilter

::ChmRangeFilter

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

count() → uint

excludeNext() → bool

static fromSubFormat(os) → ChmRangeFilter

getLast() → uint

getOpposite() → ChmRangeFilter

getOrder() → std::vector< uint,std::allocator< uint > > const &

includeNext() → bool

isDefault() → bool

isEOF() → bool

isEverything() → bool

isIndefinite() → bool

isSorted() → bool

static makeFilter(oneBasedLogicalItemsToInclude) → ChmRangeFilter

next()

returns the next ‘this’ object

rewind()

store(os)

toBitset(logicalSize) → ChmBitset

toBitsetExclude(logicalSize) → ChmBitset

toSubFormat(inputstream)

toVector(itemList, toEnd)

schrodinger.infra.canvas.ChmRangeFilter_fromSubFormat(os) → ChmRangeFilter

schrodinger.infra.canvas.ChmRangeFilter_makeFilter(oneBasedLogicalItemsToInclude) → ChmRangeFilter

class schrodinger.infra.canvas.ChmRangeUIDFilter

::ChmRangeUIDFilter

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

contains(rhs) → bool

containsKey(key) → bool

count() → uint64

static fromBlob(raw) → ChmRangeUIDFilter

static fromFile(filename) → ChmRangeUIDFilter

getFirstItem() → uint64

getHash() → uint

getOrder() → std::vector< uint64,std::allocator< uint64 > > const *

hasNext() → bool

isEOF() → bool

isSorted() → bool

logicalSize() → uint64

next() → int64

rewind()

store(os)

toBlob() → std::string

toCSV(os)

toFile(filename)

toSQL(os)

toSet(uids)

toUIDS()

schrodinger.infra.canvas.ChmRangeUIDFilter_fromBlob(raw) → ChmRangeUIDFilter

schrodinger.infra.canvas.ChmRangeUIDFilter_fromFile(filename) → ChmRangeUIDFilter

class schrodinger.infra.canvas.ChmReaction

::ChmReaction

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

canBeR1(smiles) → bool

canBeR2(smiles) → bool

getR1Info(smiles, cnt, mw)

getR2Info(smiles, cnt, mw)

name() → std::string

next()

returns the next ‘this’ object

run(reagents1, reagents2) → std::vector< std::string,std::allocator< std::string > >

run(reagents) -> std::vector< std::string,std::allocator< std::string > >

safeName() → std::string

test(r1, r2) → std::string

class schrodinger.infra.canvas.ChmRobustCtReader

::ChmRobustCtReader

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmRotBond

::ChmRotBond

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getNumRotBonds() → int

getRotBond(i, at1, at2)

isRotatable(bondIndex) → bool

isRotatableBond(arg2) → bool

next()

returns the next ‘this’ object

static printRBDef()

rotatablePair(atom1, atom2) → bool

rotatablePairByIndex(at1, at2) → bool

schrodinger.infra.canvas.ChmRotBond_printRBDef()

class schrodinger.infra.canvas.ChmRowUIDFilter

::ChmRowUIDFilter

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

contains(rhs) → bool

containsKey(key) → bool

count() → uint64

static fromBlob(raw) → ChmRangeUIDFilter

static fromFile(filename) → ChmRowUIDFilter

getFirstItem() → uint64

getHash() → uint

getOrder() → std::vector< uint64,std::allocator< uint64 > > const *

hasNext() → bool

isEOF() → bool

isSorted() → bool

logicalSize() → uint64

next() → int64

rewind()

store(os)

toBlob() → std::string

toCSV(os)

toFile(filename)

toSQL(os)

toSet(uids)

toUIDS()

schrodinger.infra.canvas.ChmRowUIDFilter_fromFile(filename) → ChmRowUIDFilter

class schrodinger.infra.canvas.ChmSDReader

::ChmSDReader

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

debug() → std::string

static estimateRecordCount(filename, scanDepth=1000, isExact=None) → uint64

estimateRecordCount(filename, scanDepth=1000) -> uint64 estimateRecordCount(filename) -> uint64

getError() → std::string

getLastRecordInfo()

getNameField() → std::string const &

getUID() → size_t

getUnionOfDataFields(selectStr, isUniform=False, removeNameField=False) → std::vector< std::string,std::allocator< std::string > >

getUnionOfDataFields(selectStr, isUniform=False) -> std::vector< std::string,std::allocator< std::string > > getUnionOfDataFields(selectStr) -> std::vector< std::string,std::allocator< std::string > > getUnionOfDataFields() -> std::vector< std::string,std::allocator< std::string > >

hasError() → bool

hasNext() → bool

isV3000() → bool

isValid() → bool

next() → ChmMol

reset()

setNameField(nameField)

class schrodinger.infra.canvas.ChmSDReaderImpl

::ChmObj< ChmSDReaderImpl >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

debug() → std::string

getUID() → size_t

isValid() → bool

next()

returns the next ‘this’ object

schrodinger.infra.canvas.ChmSDReader_estimateRecordCount(filename) → uint64

class schrodinger.infra.canvas.ChmSMARTSOut32

::ChmSMARTSOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmSMARTSOut64

::ChmSMARTSOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmScaffold

::ChmScaffold

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

contains(scaffold, countExact=False, embed=False) → bool

contains(scaffold, countExact=False) -> bool contains(scaffold) -> bool contains(scaffold, subScaffolds, countExact=False, embed=False) -> bool contains(scaffold, subScaffolds, countExact=False) -> bool contains(scaffold, subScaffolds) -> bool

containsFuzzy(scaffold, level=0, countExact=False, embed=False) → bool

containsFuzzy(scaffold, level=0, countExact=False) -> bool containsFuzzy(scaffold, level=0) -> bool containsFuzzy(scaffold) -> bool containsFuzzy(scaffold, subScaffolds, level=0, countExact=False, embed=False) -> bool containsFuzzy(scaffold, subScaffolds, level=0, countExact=False) -> bool containsFuzzy(scaffold, subScaffolds, level=0) -> bool containsFuzzy(scaffold, subScaffolds) -> bool

getAtomCount(wantHydrogens=False) → int

getAtomCount() -> int

getFuzzyScaffold(level=0) → std::string

getFuzzyScaffold() -> std::string

getLinkerAtoms(i) → std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

getLinkerCount() → int

getLinkerCount(i) -> int

getMW() → double

getRingPath(i, j) → std::vector< int,std::allocator< int > >

getRingSystemAtoms(i) → std::vector< int,std::allocator< int > >

getRingSystemCount() → int

getRingSystemSize(i) → int

getScaffoldMol() → ChmMol

getScaffoldSMARTS() → std::string

getScaffoldSMILES() → std::string

getSubScaffolds() → std::vector< ChmScaffold,std::allocator< ChmScaffold > >

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmScaffoldComplexity

::ChmScaffoldComplexity

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

heavyAtomCount

linkerCount

mw

next()

