schrodinger.infra.phase module

Phase C++ wrappers

schrodinger.infra.phase.new_instancemethod(func, inst, cls)

class schrodinger.infra.phase.SwigPyIterator(*args, **kwargs)

Bases: object

Proxy of C++ swig::SwigPyIterator class.

thisown

The membership flag

value()

SwigPyIterator_value(SwigPyIterator self) -> PyObject *

incr()

SwigPyIterator_incr(SwigPyIterator self, size_t n=1) -> SwigPyIterator

decr()

SwigPyIterator_decr(SwigPyIterator self, size_t n=1) -> SwigPyIterator

distance()

SwigPyIterator_distance(SwigPyIterator self, SwigPyIterator x) -> ptrdiff_t

equal()

SwigPyIterator_equal(SwigPyIterator self, SwigPyIterator x) -> bool

copy()

SwigPyIterator_copy(SwigPyIterator self) -> SwigPyIterator

next()

SwigPyIterator_next(SwigPyIterator self) -> PyObject *

previous()

SwigPyIterator_previous(SwigPyIterator self) -> PyObject *

advance()

SwigPyIterator_advance(SwigPyIterator self, ptrdiff_t n) -> SwigPyIterator

class schrodinger.infra.phase.PhpIntCoord

Bases: object

Proxy of C++ PhpIntCoord_ class.

thisown

The membership flag

atoms

PhpIntCoord_atoms_get(PhpIntCoord self) -> std::vector< size_t,std::allocator< size_t > > *

coords

PhpIntCoord_coords_get(PhpIntCoord self) -> std::vector< double,std::allocator< double > > *

class schrodinger.infra.phase.PhpAlignCore(*args)

Bases: object

Proxy of C++ PhpAlignCore class.

thisown

The membership flag

closeContactFailure()

PhpAlignCore_closeContactFailure(PhpAlignCore self) -> bool

getAlignedB()

PhpAlignCore_getAlignedB(PhpAlignCore self) -> std::vector< MM_Index,std::allocator< MM_Index > >

getMappings()

PhpAlignCore_getMappings(PhpAlignCore self) -> std::vector< PhpCoreMapping,std::allocator< PhpCoreMapping > >

getNumMappings()

PhpAlignCore_getNumMappings(PhpAlignCore self) -> size_t

static makeOptions(bool allowStereoFailure, bool noCarry, bool inversionsOnly, std::string const & debugMaeFile, double closeContactTol, bool allowCloseContactFailure) → PhpAlignCoreOptions

openRingFailure()

PhpAlignCore_openRingFailure(PhpAlignCore self) -> bool

stereoFailure()

PhpAlignCore_stereoFailure(PhpAlignCore self) -> bool

schrodinger.infra.phase.PhpAlignCore_makeOptions(bool allowStereoFailure, bool noCarry, bool inversionsOnly, std::string const & debugMaeFile, double closeContactTol, bool allowCloseContactFailure) → PhpAlignCoreOptions

class schrodinger.infra.phase.PhpAlignCoreOptions

Bases: object

Proxy of C++ PhpAlignCoreOptions class.

thisown

The membership flag

stereo_change

PhpAlignCoreOptions_stereo_change_get(PhpAlignCoreOptions self) -> PhpStereoChange

stereo_change_action

PhpAlignCoreOptions_stereo_change_action_get(PhpAlignCoreOptions self) -> PhpStereoChangeAction

close_contact_tol

PhpAlignCoreOptions_close_contact_tol_get(PhpAlignCoreOptions self) -> double

close_contact_action

PhpAlignCoreOptions_close_contact_action_get(PhpAlignCoreOptions self) -> PhpCloseContactAction

open_ring_policy

PhpAlignCoreOptions_open_ring_policy_get(PhpAlignCoreOptions self) -> PhpOpenRingPolicy

open_ring_action

PhpAlignCoreOptions_open_ring_action_get(PhpAlignCoreOptions self) -> PhpOpenRingAction

atom_movement

PhpAlignCoreOptions_atom_movement_get(PhpAlignCoreOptions self) -> PhpAtomMovement

debug_maefile

PhpAlignCoreOptions_debug_maefile_get(PhpAlignCoreOptions self) -> std::string const &

class schrodinger.infra.phase.PhpComplex(*args)

Bases: object

Proxy of C++ PhpComplex class.

thisown

The membership flag

create()

PhpComplex_create(PhpComplex self, MM_Index ligandCt, MM_Index receptorCt, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, std::string const & hypoID, double level=0.5, bool proj=False, bool HR=False, bool RH=False, bool RRdisp=False, bool xvol=False, bool rhypo=False, bool single=False) -> std::vector< std::pair< PhpSite,PhpSite >,std::allocator< std::pair< PhpSite,PhpSite > > >

getErrMesg()

PhpComplex_getErrMesg(PhpComplex self) -> std::string

getLimits()