returns the next ‘this’ object

ringSystemCount

smiles

class schrodinger.infra.canvas.ChmScaffoldFinder

::ChmScaffoldFinder

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

exportScaffolds(outFile, base=0)

exportScaffolds(outFile) exportScaffolds(outStream, base=0) exportScaffolds(outStream)

getExocyc() → std::vector< std::string,std::allocator< std::string > >

getExolink() → std::vector< std::string,std::allocator< std::string > >

getScaffold(i) → ChmScaffold

getScaffoldCount() → int

getScaffoldSources(i, embed=False) → std::vector< int,std::allocator< int > >

getScaffoldSources(i) -> std::vector< int,std::allocator< int > >

getScaffoldSourcesCount(i, embed=False) → int

getScaffoldSourcesCount(i) -> int

getScaffolds() → std::vector< ChmScaffold,std::allocator< ChmScaffold > >

getSubScaffolds(i, embed=False) → std::vector< int,std::allocator< int > >

getSubScaffolds(i) -> std::vector< int,std::allocator< int > >

getSubScaffoldsCount(i, embed=False) → int

getSubScaffoldsCount(i) -> int

getSuperScaffolds(i, embed=False) → std::vector< int,std::allocator< int > >

getSuperScaffolds(i) -> std::vector< int,std::allocator< int > >

getSuperScaffoldsCount(i, embed=False) → int

getSuperScaffoldsCount(i) -> int

next()

returns the next ‘this’ object

saveObject(outFile)

saveObject(outStream)

class schrodinger.infra.canvas.ChmScaffoldMatcher

::ChmScaffoldMatcher

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getFuzzyMatches(mol, level=0, embed=False) → std::vector< int,std::allocator< int > >

getFuzzyMatches(mol, level=0) -> std::vector< int,std::allocator< int > > getFuzzyMatches(mol) -> std::vector< int,std::allocator< int > > getFuzzyMatches(smiles, level=0, embed=False) -> std::vector< int,std::allocator< int > > getFuzzyMatches(smiles, level=0) -> std::vector< int,std::allocator< int > > getFuzzyMatches(smiles) -> std::vector< int,std::allocator< int > >

getMatches(mol, embed=False) → std::vector< int,std::allocator< int > >

getMatches(mol) -> std::vector< int,std::allocator< int > > getMatches(smiles, embed=False) -> std::vector< int,std::allocator< int > > getMatches(smiles) -> std::vector< int,std::allocator< int > >

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmScaffoldRunner

::ChmScaffoldRunner

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

findFastScaffolds(smiles, exocyc, exolink, verbose=False) → std::vector< ChmScaffoldComplexity,std::allocator< ChmScaffoldComplexity > >

findFastScaffolds(smiles, exocyc, exolink) -> std::vector< ChmScaffoldComplexity,std::allocator< ChmScaffoldComplexity > >

getFinder() → ChmScaffoldFinder

getMatcher() → ChmScaffoldMatcher

getOptions() → std::map< std::string,std::string,std::less< std::string >,std::allocator< std::pair< std::string const,std::string > > >

hasMatcher() → bool

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmSearchKey

::ChmSearchKeyT< 8 >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

bits() → uint

bytes() → uint

chmtostring() → std::string

clear()

count() → uint

dbTestIdentity(target) → int

dbTestSubstructure(target) → int

dbTestSuperstructure(target) → int

static fromBinary(arg1) → ChmSearchKey

static fromHex(data) → ChmSearchKey

hash() → uint

hash64() → uint64

isEmpty() → bool

isFull() → bool

next()

returns the next ‘this’ object

set()

size() → uint

testIdentity(query) → int

testSubstructure(query) → int

testSuperstructure(query) → int

toBinary() → std::vector< uint64,std::allocator< uint64 > >

toBitset() → ChmBitset

toHex() → std::string

toSqlite() → std::string

toSqlite(os)

schrodinger.infra.canvas.ChmSearchKey_fromBinary(arg2) → ChmSearchKey

schrodinger.infra.canvas.ChmSearchKey_fromHex(data) → ChmSearchKey

class schrodinger.infra.canvas.ChmSmiles

::ChmSmiles

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

setSmiles(smiles)

class schrodinger.infra.canvas.ChmSmilesFileReader

::ChmSmilesFileReader

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

close()

directorySeparator = '/'

getCumulativeLinesRead() → uint64

getError() → std::string

getFailureCount() → size_t

getFilename() → std::string const &

getLastName() → std::string

getLastPos() → uint64

getLastRecordInfo(name, moldata)

getLastSMILES() → std::string

getLineNumber() → uint64

getPos() → uint64

getStream() → std::istream &

getSuccessCount() → size_t

hasError() → bool

hasNextLine() → bool

hasNextMol() → bool

static isCompressedFileName(filename) → bool

static isZipped(filename) → bool

next()

returns the next ‘this’ object

nextLine() → std::string

nextLine(line)

nextMol() → ChmMol

open(filename, isZipped=False)

open(filename)

peekNextLine(line) → bool

reset()

rewind()

seekg(pos)

setPos(pos)

skip()

tellg() → uint64

totalBytes() → uint64

class schrodinger.infra.canvas.ChmSmilesGenerator

::ChmSmilesGenerator

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clone() → ChmSmilesGenerator

getSmiles(mol, test=False, forceOrder=False, rigorousAromaticy=True) → std::string

getSmiles(mol, test=False, forceOrder=False) -> std::string getSmiles(mol, test=False) -> std::string getSmiles(mol) -> std::string getSmiles(mol, mapping, test=False, forceOrder=False, rigorousAromaticy=True) -> std::string getSmiles(mol, mapping, test=False, forceOrder=False) -> std::string getSmiles(mol, mapping, test=False) -> std::string getSmiles(mol, mapping) -> std::string

getSmilesAndMap(mol, test=False, forceOrder=False, rigorousAromaticy=True) → std::string

getSmilesAndMap(mol, test=False, forceOrder=False) -> std::string getSmilesAndMap(mol, test=False) -> std::string getSmilesAndMap(mol) -> std::string

next()