PhpComplex_getLimits(PhpComplex self, std::string const & parName) -> std::vector< double,std::allocator< double > >

setDefaultLimits()

PhpComplex_setDefaultLimits(PhpComplex self)

setLimits()

PhpComplex_setLimits(PhpComplex self, std::string const & parName, double parStrict, double parRelaxed)

class schrodinger.infra.phase.PhpConfOptions(*args)

Bases: object

Proxy of C++ PhpConfOptions class.

thisown

The membership flag

getAppendConfs()

PhpConfOptions_getAppendConfs(PhpConfOptions self) -> bool

getEnergyWindow()

PhpConfOptions_getEnergyWindow(PhpConfOptions self) -> double

getForceField()

PhpConfOptions_getForceField(PhpConfOptions self) -> PhpConfForceField

static getForceFieldCommonName(std::string const & ff_name) → std::string

getForceFieldCommonName(PhpConfForceField ff) -> std::string

static getForceFieldDisplayName(std::string const & ff_name) → std::string

getForceFieldDisplayName(PhpConfForceField ff) -> std::string

getMaxConfs()

PhpConfOptions_getMaxConfs(PhpConfOptions self) -> int

getSamplingMethod()

PhpConfOptions_getSamplingMethod(PhpConfOptions self) -> PhpConfSamplingMethod

static getSamplingMethodDisplayName(PhpConfSamplingMethod method) → std::string

setAppendConfs()

PhpConfOptions_setAppendConfs(PhpConfOptions self, bool append_confs)

setEnergyWindow()

PhpConfOptions_setEnergyWindow(PhpConfOptions self, double energy_window)

setForceField()

PhpConfOptions_setForceField(PhpConfOptions self, PhpConfForceField force_field)

setMaxConfs()

PhpConfOptions_setMaxConfs(PhpConfOptions self, int max_confs)

setSamplingMethod()

PhpConfOptions_setSamplingMethod(PhpConfOptions self, PhpConfSamplingMethod sampling_method)

schrodinger.infra.phase.PhpConfOptions_getForceFieldCommonName(*args) → std::string

getForceFieldCommonName(std::string const & ff_name) -> std::string PhpConfOptions_getForceFieldCommonName(PhpConfForceField ff) -> std::string

schrodinger.infra.phase.PhpConfOptions_getForceFieldDisplayName(*args) → std::string

getForceFieldDisplayName(std::string const & ff_name) -> std::string PhpConfOptions_getForceFieldDisplayName(PhpConfForceField ff) -> std::string

schrodinger.infra.phase.PhpConfOptions_getSamplingMethodDisplayName(PhpConfSamplingMethod method) → std::string

class schrodinger.infra.phase.PhpDatabaseFp(dbName: std::string const &)

Bases: object

Proxy of C++ PhpDatabaseFp class.

thisown

The membership flag

static distEuclidean(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

static distHamming(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

static distSoergel(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

getAllIDs()

PhpDatabaseFp_getAllIDs(PhpDatabaseFp self) -> std::vector< size_t,std::allocator< size_t > >

static getCommonCount(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → size_t

getCt()

PhpDatabaseFp_getCt(PhpDatabaseFp self, size_t molID) -> MM_Index

getCts()

PhpDatabaseFp_getCts(PhpDatabaseFp self, std::vector< size_t,std::allocator< size_t > > const & molIDs) -> std::vector< MM_Index,std::allocator< MM_Index > >

getFp()

PhpDatabaseFp_getFp(PhpDatabaseFp self, PhpFpType fpType, size_t molID, bool allowMissing=True) -> std::vector< unsigned int,std::allocator< unsigned int > >

getFps()

PhpDatabaseFp_getFps(PhpDatabaseFp self, PhpFpType fpType, std::vector< size_t,std::allocator< size_t > > const & molIDs, bool allowMissing=True) -> std::vector< std::vector< unsigned int,std::allocator< unsigned int > >,std::allocator< std::vector< unsigned int,std::allocator< unsigned int > > > >

getFpTypesStored()

PhpDatabaseFp_getFpTypesStored(PhpDatabaseFp self) -> std::vector< PhpFpType,std::allocator< PhpFpType > >

isStored()

PhpDatabaseFp_isStored(PhpDatabaseFp self, PhpFpType fpType) -> bool

static packFp(std::vector< unsigned int, std::allocator< unsigned int > > const & onBits, size_t molID=0) → PhpPackedFp

static simCosine(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

static simDice(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

static simTanimoto(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

static unpackFp(PhpPackedFp packedFp) → std::vector< unsigned int,std::allocator< unsigned int > >

schrodinger.infra.phase.PhpDatabaseFp_distEuclidean(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

schrodinger.infra.phase.PhpDatabaseFp_distHamming(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

schrodinger.infra.phase.PhpDatabaseFp_distSoergel(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

schrodinger.infra.phase.PhpDatabaseFp_getCommonCount(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → size_t

schrodinger.infra.phase.PhpDatabaseFp_packFp(std::vector< unsigned int, std::allocator< unsigned int > > const & onBits, size_t molID=0) → PhpPackedFp

schrodinger.infra.phase.PhpDatabaseFp_simCosine(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

schrodinger.infra.phase.PhpDatabaseFp_simDice(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

schrodinger.infra.phase.PhpDatabaseFp_simTanimoto(std::vector< unsigned int, std::allocator< unsigned int > > const & fp1, std::vector< unsigned int, std::allocator< unsigned int > > const & fp2) → double

schrodinger.infra.phase.PhpDatabaseFp_unpackFp(PhpPackedFp packedFp) → std::vector< unsigned int,std::allocator< unsigned int > >

class schrodinger.infra.phase.PhpDeltaHypoSite

Bases: object

Proxy of C++ PhpDeltaHypoSite_ class.

thisown

The membership flag

siteNumber

PhpDeltaHypoSite_siteNumber_get(PhpDeltaHypoSite self) -> size_t

siteType

PhpDeltaHypoSite_siteType_get(PhpDeltaHypoSite self) -> char

deltaXYZ

PhpDeltaHypoSite_deltaXYZ_get(PhpDeltaHypoSite self) -> double

class schrodinger.infra.phase.PhpDeltaHypo(*args)

Bases: object

Proxy of C++ PhpDeltaHypo class.

thisown

The membership flag

addSiteData(char siteType, double deltaXYZ)

addSiteData(size_t siteNumber, char siteType, double deltaXYZ) PhpDeltaHypo_addSiteData(PhpDeltaHypo self, PhpDeltaHypoSite siteData)

clear()

PhpDeltaHypo_clear(PhpDeltaHypo self)

exportToFile()

PhpDeltaHypo_exportToFile(PhpDeltaHypo self, std::string const & fileName)

exportToStream()

PhpDeltaHypo_exportToStream(PhpDeltaHypo self, std::ostream & outStream)

getDeltaXYZ()

PhpDeltaHypo_getDeltaXYZ(PhpDeltaHypo self, size_t siteIndex) -> double

getSiteData()

PhpDeltaHypo_getSiteData(PhpDeltaHypo self, size_t siteIndex) -> PhpDeltaHypoSite

getSiteNumber()

PhpDeltaHypo_getSiteNumber(PhpDeltaHypo self, size_t siteIndex) -> size_t

getSiteType()

PhpDeltaHypo_getSiteType(PhpDeltaHypo self, size_t siteIndex) -> char

importFromFile()

PhpDeltaHypo_importFromFile(PhpDeltaHypo self, std::string const & fileName)

importFromStream()

PhpDeltaHypo_importFromStream(PhpDeltaHypo self, std::istream & inStream)

numSites()

PhpDeltaHypo_numSites(PhpDeltaHypo self) -> size_t

class schrodinger.infra.phase.PhpSiteWithAtoms

Bases: object

Proxy of C++ PhpSiteWithAtoms class.

thisown

The membership flag

site

PhpSiteWithAtoms_site_get(PhpSiteWithAtoms self) -> PhpSite

atoms

PhpSiteWithAtoms_atoms_get(PhpSiteWithAtoms self) -> std::set< int >

class schrodinger.infra.phase.PhpDeNovoPharm(*args)

Bases: object

Proxy of C++ PhpDeNovoPharm class.

thisown

The membership flag

getCentroid()

PhpDeNovoPharm_getCentroid(PhpDeNovoPharm self) -> std::vector< double,std::allocator< double > >

getCentroidHypo()

PhpDeNovoPharm_getCentroidHypo(PhpDeNovoPharm self, std::string const & hypoID) -> PhpHypoAdaptor

getLigandHypo()

PhpDeNovoPharm_getLigandHypo(PhpDeNovoPharm self, std::string const & hypoID) -> PhpHypoAdaptor

getReceptorHypo()

PhpDeNovoPharm_getReceptorHypo(PhpDeNovoPharm self, std::string const & hypoID) -> PhpHypoAdaptor

getSiteCount()

PhpDeNovoPharm_getSiteCount(PhpDeNovoPharm self) -> int

getSitePairs()

PhpDeNovoPharm_getSitePairs(PhpDeNovoPharm self) -> std::vector< std::pair< PhpSite,PhpSite >,std::allocator< std::pair< PhpSite,PhpSite > > >

exception schrodinger.infra.phase.PhpException(*args)

Bases: Exception

Proxy of C++ PhpException class.

what()

PhpException_what(PhpException self) -> char const *

class schrodinger.infra.phase.PhpExclVolSphere

Bases: object

Proxy of C++ PhpExclVolSphere_ class.