returns the next ‘this’ object

wantAllBondOrders(on)

wantAllBondOrders() -> bool

wantAllClosureBonds(on)

wantAllClosureBonds() -> bool

wantAllHydrogens(newval)

wantAllHydrogens() -> bool

wantAromaticity() → bool

wantAromaticity(newval)

wantAtomicNumber() → bool

wantAtomicNumber(newval)

wantBondOrder() → bool

wantBondOrder(newval)

wantCharge() → bool

wantCharge(newval)

wantKekulized() → bool

wantKekulized(newval)

wantMapping() → bool

wantMapping(newval)

wantStereo() → bool

wantStereo(newval)

class schrodinger.infra.canvas.ChmSmilesGeneratorState

::ChmSmilesGeneratorState

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

wantAllBondOrders

wantAllClosureBonds

wantAllHydrogens

wantAromaticity

wantAtomicNumber

wantBondOrder

wantCharge

wantKekule

wantMapping

wantStereo

class schrodinger.infra.canvas.ChmSparseBitset

::ChmSparseBitset

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__() → uint64

accumulate(total)

accumulate(total)

append()

appends another ‘this’ object

chmtostring() → std::string

contains(rhs) → bool

contains(key) -> bool

contract()

count() → uint64

countCommonOff(rhs) → uint64

countCommonOff(rhs) -> uint64

countCommonOn(rhs) → uint64

countCommonOn(rhs) -> uint64

countDifference(rhs) → uint64

countDifference(rhs) -> uint64

static createModal(toCombine) → ChmSparseBitset

density() → double

digest(arg2)

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

empty() → bool

expand(forceBinary=False)

expand()

foldXOR(dest, scale=7)

foldXOR(dest) foldXOR(scale=7) -> ChmBitset foldXOR() -> ChmBitset

static fromBlob(raw) → ChmSparseBitset

static fromString(idstring, logicalSize) → ChmSparseBitset

fromString(idstring) -> ChmSparseBitset

getHash() → int

getHash64() → int64

getMaxXY(rhs) → double

getMaxXY(rhs) -> double

getMinXY(rhs) → double

getMinXY(rhs) -> double

getScaleType() → FingerprintScaleType

getSumX() → double

getType() → int

getValue(pos) → float

getValues() → std::vector< float,std::allocator< float > > const &

getX2() → double

getXY(rhs) → double

getXY(rhs) -> double

hasDifference(rhs) → bool

hasValues(strict) → bool

hasValues() -> bool

intersects(rhs) → bool

isSubsetOf(rhs) → bool

move(offset)

next()

returns the next ‘this’ object

pack()

positionOf(key) → int

reduceToBitset(size) → ChmBitset

rescale(scale)

setCompressedSource(cs)

setScaleType(type)

setValues(values, swap=False)

setValues(values)

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

store(sdata)

store(os)

swap(rhs)

toBitset() → ChmBitset

toBlob() → std::string

toVector() → std::vector< ChmSparseBitset::key_type,std::allocator< ChmSparseBitset::key_type > >

class schrodinger.infra.canvas.ChmSparseBitset64

::ChmSparseBitset64

__contains__(key, /)

Return key in self.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__() → uint64

append()

appends another ‘this’ object

chmtostring() → std::string

contains(rhs) → bool

contains(key) -> bool

contract()

count() → uint64

countCommonOff(rhs) → uint64

countCommonOff(rhs) -> uint64

countCommonOn(rhs) → uint64

countCommonOn(rhs) -> uint64

countDifference(rhs) → uint64

countDifference(rhs) -> uint64

static createModal(toCombine) → ChmSparseBitset64

density() → double

digest(arg2)

distDixon(rhs, forceBinary=False) → double

distDixon(rhs) -> double

distEuclidean(rhs, forceBinary=False) → double

distEuclidean(rhs) -> double

distHamming(rhs, normalized=False, forceBinary=False, overrideSize=None) → double

distHamming(rhs, normalized=False, forceBinary=False) -> double distHamming(rhs, normalized=False) -> double distHamming(rhs) -> double

distPatternDifference(rhs, forceBinary=False, overrideSize=None) → double

distPatternDifference(rhs, forceBinary=False) -> double distPatternDifference(rhs) -> double

distShape(rhs, forceBinary=False, overrideSize=None) → double

distShape(rhs, forceBinary=False) -> double distShape(rhs) -> double

distSize(rhs, forceBinary=False, overrideSize=None) → double

distSize(rhs, forceBinary=False) -> double distSize(rhs) -> double

distSoergel(rhs, forceBinary=False) → double

distSoergel(rhs) -> double

distSquaredEuclidean(rhs, forceBinary=False) → double

distSquaredEuclidean(rhs) -> double

distTanimoto(rhs, forceBinary=False) → double

distTanimoto(rhs) -> double

distVariance(rhs, forceBinary=False, overrideSize=None) → double

distVariance(rhs, forceBinary=False) -> double distVariance(rhs) -> double

empty() → bool

expand(forceBinary=False)

expand()

foldXOR(dest, scale=7)

foldXOR(dest) foldXOR(scale=7) -> ChmBitset foldXOR() -> ChmBitset

static fromBlob(raw) → ChmSparseBitset64

static fromString(idstring, logicalSize) → ChmSparseBitset64

fromString(idstring) -> ChmSparseBitset64

getHash() → int

getHash64() → int64

getMaxXY(rhs) → double

getMaxXY(rhs) -> double

getMinXY(rhs) → double

getMinXY(rhs) -> double

getScaleType() → FingerprintScaleType

getSumX() → double

getType() → int

getValue(pos) → float

getValues() → std::vector< float,std::allocator< float > > const &

getX2() → double

getXY(rhs) → double

getXY(rhs) -> double

hasDifference(rhs) → bool

hasValues(strict) → bool

hasValues() -> bool

intersects(rhs) → bool

isSubsetOf(rhs) → bool

move(offset)

next()

returns the next ‘this’ object

pack()

positionOf(key) → int

reduceToBitset(size) → ChmBitset

reduceToBitset64(size) → ChmBitset64

rescale(scale)

setCompressedSource(cs)

setScaleType(type)

setValues(values, swap=False)

setValues(values)