thisown

The membership flag

x

PhpExclVolSphere_x_get(PhpExclVolSphere self) -> double

y

PhpExclVolSphere_y_get(PhpExclVolSphere self) -> double

z

PhpExclVolSphere_z_get(PhpExclVolSphere self) -> double

r

PhpExclVolSphere_r_get(PhpExclVolSphere self) -> double

class schrodinger.infra.phase.PhpExclVol(*args)

Bases: object

Proxy of C++ PhpExclVol class.

thisown

The membership flag

addSphere(double x, double y, double z, double r)

PhpExclVol_addSphere(PhpExclVol self, PhpExclVolSphere sphere)

append()

PhpExclVol_append(PhpExclVol self, PhpExclVol xvol)

clear()

PhpExclVol_clear(PhpExclVol self)

exportToFile()

PhpExclVol_exportToFile(PhpExclVol self, std::string const & fileName)

exportToMMTableFile()

PhpExclVol_exportToMMTableFile(PhpExclVol self, std::string const & fileName)

exportToStream()

PhpExclVol_exportToStream(PhpExclVol self, std::ostream & outStream)

filter()

PhpExclVol_filter(PhpExclVol self, MM_Index ct, bool treatHydrogens) -> PhpExclVol

findViolations()

PhpExclVol_findViolations(PhpExclVol self, MM_Index ctHandle, size_t maxViolations) -> std::vector< size_t,std::allocator< size_t > >

getSphere()

PhpExclVol_getSphere(PhpExclVol self, size_t sphereIndex) -> PhpExclVolSphere

getSphereRadius()

PhpExclVol_getSphereRadius(PhpExclVol self, size_t sphereIndex) -> double

getSpheres()

PhpExclVol_getSpheres(PhpExclVol self) -> std::vector< PhpExclVolSphere,std::allocator< PhpExclVolSphere > >

getSphereXYZ()

PhpExclVol_getSphereXYZ(PhpExclVol self, size_t sphereIndex)

getTreatHydrogens()

PhpExclVol_getTreatHydrogens(PhpExclVol self) -> bool

importFromAnyFile()

PhpExclVol_importFromAnyFile(PhpExclVol self, std::string const & fileName)

importFromFile()

PhpExclVol_importFromFile(PhpExclVol self, std::string const & fileName)

importFromMMTableFile()

PhpExclVol_importFromMMTableFile(PhpExclVol self, std::string const & fileName)

importFromStream()

PhpExclVol_importFromStream(PhpExclVol self, std::istream & inStream)

numShapes()

PhpExclVol_numShapes(PhpExclVol self) -> size_t

numSpheres()

PhpExclVol_numSpheres(PhpExclVol self) -> size_t

removeSphere()

PhpExclVol_removeSphere(PhpExclVol self, size_t sphereIndex)

setSphereRadius()

PhpExclVol_setSphereRadius(PhpExclVol self, size_t sphereIndex, double r)

setSphereXYZ()

PhpExclVol_setSphereXYZ(PhpExclVol self, size_t sphereIndex, double x, double y, double z)

setTreatHydrogens()

PhpExclVol_setTreatHydrogens(PhpExclVol self, bool treatHydrogens)

class schrodinger.infra.phase.PhpFastShapePair

Bases: object

Proxy of C++ PhpFastShapePair_ class.

thisown

The membership flag

i1

PhpFastShapePair_i1_get(PhpFastShapePair self) -> size_t

i2

PhpFastShapePair_i2_get(PhpFastShapePair self) -> size_t

a

PhpFastShapePair_a_get(PhpFastShapePair self) -> double

b

PhpFastShapePair_b_get(PhpFastShapePair self) -> double

c

PhpFastShapePair_c_get(PhpFastShapePair self) -> double

class schrodinger.infra.phase.PhpFastShape(*args)

Bases: object

Proxy of C++ PhpFastShape class.

thisown

The membership flag

alignCt()

PhpFastShape_alignCt(PhpFastShape self, MM_Index ctHandle)

alignCtPy()

PhpFastShape_alignCtPy(PhpFastShape self, MM_Index ctHandle, std::vector< double,std::allocator< double > > const & simTrans)

computeShapeSimPy()

PhpFastShape_computeShapeSimPy(PhpFastShape self, MM_Index ctHandle, bool first, bool inplace) -> std::vector< double,std::allocator< double > >

computeShapeSim(std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & xyz, std::vector< double, std::allocator< double > > const & r, bool first, bool inplace)

computeShapeSim(std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > const & xyz, std::vector< double,std::allocator< double > > const & r, std::vector< int,std::allocator< int > > const & stype, bool first, bool inplace) computeShapeSim(MM_Index ctHandle, bool first, bool inplace) PhpFastShape_computeShapeSim(PhpFastShape self, std::vector< PhpSite,std::allocator< PhpSite > > const & sites, PhpLcsMap const & lcsMap, bool first, bool inplace)

setDebug()

PhpFastShape_setDebug(PhpFastShape self, bool debug)

class schrodinger.infra.phase.PhpFragPair

Bases: object

Proxy of C++ PhpFragPair_ class.

thisown

The membership flag

fragType

PhpFragPair_fragType_get(PhpFragPair self) -> std::string const &

projType

PhpFragPair_projType_get(PhpFragPair self) -> int

schrodinger.infra.phase.addStaticDummyAtom(MM_Index staticFrag, std::string const & fragType, std::vector< double, std::allocator< double > > const & xyz, int bondedTo=0)

schrodinger.infra.phase.checkStaticFrag(std::string const & fragType, size_t npoints, std::string mesg)

schrodinger.infra.phase.coordsMatch(MM_Index ct, int atom, std::vector< double, std::allocator< double > > const & coords, double tol) → bool

schrodinger.infra.phase.createLocateSite(PhpBaseFeature const & bf) → PhpLocateSitePoint *

schrodinger.infra.phase.createStaticFrag(PhpSite staticSite) → MM_Index

schrodinger.infra.phase.createStaticMol(std::vector< PhpSite, std::allocator< PhpSite > > const & sites, MM_Index ctStart) → MM_Index

schrodinger.infra.phase.createStaticSite(std::string const & fragType, std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & xyz) → PhpSite

createStaticSite(PhpSite site) -> PhpSite

schrodinger.infra.phase.deleteAllAtoms(MM_Index ct)

schrodinger.infra.phase.findFirstQSite(std::vector< PhpSite, std::allocator< PhpSite > > const & sites) → size_t

schrodinger.infra.phase.generateLcsMapFromBaseFeatures(std::vector< PhpBaseFeature, std::allocator< PhpBaseFeature > > const & features) → PhpLcsMap

schrodinger.infra.phase.generateSitesFromBaseFeatures(std::vector< PhpBaseFeature, std::allocator< PhpBaseFeature > > const & features, std::vector< PhpAtom, std::allocator< PhpAtom > > const & atoms) → std::vector< PhpSite,std::allocator< PhpSite > >

schrodinger.infra.phase.getFragAtoms(MM_Index ct, PhpSite site, double tol) → std::vector< int,std::allocator< int > >

schrodinger.infra.phase.getFragAtomID(std::string const & fragType, size_t atomIndex) → std::string

schrodinger.infra.phase.getListOfBondedAtoms(MM_Index ct, size_t atom) → std::vector< size_t,std::allocator< size_t > >

schrodinger.infra.phase.getNonQCount(std::vector< PhpBaseFeature, std::allocator< PhpBaseFeature > > const & features) → int

class schrodinger.infra.phase.PhpFeatureData(*args)

Bases: object

Proxy of C++ PhpFeatureData class.

thisown

The membership flag

clear()

PhpFeatureData_clear(PhpFeatureData self)

exportToFile()

PhpFeatureData_exportToFile(PhpFeatureData self, char const * fileName)

exportToStream()

PhpFeatureData_exportToStream(PhpFeatureData self, std::ostream & outStream)

getDataColumn()

PhpFeatureData_getDataColumn(PhpFeatureData self, std::string const & variant, size_t dataColumn=0) -> std::vector< double,std::allocator< double > >

getDataRow()

PhpFeatureData_getDataRow(PhpFeatureData self, char featureType) -> std::vector< double,std::allocator< double > >

getDataValue()

PhpFeatureData_getDataValue(PhpFeatureData self, char featureType) -> double

importFromFile()

PhpFeatureData_importFromFile(PhpFeatureData self, char const * fileName)

importFromStream()

PhpFeatureData_importFromStream(PhpFeatureData self, std::istream & inStream)

numDataColumns()

PhpFeatureData_numDataColumns(PhpFeatureData self) -> size_t

setDataRow()

PhpFeatureData_setDataRow(PhpFeatureData self, char featureType, std::vector< double,std::allocator< double > > const & dataRow)

setDataValue()

PhpFeatureData_setDataValue(PhpFeatureData self, char featureType, double dataValue)

setDefaultDataRow()

PhpFeatureData_setDefaultDataRow(PhpFeatureData self, std::vector< double,std::allocator< double > > const & dataRow)

setDefaultDataValue()

PhpFeatureData_setDefaultDataValue(PhpFeatureData self, double dataValue)

class schrodinger.infra.phase.PhpFeatureDefinition(*args)

Bases: object

Proxy of C++ PhpFeatureDefinition class.

thisown

The membership flag

getFeatureNumber()

PhpFeatureDefinition_getFeatureNumber(PhpFeatureDefinition self) -> size_t

setFeatureNumber()

PhpFeatureDefinition_setFeatureNumber(PhpFeatureDefinition self, size_t a_i)

getFeatureType()