simBuser(rhs, forceBinary=False, overrideSize=None) → double

simBuser(rhs, forceBinary=False) -> double simBuser(rhs) -> double

simCosine(rhs, forceBinary=False) → double

simCosine(rhs) -> double

simDice(rhs, forceBinary=False) → double

simDice(rhs) -> double

simHamann(rhs, forceBinary=False, overrideSize=None) → double

simHamann(rhs, forceBinary=False) -> double simHamann(rhs) -> double

simKulczynski(rhs, forceBinary=False) → double

simKulczynski(rhs) -> double

simMatching(rhs, forceBinary=False, overrideSize=None) → double

simMatching(rhs, forceBinary=False) -> double simMatching(rhs) -> double

simMcConnaughey(rhs, forceBinary=False) → double

simMcConnaughey(rhs) -> double

simMinMax(rhs, forceBinary=False) → double

simMinMax(rhs) -> double

simModifiedTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simModifiedTanimoto(rhs, forceBinary=False) -> double simModifiedTanimoto(rhs) -> double

simPearson(rhs, forceBinary=False, overrideSize=None) → double

simPearson(rhs, forceBinary=False) -> double simPearson(rhs) -> double

simPetke(rhs, forceBinary=False) → double

simPetke(rhs) -> double

simRogersTanimoto(rhs, forceBinary=False, overrideSize=None) → double

simRogersTanimoto(rhs, forceBinary=False) -> double simRogersTanimoto(rhs) -> double

simSimpson(rhs, forceBinary=False) → double

simSimpson(rhs) -> double

simTanimoto(rhs, forceBinary=False) → double

simTanimoto(rhs) -> double

simTversky(rhs, alpha, beta, forceBinary=False) → double

simTversky(rhs, alpha, beta) -> double

simYule(rhs, forceBinary=False, overrideSize=None) → double

simYule(rhs, forceBinary=False) -> double simYule(rhs) -> double

size() → uint64

store(sdata)

store(os)

swap(rhs)

toBitset() → ChmBitset

toBitset64() → ChmBitset64

toBlob() → std::string

toVector() → std::vector< ChmSparseBitset64::key_type,std::allocator< ChmSparseBitset64::key_type > > const

schrodinger.infra.canvas.ChmSparseBitset64_createModal(toCombine) → ChmSparseBitset64

schrodinger.infra.canvas.ChmSparseBitset64_fromBlob(raw) → ChmSparseBitset64

schrodinger.infra.canvas.ChmSparseBitset64_fromString(idstring) → ChmSparseBitset64

schrodinger.infra.canvas.ChmSparseBitset_createModal(toCombine) → ChmSparseBitset

schrodinger.infra.canvas.ChmSparseBitset_fromBlob(raw) → ChmSparseBitset

schrodinger.infra.canvas.ChmSparseBitset_fromString(idstring) → ChmSparseBitset

class schrodinger.infra.canvas.ChmStringTokenizer

::ChmStringTokenizer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

hasNext() → bool

next() → char *

next(token) -> char next(leftToken, rightToken) -> char

nextDouble() → double

nextDouble(token) -> double nextDouble(leftToken, rightToken) -> double

nextFloat() → float

nextFloat(token) -> float nextFloat(leftToken, rightToken) -> float

nextInt() → int

nextInt(token) -> int nextInt(leftToken, rightToken) -> int

nextString() → std::string

nextString(token) -> std::string nextString(leftToken, rightToken) -> std::string

class schrodinger.infra.canvas.ChmSymmetricMatrixUnsignedInt

::ChmSymmetricMatrix< uint >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

autoScale(tolerance=1.0e-24)

autoScale()

base() → unsigned int const *

center()

chmtostring() → std::string

clear()

cols() → uint

doubleCenter()

fastItem(i, j) → unsigned int &

fastReadItem(i, j) → unsigned int const &

fill(value)

getColumnMeans(means)

getColumnMeansAndDeviations(means, stdDeviations)

getCovariance(covariance)

getCovariance(rhs, covariance) getCovariance(covariance, means) getCovariance(covariance, means, scalingFactors, tolerance=1.0e-24) getCovariance(covariance, means, scalingFactors)

getDM(distanceMatrix, lambda1=2, lambda2=0.5)

getDM(distanceMatrix, lambda1=2) getDM(distanceMatrix)

getItem(i, j) → unsigned int

getLaplacian(laplacian)

getLaplacian(laplacian)

getMahalanobisDM(distanceMatrix, lambda1=2, lambda2=0.5) → int

getMahalanobisDM(distanceMatrix, lambda1=2) -> int getMahalanobisDM(distanceMatrix) -> int

getRMSD(rmsd)

getRMSD(rhs, rmsd)

getScaledCovariance(covariance, tolerance=1.0e-24)

getScaledCovariance(covariance) getScaledCovariance(rhs, covariance, tolerance=1.0e-24) getScaledCovariance(rhs, covariance)

getScaledMahalanobisDM(distanceMatrix, lambda1=2, lambda2=0.5, tolerance=1.0e-24) → int

getScaledMahalanobisDM(distanceMatrix, lambda1=2, lambda2=0.5) -> int getScaledMahalanobisDM(distanceMatrix, lambda1=2) -> int getScaledMahalanobisDM(distanceMatrix) -> int

invert()

isSquare() → bool

item(i, j) → unsigned int &

next()

returns the next ‘this’ object

pivot(piv) → ChmMatrixUnsignedInt

pivot(piv, fromIndex, toIndex) -> ChmMatrixUnsignedInt

readItem(i, j) → unsigned int const &

resize(dim)

resize(rows, cols)

rows() → uint

swap(rhs)

transpose() → ChmSymmetricMatrixUnsignedInt

type() → bool

class schrodinger.infra.canvas.ChmTautomericAtomTyper

::ChmTautomericAtomTyper

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

calculateScalar(mol, wantImplicitHydrogens=False, et) → double

calculateScalar(mol, wantImplicitHydrogens=False) -> double calculateScalar(mol) -> double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False, et) → double

calculateWeightedScalar(mol, smoothingWeights, wantImplicitHydrogens=False) -> double calculateWeightedScalar(mol, smoothingWeights) -> double

chmtostring() → std::string

debug() → std::string

extendedType(mol, wantImplicitHydrogens=False) → ChmExtendedAssignments

extendedType(mol) -> ChmExtendedAssignments

extendedTypeAvg = 1

extendedTypeLast = 0

extendedTypeSum = 2

extendedValueTypeMean(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeMean(mol) -> ChmValueAssignmentIterator

extendedValueTypeSum(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

extendedValueTypeSum(mol) -> ChmValueAssignmentIterator

getAllPossibleAssignments() → ChmValueAssignmentIterator

getUID() → size_t

isValid() → bool

makeGaussianWeights(maxPath, sigma) → std::vector< double,std::allocator< double > >