PhpFeatureDefinition_getFeatureType(PhpFeatureDefinition self) -> char

setFeatureType()

PhpFeatureDefinition_setFeatureType(PhpFeatureDefinition self, char a_type)

getFeatureName()

PhpFeatureDefinition_getFeatureName(PhpFeatureDefinition self) -> std::string

setFeatureName()

PhpFeatureDefinition_setFeatureName(PhpFeatureDefinition self, std::string const & a_name)

getFeatureComment()

PhpFeatureDefinition_getFeatureComment(PhpFeatureDefinition self) -> std::string

setFeatureComment()

PhpFeatureDefinition_setFeatureComment(PhpFeatureDefinition self, std::string const a_comment)

getNumIncludes()

PhpFeatureDefinition_getNumIncludes(PhpFeatureDefinition self) -> size_t

getNumExcludes()

PhpFeatureDefinition_getNumExcludes(PhpFeatureDefinition self) -> size_t

getAllIncludes()

PhpFeatureDefinition_getAllIncludes(PhpFeatureDefinition self) -> std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > >

getIncludePattern()

PhpFeatureDefinition_getIncludePattern(PhpFeatureDefinition self, size_t a_i) -> PhpFeaturePattern

setAllIncludes()

PhpFeatureDefinition_setAllIncludes(PhpFeatureDefinition self, std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > > & rhs)

setIncludePattern()

PhpFeatureDefinition_setIncludePattern(PhpFeatureDefinition self, PhpFeaturePattern rhs)

getAllExcludes()

PhpFeatureDefinition_getAllExcludes(PhpFeatureDefinition self) -> std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > >

getExcludePattern()

PhpFeatureDefinition_getExcludePattern(PhpFeatureDefinition self, size_t a_i) -> PhpFeaturePattern

setAllExcludes()

PhpFeatureDefinition_setAllExcludes(PhpFeatureDefinition self, std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > > & rhs)

setExcludePattern()

PhpFeatureDefinition_setExcludePattern(PhpFeatureDefinition self, PhpFeaturePattern rhs)

setProjectedTypeOn()

PhpFeatureDefinition_setProjectedTypeOn(PhpFeatureDefinition self)

setProjectedTypeOff()

PhpFeatureDefinition_setProjectedTypeOff(PhpFeatureDefinition self)

getProjectedType()

PhpFeatureDefinition_getProjectedType(PhpFeatureDefinition self) -> bool

setExtendDistance()

PhpFeatureDefinition_setExtendDistance(PhpFeatureDefinition self, double const a_d)

getExtendDistance()

PhpFeatureDefinition_getExtendDistance(PhpFeatureDefinition self) -> double

setSasOptions()

PhpFeatureDefinition_setSasOptions(PhpFeatureDefinition self, PhpSASOptions const & a_sas)

getSasOptions()

PhpFeatureDefinition_getSasOptions(PhpFeatureDefinition self) -> PhpSASOptions

clear()

PhpFeatureDefinition_clear(PhpFeatureDefinition self)

addStaticFragmentPatterns()

PhpFeatureDefinition_addStaticFragmentPatterns(PhpFeatureDefinition self)

class schrodinger.infra.phase.PhpFeatureFinder(*args)

Bases: object

Proxy of C++ PhpFeatureFinder class.

thisown

The membership flag

setCTSource()

PhpFeatureFinder_setCTSource(PhpFeatureFinder self, int a_ct)

setFeatureDefinitions()

PhpFeatureFinder_setFeatureDefinitions(PhpFeatureFinder self, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & a_fd)

getAllFeatures()

PhpFeatureFinder_getAllFeatures(PhpFeatureFinder self) -> std::vector< PhpBaseFeature,std::allocator< PhpBaseFeature > >

execute()

PhpFeatureFinder_execute(PhpFeatureFinder self)

class schrodinger.infra.phase.PhpFeaturePattern(*args)

Bases: object

Proxy of C++ PhpFeaturePattern class.

thisown

The membership flag

getPattern()

PhpFeaturePattern_getPattern(PhpFeaturePattern self) -> std::string

setPattern()

PhpFeaturePattern_setPattern(PhpFeaturePattern self, std::string const & a_pattern)

getPatternID()

PhpFeaturePattern_getPatternID(PhpFeaturePattern self) -> int

setPatternID()

PhpFeaturePattern_setPatternID(PhpFeaturePattern self, int a_patternID)

getGeometry()

PhpFeaturePattern_getGeometry(PhpFeaturePattern self) -> std::string

setGeometry()

PhpFeaturePattern_setGeometry(PhpFeaturePattern self, std::string const & a_geometry)

getType()

PhpFeaturePattern_getType(PhpFeaturePattern self) -> int

setType()

PhpFeaturePattern_setType(PhpFeaturePattern self, int a_type)

getProjectedType()