makeWeights(maxPath, fallOffPower) → std::vector< double,std::allocator< double > >

next()

returns the next ‘this’ object

setRules(rulesString)

setRulesFile(rulesFile)

setup(considerCharge, considerIsotope)

type(mol, arg3=False) → ChmAssignments

type(mol) -> ChmAssignments

valueType(mol, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueType(mol) -> ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights, wantImplicitHydrogens=False) → ChmValueAssignmentIterator

valueTypeWithSmoothing(mol, smoothingWeights) -> ChmValueAssignmentIterator

class schrodinger.infra.canvas.ChmTmpFile

::ChmTmpFile

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

close()

copyFrom(name) → uint64

flush()

getName() → std::string const &

getStream() → std::ostream &

static getTempFileName(ext) → std::string

getTempFileName() -> std::string

static hardLink(existingFile, anAlias) → bool

next()

returns the next ‘this’ object

static rename(oldname, newname)

reset()

static swap(file1, file2)

schrodinger.infra.canvas.ChmTmpFile_getTempFileName() → std::string

schrodinger.infra.canvas.ChmTmpFile_hardLink(existingFile, anAlias) → bool

schrodinger.infra.canvas.ChmTmpFile_rename(oldname, newname)

schrodinger.infra.canvas.ChmTmpFile_swap(file1, file2)

class schrodinger.infra.canvas.ChmTokenizer

::ChmTokenizer

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

hasNext() → bool

next() → char *

next(token) -> char next(leftToken, rightToken) -> char

nextDouble() → double

nextDouble(token) -> double nextDouble(leftToken, rightToken) -> double

nextFloat() → float

nextFloat(token) -> float nextFloat(leftToken, rightToken) -> float

nextInt() → int

nextInt(token) -> int nextInt(leftToken, rightToken) -> int

nextInt64() → int64

nextInt64(token) -> int64 nextInt64(leftToken, rightToken) -> int64

nextString() → std::string

nextString(token) -> std::string nextString(leftToken, rightToken) -> std::string

class schrodinger.infra.canvas.ChmTopologicalTorsionOut32

::ChmTopologicalTorsionOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmTopologicalTorsionOut64

::ChmTopologicalTorsionOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmTripletOut32

::ChmTripletOut32

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset

generate(mol) -> ChmSparseBitset generate(distanceMatrix) -> ChmSparseBitset

generateMap(mol, distanceMatrix=None) → ChmFPMap32

generateMap(mol) -> ChmFPMap32 generateMap(distanceMatrix) -> ChmFPMap32

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

set3D(on)

setBinWidth(width)

setFuzzyDistance(fuzzy)

setMaxDistance(max)

setMinDistance(min)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmTripletOut64

::ChmTripletOut64

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

addZeros(toAdd)

append()

appends another ‘this’ object

close()

close(minFreq, maxFreq, maxBits) close(minFreq, maxFreq, maxBits, reduceBits)

generate(mol, distanceMatrix=None) → ChmSparseBitset64

generate(mol) -> ChmSparseBitset64 generate(distanceMatrix) -> ChmSparseBitset64

generateMap(mol, distanceMatrix=None) → ChmFPMap64

generateMap(mol) -> ChmFPMap64 generateMap(distanceMatrix) -> ChmFPMap64

getCurrentRowCount() → uint

getFilename() → std::string

getTypeInfo() → std::string

m_scaleType

needsDM() → bool

needsStereo() → bool

next()

returns the next ‘this’ object

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False, omitJobDir=False)

open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False, noSummary=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None, summaryOnly=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18, requiredBits=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False, maxLog2=18) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None, compressed=False) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone, overrideTypeInfo=None) open(filename, dataFields=None, logicalSize=None, scaleType=FPScaleNone) open(filename, dataFields=None, logicalSize=None) open(filename, dataFields=None) open(filename)

set3D(on)

setBinWidth(width)

setFuzzyDistance(fuzzy)

setMaxDistance(max)

setMinDistance(min)

write(mol, excludeAtomMask=None)

write(mol) write(mol, extraData, excludeAtomMask=None) write(mol, extraData) write(mol, id, excludeAtomMask=None) write(mol, id) write(mol, id, extraData, excludeAtomMask=None) write(mol, id, extraData)

writeNameAndProps(mol, id, extraData)

class schrodinger.infra.canvas.ChmUniqueSmilesGenerator

::ChmUniqueSmilesGenerator

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

clone() → ChmUniqueSmilesGenerator

getHash(mol) → uint

getHash(uniqueSmiles) -> uint

getHash64(mol) → uint64

getHash64(uniqueSmiles) -> uint64

getSmiles(mol, test=False) → std::string

getSmiles(mol) -> std::string getSmiles(mol, mapping) -> std::string

getSmilesAndMap(mol, test=False) → std::string

getSmilesAndMap(mol) -> std::string

next()

returns the next ‘this’ object

wantAllBondOrders(on)

wantAllBondOrders() -> bool

wantAllClosureBonds(on)

wantAllClosureBonds() -> bool

wantAllHydrogens(newval)

wantAllHydrogens() -> bool

wantCharge(on)

wantCharge() -> bool

wantStereo() → bool

wantStereo(newval)

class schrodinger.infra.canvas.ChmUniqueSmilesGeneratorState

::ChmUniqueSmilesGeneratorState

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

wantAllBondOrders

wantAllClosureBonds

wantAllHydrogens

wantCharge

wantStereo

class schrodinger.infra.canvas.ChmValueAssignment

::ChmValueAssignment

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

chmtostring() → std::string

getKey() → int64

getName() → std::string const &

getValue() → double

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.ChmValueAssignmentIterator

::ChmIterator< ChmValueAssignment >

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

__len__()

Return len(self).

append()

appends another ‘this’ object

asVector() → std::vector< ChmValueAssignment,std::allocator< ChmValueAssignment > > const &

asVector() -> std::vector< ChmValueAssignment,std::allocator< ChmValueAssignment > >

at(index) → ChmValueAssignment

at(index) -> ChmValueAssignment

chmtostring() → std::string

hasNext() → bool

hasPrev() → bool

isValid() → bool

next() → ChmValueAssignment

prev() → ChmValueAssignment

rewind()

size() → int

sort()

class schrodinger.infra.canvas.ClusterItem

::ClusterItem

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

avgDistanceToCentroid

avgPairwiseDist

clusterNumber

distNext

distPrev

distanceToCentroid

isFarthestToCentroid

isNearestToCentroid

label

next()

returns the next ‘this’ object

order

originalIndex

radius

variance

exception schrodinger.infra.canvas.CtAssertion

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.infra.canvas.CtException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.infra.canvas.CtMsgException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.infra.canvas.CtRdrException