PhpFeaturePattern_getProjectedType(PhpFeaturePattern self) -> int

setProjectedType()

PhpFeaturePattern_setProjectedType(PhpFeaturePattern self, int a_type)

getTypeSimilarity()

PhpFeaturePattern_getTypeSimilarity(PhpFeaturePattern self) -> int

setTypeSimilarity()

PhpFeaturePattern_setTypeSimilarity(PhpFeaturePattern self, int a_typeSimilarity)

getAtomList()

PhpFeaturePattern_getAtomList(PhpFeaturePattern self) -> std::vector< size_t,std::allocator< size_t > >

setAtomList()

PhpFeaturePattern_setAtomList(PhpFeaturePattern self, std::vector< size_t,std::allocator< size_t > > & rhs)

setUsedOn()

PhpFeaturePattern_setUsedOn(PhpFeaturePattern self)

setUsedOff()

PhpFeaturePattern_setUsedOff(PhpFeaturePattern self)

getUsedStatus()

PhpFeaturePattern_getUsedStatus(PhpFeaturePattern self) -> bool

setEditOn()

PhpFeaturePattern_setEditOn(PhpFeaturePattern self)

setEditOff()

PhpFeaturePattern_setEditOff(PhpFeaturePattern self)

getEditStatus()

PhpFeaturePattern_getEditStatus(PhpFeaturePattern self) -> bool

setPattyHandle()

PhpFeaturePattern_setPattyHandle(PhpFeaturePattern self, int const a_handle)

getPattyHandle()

PhpFeaturePattern_getPattyHandle(PhpFeaturePattern self) -> int

setExtendDistance()

PhpFeaturePattern_setExtendDistance(PhpFeaturePattern self, double const a_d)

getExtendDistance()

PhpFeaturePattern_getExtendDistance(PhpFeaturePattern self) -> double

getSummary()

PhpFeaturePattern_getSummary(PhpFeaturePattern self) -> std::string

class schrodinger.infra.phase.PhpFeatureRules(*args)

Bases: object

Proxy of C++ PhpFeatureRules class.

thisown

The membership flag

addRule()

PhpFeatureRules_addRule(PhpFeatureRules self, size_t siteNumber, std::string const & permitted, std::string const & prohibited)

clear()

PhpFeatureRules_clear(PhpFeatureRules self)

containsVariant()

PhpFeatureRules_containsVariant(PhpFeatureRules self, std::string const & variant) -> bool

exportToFile()

PhpFeatureRules_exportToFile(PhpFeatureRules self, std::string const & ruleFile)

exportToStream()

PhpFeatureRules_exportToStream(PhpFeatureRules self, std::ostream & ruleStream)

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

PhpFeatureRules_getPermittedFeatures(PhpFeatureRules self, size_t siteIndex) -> std::string

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

PhpFeatureRules_getProhibitedFeatures(PhpFeatureRules self, size_t siteIndex) -> std::string

getSiteNumber()

PhpFeatureRules_getSiteNumber(PhpFeatureRules self, size_t siteIndex) -> size_t

getVariant()

PhpFeatureRules_getVariant(PhpFeatureRules self) -> std::string

hasMixedFeatures()

PhpFeatureRules_hasMixedFeatures(PhpFeatureRules self) -> bool

importFromFile()

PhpFeatureRules_importFromFile(PhpFeatureRules self, std::string const & ruleFile)

importFromStream()

PhpFeatureRules_importFromStream(PhpFeatureRules self, std::istream & ruleStream)

numSites()

PhpFeatureRules_numSites(PhpFeatureRules self) -> size_t

schrodinger.infra.phase.countStructuresMaeOrSD(std::string const & file_name) → int

schrodinger.infra.phase.deleteCtVector(std::vector< MM_Index, std::allocator< MM_Index > > const & cts)

schrodinger.infra.phase.initMMlibs()

schrodinger.infra.phase.getCtTitle(MM_Index ctHandle) → std::string

schrodinger.infra.phase.getDefaultFdFileBaseName() → std::string

schrodinger.infra.phase.getDefaultFdFilePath() → std::string

schrodinger.infra.phase.getLongLine(std::istream & istr, std::string & s) → std::istream &

schrodinger.infra.phase.get_phase_file_format(std::string const & file_name) → PhpFileFormat

schrodinger.infra.phase.getPhpFunction(std::string const & boostFunction) → std::string

schrodinger.infra.phase.getTopoDistanceMatrix(MM_Index ctHandle) → std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

getTopoDistanceMatrix(MM_Index ctHandle, std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > > const & brokenBonds) -> std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

schrodinger.infra.phase.is_connected_subgraph(MM_Index ct, std::vector< size_t, std::allocator< size_t > > const & atom_subset) → bool

schrodinger.infra.phase.isInVector(std::vector< int, std::allocator< int > > const & values, int value) → bool

schrodinger.infra.phase.isNanValue(double const & value) → bool

schrodinger.infra.phase.partitionValues(int num_values, int num_bins) → std::vector< int,std::allocator< int > >

schrodinger.infra.phase.printVectorValues(std::vector< int, std::allocator< int > > const & values, std::string sep, std::string lastSep) → std::string

schrodinger.infra.phase.tokenizeDelimitedString(std::string const & s, char sep, bool trim=False) → std::vector< std::string,std::allocator< std::string > >

schrodinger.infra.phase.valueIsNumeric(std::string const & s) → bool

class schrodinger.infra.phase.PhpHiClusterPair

Bases: object

Proxy of C++ PhpHiClusterPair_ class.