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.infra.canvas.GetEigenVectorAndValues(matrix, eigenVector, eigenValues, dimensions, rank)

GetEigenVectorAndValues(matrix, eigenVector, eigenValues, dimensions)

schrodinger.infra.canvas.INITSTREAM(os, doublePrecision=True)

INITSTREAM(os)

class schrodinger.infra.canvas.InteractionInfo

::InteractionInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

static getOneLetterCode(threeLetterCode) → char

static getThreeLetterCode(oneLetterCode) → std::string

static int64ToPdb(code) → InteractionInfo

m_intType

m_pdb

m_resCode

m_resIndex

next()

returns the next ‘this’ object

static pdbToInt64(pdbCode, residueIndex, residueCode=0, interactionType=0) → uint64

pdbToInt64(pdbCode, residueIndex, residueCode=0) -> uint64 pdbToInt64(pdbCode, residueIndex) -> uint64 pdbToInt64(pdbCode, residueIndex, threeLetterCode, interactionType=0) -> uint64 pdbToInt64(pdbCode, residueIndex, threeLetterCode) -> uint64

toInt64() → uint64

toString(separator, indexWidth=4, typeWidth=2) → std::string

toString(separator, indexWidth=4) -> std::string toString(separator) -> std::string toString() -> std::string

schrodinger.infra.canvas.InteractionInfo_getOneLetterCode(threeLetterCode) → char

schrodinger.infra.canvas.InteractionInfo_getThreeLetterCode(oneLetterCode) → std::string

schrodinger.infra.canvas.InteractionInfo_int64ToPdb(code) → InteractionInfo

schrodinger.infra.canvas.InteractionInfo_pdbToInt64(pdbCode, residueIndex, threeLetterCode) → uint64

class schrodinger.infra.canvas.MCSByWeight

::MCSByWeight

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.MCSsettings

::MCSsettings

MCSStop

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

allH

allowDisconnect

append()

appends another ‘this’ object

atomTyping

collectAfterBond

configuration_problem

deleteInput

elementsToken

exclusive

forceDetail

fromCanvasGUI

getElapsedTime() → double

static isFEPAtomtype(x) → bool

isFEPAtomtype() -> bool

isPW

maxCount

minCount

minPathLength

next()

returns the next ‘this’ object

noDetail

nobreakaring

nobreakring

ordinal

outputDelim

outputRequiresCoords

pathLength

prochiral

ringPathLength

scaleXYZ

showAllMatches

shuffleAtomOrder

silent

sortName

throwIfDurationTooLong()

timeout

uniqueSMILES

v3SDF

wantH

wantRingCodes

wantX

class schrodinger.infra.canvas.SortChmMCSRecordByScore

::SortChmMCSRecordByScore

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.SortChmMCSRecordByScoreAndWeight

::SortChmMCSRecordByScoreAndWeight

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.SortChmMCSRecordByWeight

::SortChmMCSRecordByWeight

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.SortFPUniqueItem

::SortFPUniqueItem

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.SortFPUniqueItem3

::SortFPUniqueItem3

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

class schrodinger.infra.canvas.SortFrag

::SortFrag

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

schrodinger.infra.canvas.TESTMATCH(s)

schrodinger.infra.canvas.TESTSMILES(s)

class schrodinger.infra.canvas.XYZ

::XYZ

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

isDefined() → bool

next()

returns the next ‘this’ object

x

y

z

schrodinger.infra.canvas.alignMolecule(reference, toBeAligned, matchinfo, baseOfMatchInfo, overrideWeights=None) → ChmMol

alignMolecule(reference, toBeAligned, matchinfo, baseOfMatchInfo) -> ChmMol

schrodinger.infra.canvas.allTrim(str)

allTrim(str, c)

schrodinger.infra.canvas.bit_reverse(x) → uint

schrodinger.infra.canvas.cbstest(minlen, maxlen, reps) → bool

schrodinger.infra.canvas.checkCanvasElementsLicense(lic1, lic2, elemPass, driver, host, want_exit=True)

checkCanvasElementsLicense(lic1, lic2, elemPass, driver, host)

schrodinger.infra.canvas.checkLicense(licenseMask, className=None) → int

checkLicense(licenseMask) -> int

schrodinger.infra.canvas.chmCleanPath(path) → std::string

schrodinger.infra.canvas.chmDouble(str, toDouble) → std::string

chmDouble(str) -> std::string

schrodinger.infra.canvas.chmHasTerminal() → bool

schrodinger.infra.canvas.chmIsFileOpen(filename) → bool

schrodinger.infra.canvas.chmReadNullTerminatedString(source, dest) → bool

schrodinger.infra.canvas.chmTermFormat(text, color=foreground_black, attr=attr_none, hasTTY=True) → std::string

chmTermFormat(text, color=foreground_black, attr=attr_none) -> std::string chmTermFormat(text, color=foreground_black) -> std::string chmTermFormat(text) -> std::string

schrodinger.infra.canvas.chmTestYes(v) → bool

schrodinger.infra.canvas.chmUndouble(str, toUndouble) → std::string

chmUndouble(str) -> std::string

schrodinger.infra.canvas.chm_mkdir(dirname, permissionsInOctal=0o755) → bool

chm_mkdir(dirname) -> bool

schrodinger.infra.canvas.chmacos(x) → double

schrodinger.infra.canvas.chmatod(toConvert) → double

schrodinger.infra.canvas.chmatof(toConvert) → float

schrodinger.infra.canvas.chmatoi64(buf, base=10) → int64

chmatoi64(buf) -> int64

schrodinger.infra.canvas.chmatoui(buf, base=10) → uint

chmatoui(buf) -> uint

schrodinger.infra.canvas.chmatoui64(buf, base=10) → uint64

chmatoui64(buf) -> uint64

schrodinger.infra.canvas.chmatoull(toConvert) → uint64

schrodinger.infra.canvas.chmcos(radians) → double

schrodinger.infra.canvas.chmdtoa(value, precision) → std::string

chmdtoa(value) -> std::string

schrodinger.infra.canvas.chmendl(os) → std::ostream &

schrodinger.infra.canvas.chmitoa(value, str, base=10)

chmitoa(value, str)

schrodinger.infra.canvas.chmitoa64(value, str)

schrodinger.infra.canvas.chmmemcmp(ptr1, ptr2, num) → int

schrodinger.infra.canvas.chmremovefile(f) → bool

schrodinger.infra.canvas.chmround(val) → double

schrodinger.infra.canvas.chmsin(radians) → double

schrodinger.infra.canvas.chmstricmp(c1, c2) → int

schrodinger.infra.canvas.chmuitoa(value, str, base=10)

chmuitoa(value, str)

schrodinger.infra.canvas.chmuitoa64(value, str)

schrodinger.infra.canvas.cleanup(molUI)

cleanup(inner)

class schrodinger.infra.canvas.connectInfo

::connectInfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getConnectionOrder() → int

m_centralAtom

m_firstAtom

m_restOfAtoms

next()

returns the next ‘this’ object

toString() → std::string

schrodinger.infra.canvas.considersOffBits(value) → bool

schrodinger.infra.canvas.contains(target, pattern) → bool

contains(target, pattern, pos) -> bool

schrodinger.infra.canvas.count(source, toCount) → size_t

schrodinger.infra.canvas.createElementsToken() → std::string

schrodinger.infra.canvas.doAlphaNumericCompare(left, right) → int

schrodinger.infra.canvas.doAlphaNumericCompare2(left, right) → int

schrodinger.infra.canvas.doAnd(x, y, wantPopulationCount) → ChmCompressedBitset

doAnd(x, y, wantPopulationCount) -> ChmCompressedBitset64

schrodinger.infra.canvas.doOr(x, y, wantPopulationCount) → ChmCompressedBitset

doOr(x, y, wantPopulationCount) -> ChmCompressedBitset64

schrodinger.infra.canvas.doPairwiseInner(index1, index2, molecules, settings, output, molUI, sssrRings, conntabs, heavy, bonds2Atoms)

schrodinger.infra.canvas.doXor(x, y, wantPopulationCount) → ChmCompressedBitset

doXor(x, y, wantPopulationCount) -> ChmCompressedBitset64

schrodinger.infra.canvas.endsWith(s, substr) → bool

schrodinger.infra.canvas.estimateLineCount(filename, maxSample=100, isExact=None) → uint64

estimateLineCount(filename, maxSample=100) -> uint64 estimateLineCount(filename) -> uint64

schrodinger.infra.canvas.fastatof(p, len=18) → double

fastatof(p) -> double

schrodinger.infra.canvas.fastatoi(p, len=10) → int

fastatoi(p) -> int

schrodinger.infra.canvas.fixupAtomsAndBondsGeneral(molecules, output, settings)

schrodinger.infra.canvas.fixupAtomsAndBondsPairwise(localMols, output, settings)

schrodinger.infra.canvas.getAllowedMem() → double

schrodinger.infra.canvas.getAutoscaleFactor(variance, varianceCutoff) → double

schrodinger.infra.canvas.getBestAtomMapping(m1, m2, atomMappings, baseForMappings=1, distanceCutoff=1e99, xyzScale=1.0, removeBrokenRings=True, wantHydrogens=False) → double

getBestAtomMapping(m1, m2, atomMappings, baseForMappings=1, distanceCutoff=1e99, xyzScale=1.0, removeBrokenRings=True) -> double getBestAtomMapping(m1, m2, atomMappings, baseForMappings=1, distanceCutoff=1e99, xyzScale=1.0) -> double getBestAtomMapping(m1, m2, atomMappings, baseForMappings=1, distanceCutoff=1e99) -> double getBestAtomMapping(m1, m2, atomMappings, baseForMappings=1) -> double getBestAtomMapping(m1, m2, atomMappings) -> double

schrodinger.infra.canvas.getCanvasType(filename) → canvasFileType

schrodinger.infra.canvas.getDelim(flag, defaultDelim) → char

getDelim(flag) -> char

schrodinger.infra.canvas.getFPInfo(filename) → ChmFPTypeInfo

schrodinger.infra.canvas.getFPPrecision(filename) → int

schrodinger.infra.canvas.getLineCount(filename) → uint64

schrodinger.infra.canvas.getMapping(item, outputDelim, onebased) → std::string

schrodinger.infra.canvas.getMetricString(value) → std::string

schrodinger.infra.canvas.getMetricStyle(value) → ChmMetricStyle

schrodinger.infra.canvas.getNumberOfUniqueValues(filename) → uint64

schrodinger.infra.canvas.getSize(overrideSize, logicalSize) → CANVAS_MAXFPLEN_TYPE

schrodinger.infra.canvas.hasBrokenRings(mol, sssrRings, conntab, bonds, ignoreAliphatic=False) → bool

hasBrokenRings(mol, sssrRings, conntab, bonds) -> bool

schrodinger.infra.canvas.hasFraction(source) → bool

schrodinger.infra.canvas.hasPolymerInfo(mol) → bool

schrodinger.infra.canvas.hex2String(source, dest)

schrodinger.infra.canvas.incrementAlphaNum(source, separator1, separator2) → std::string

incrementAlphaNum(source, separator1) -> std::string incrementAlphaNum(source) -> std::string

schrodinger.infra.canvas.interpretPolymerInfo(mol) → bool

schrodinger.infra.canvas.isFepJob(options, inmae) → bool

schrodinger.infra.canvas.isMaeProperty(prop) → bool

schrodinger.infra.canvas.isMetricADistance(value) → bool

schrodinger.infra.canvas.isMetricASimilarity(value) → bool

schrodinger.infra.canvas.isMonomer(mol) → bool

schrodinger.infra.canvas.isValidSMARTS(smarts) → bool

schrodinger.infra.canvas.leftTrim(str)

leftTrim(str, c)

schrodinger.infra.canvas.loadReactions(instream, test=True) → std::vector< ChmReaction,std::allocator< ChmReaction > >

loadReactions(instream) -> std::vector< ChmReaction,std::allocator< ChmReaction > >

schrodinger.infra.canvas.lowerCase(source) → std::string

schrodinger.infra.canvas.maeDecode(source) → std::string

schrodinger.infra.canvas.maeEncode(source) → std::string

schrodinger.infra.canvas.makeMask(index) → uint

schrodinger.infra.canvas.makeMaskLL(index) → uint64

schrodinger.infra.canvas.matchChiralities(m1, atomMappings1, bondMappings1, base1, m2, atomMappings2, bondMappings2, base2) → bool

schrodinger.infra.canvas.matchStereo(m1, atomMappings1, bondMappings1, base1, m2, atomMappings2, bondMappings2, base2) → bool

schrodinger.infra.canvas.mmctToString(ctHandle, mmctString, allProps, depProps)

schrodinger.infra.canvas.mol2grid(mol, atomProps, dest, sigma)

class schrodinger.infra.canvas.molecularinfo

::molecularinfo

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

getBonds() → std::vector< std::pair< int,int >,std::allocator< std::pair< int,int > > > const &

getDM() → ChmSymmetricMatrixUnsignedInt

getDegrees() → std::vector< uint,std::allocator< uint > > const &

next()

returns the next ‘this’ object

schrodinger.infra.canvas.nChooseK(bs) → uint64

schrodinger.infra.canvas.openPWM(filename, rowflag, colflag, checkSquare=False, checkDiag=False, checkSingular=False) → ChmPairwiseFPIn

openPWM(filename, rowflag, colflag, checkSquare=False, checkDiag=False) -> ChmPairwiseFPIn openPWM(filename, rowflag, colflag, checkSquare=False) -> ChmPairwiseFPIn openPWM(filename, rowflag, colflag) -> ChmPairwiseFPIn

class schrodinger.infra.canvas.optionMDL

::optionMDL

H_All = 3

H_AsWritten = 1

H_Chiral = 4

H_Default = 0

H_Never = 0

H_Polar = 2

H_Visible = 5

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

static translate(val) → ChmAtomOption::H

schrodinger.infra.canvas.optionMDL_translate(val) → ChmAtomOption::H

class schrodinger.infra.canvas.optionSMARTS

::optionSMARTS

H_Always = 1

H_Default = 0

H_Never = -1

H_SMILES_behavior = 0

X_Always = 2

X_AromaticNitrogensOnly = 1

X_Default = 1

X_No = 0

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

schrodinger.infra.canvas.parseAlphaNum(source, alphaPart, numPart)

schrodinger.infra.canvas.printoutMCS(molecules, mcsItems, outputFile, toMae, toSD, toCSV, colorCode, useMolIndex, v3SDF, onebased, wantUniqueSMILES)

schrodinger.infra.canvas.printoutMCSFromCts(molecules, records, outputFile, colorCode, useMolIndex)

schrodinger.infra.canvas.printoutPWMCS(molecules, rec1, rec2, output, onebasedCSV, wantUniqueSMILES)

schrodinger.infra.canvas.readBSFile(bsFileName, prefix, mask32, mask64)

schrodinger.infra.canvas.removeAllNotOf(s, allowedChars) → size_t

schrodinger.infra.canvas.removeAllOf(s, disallowedChars) → size_t

schrodinger.infra.canvas.removeExistingFilterInfo(typeinfo) → std::string

schrodinger.infra.canvas.removeMaePrefix(prop) → std::string

removeMaePrefix(prop, app, type) -> std::string

schrodinger.infra.canvas.replaceAll(target, oldSubstring, newSubstring)

schrodinger.infra.canvas.replaceFirst(target, oldSubstring, newSubstring)

schrodinger.infra.canvas.replaceLast(target, oldSubstring, newSubstring)

schrodinger.infra.canvas.resolveConnectivityIssues(m1, m2, atomMappings, base) → bool

schrodinger.infra.canvas.rightTrim(str)

rightTrim(str, c)

schrodinger.infra.canvas.runAllPairwiseMCS(molecules, settings) → std::vector< ChmPairwiseMCSRecord,std::allocator< ChmPairwiseMCSRecord > >

schrodinger.infra.canvas.runMCS(molecules, settings, allow_any_atom_type=False) → std::vector< ChmMCSRecord,std::allocator< ChmMCSRecord > >

runMCS(molecules, settings) -> std::vector< ChmMCSRecord,std::allocator< ChmMCSRecord > >

schrodinger.infra.canvas.runMCSPairwiseRefinement(settings, molecules, index1, index2, heavy, sssrRings, conntabs, bonds2Atoms, output)

schrodinger.infra.canvas.runPairwiseMCS(molecules, settings, whichPairs) → std::vector< ChmPairwiseMCSRecord,std::allocator< ChmPairwiseMCSRecord > >

schrodinger.infra.canvas.scoreAtomMapping(m1, m2, atomMappings, baseForMappings=1, xyzScale=1.0, scores=None, allowRingBreak=False) → double

scoreAtomMapping(m1, m2, atomMappings, baseForMappings=1, xyzScale=1.0, scores=None) -> double scoreAtomMapping(m1, m2, atomMappings, baseForMappings=1, xyzScale=1.0) -> double scoreAtomMapping(m1, m2, atomMappings, baseForMappings=1) -> double scoreAtomMapping(m1, m2, atomMappings) -> double

schrodinger.infra.canvas.scoreAtomMapping2(m1, m2, atomMappings, baseForMappings=1, xyzScale=1.0) → double

scoreAtomMapping2(m1, m2, atomMappings, baseForMappings=1) -> double scoreAtomMapping2(m1, m2, atomMappings) -> double

schrodinger.infra.canvas.setAllowedMem(mem) → bool

schrodinger.infra.canvas.setEnv(varName, value, overwrite=False) → bool

setEnv(varName, value) -> bool

schrodinger.infra.canvas.split(s, delim, yourTokens, allowEmpty=True)

split(s, delim, yourTokens) split(s, delim, yourTokens, allowEmpty=True) split(s, delim, yourTokens)

schrodinger.infra.canvas.ssreset(oss)

schrodinger.infra.canvas.startsWith(s, substr) → bool

schrodinger.infra.canvas.string2Hex(source, dest)

schrodinger.infra.canvas.swap(a, b)

schrodinger.infra.canvas.toLowerCase(toTransform)

schrodinger.infra.canvas.toUpperCase(toTransform)

class schrodinger.infra.canvas.topologicalDescriptors

::topologicalDescriptors

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

append()

appends another ‘this’ object

next()

returns the next ‘this’ object

randicIndex() → double

wienerIndex() → uint

zagreb_m1() → uint

zagreb_m2() → uint

schrodinger.infra.canvas.transpose(src, dest)

transpose(src, dest)

schrodinger.infra.canvas.upperCase(source) → std::string

schrodinger.infra.canvas.utf_strlen(s) → size_t

schrodinger.infra.canvas.weakref_proxy()

proxy(object[, callback]) – create a proxy object that weakly references ‘object’. ‘callback’, if given, is called with a reference to the proxy when ‘object’ is about to be finalized.

schrodinger.infra.canvas.writeBSFile(bsFileName, fpFileName, prefix)