thisown

The membership flag

cluster1

PhpHiClusterPair_cluster1_get(PhpHiClusterPair self) -> std::vector< size_t,std::allocator< size_t > > *

cluster2

PhpHiClusterPair_cluster2_get(PhpHiClusterPair self) -> std::vector< size_t,std::allocator< size_t > > *

d12

PhpHiClusterPair_d12_get(PhpHiClusterPair self) -> double

class schrodinger.infra.phase.PhpHiCluster(*args)

Bases: object

Proxy of C++ PhpHiCluster class.

thisown

The membership flag

clear()

PhpHiCluster_clear(PhpHiCluster self)

clearClusters()

PhpHiCluster_clearClusters(PhpHiCluster self)

createClusters()

PhpHiCluster_createClusters(PhpHiCluster self)

getClusterCutPoints()

PhpHiCluster_getClusterCutPoints(PhpHiCluster self, size_t numClusters) -> std::vector< size_t,std::allocator< size_t > >

getClusters()

PhpHiCluster_getClusters(PhpHiCluster self, size_t numClusters) -> std::vector< std::vector< size_t,std::allocator< size_t > >,std::allocator< std::vector< size_t,std::allocator< size_t > > > >

getClusterSizes()

PhpHiCluster_getClusterSizes(PhpHiCluster self, size_t numClusters) -> std::vector< size_t,std::allocator< size_t > >

getClustersMerged()

PhpHiCluster_getClustersMerged(PhpHiCluster self, size_t numClusters) -> PhpHiClusterPair

numObs()

PhpHiCluster_numObs(PhpHiCluster self) -> size_t

printSummary()

PhpHiCluster_printSummary(PhpHiCluster self, std::ostream & outStream, size_t base=0)

setDmatrix()

PhpHiCluster_setDmatrix(PhpHiCluster self, std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > const & dmatrix)

setLinkageType()

PhpHiCluster_setLinkageType(PhpHiCluster self, int const linkageType)

class schrodinger.infra.phase.PhpHypoAdaptor(*args)

Bases: object

Proxy of C++ PhpHypoAdaptor class.

thisown

The membership flag

addAttr()

PhpHypoAdaptor_addAttr(PhpHypoAdaptor self, std::string const & fileName, bool hydrogens=False)

addCnst()

PhpHypoAdaptor_addCnst(PhpHypoAdaptor self, PhpSiteConstrainer cnst)

addCt()

PhpHypoAdaptor_addCt(PhpHypoAdaptor self, MM_Index ctHandle, std::string const & role)

addIvol()

PhpHypoAdaptor_addIvol(PhpHypoAdaptor self, PhpExclVol ivol)

addMask()

PhpHypoAdaptor_addMask(PhpHypoAdaptor self, PhpSiteMask mask)

addProp(std::string const & propName, std::string const & propValue)

addProp(std::string const & propName, int propValue) PhpHypoAdaptor_addProp(PhpHypoAdaptor self, std::string const & propName, double propValue)

addQsar()

PhpHypoAdaptor_addQsar(PhpHypoAdaptor self, PhpQSAR qsar)

addRad()

PhpHypoAdaptor_addRad(PhpHypoAdaptor self, PhpFeatureData rad)

addRules()

PhpHypoAdaptor_addRules(PhpHypoAdaptor self, PhpFeatureRules rules)

addSite()

PhpHypoAdaptor_addSite(PhpHypoAdaptor self, PhpSite site)

addTol()

PhpHypoAdaptor_addTol(PhpHypoAdaptor self, PhpDeltaHypo tol)

addTolByType()

PhpHypoAdaptor_addTolByType(PhpHypoAdaptor self, PhpFeatureData tol)

addXvol()

PhpHypoAdaptor_addXvol(PhpHypoAdaptor self, PhpExclVol xvol, bool hydrogens=False)

buildAllAttr()

PhpHypoAdaptor_buildAllAttr(PhpHypoAdaptor self, bool alwaysBuild=False)

convert()

PhpHypoAdaptor_convert(PhpHypoAdaptor self, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd)

convertToStatic(std::vector< PhpFeatureDefinition, std::allocator< PhpFeatureDefinition > > const & fd)

PhpHypoAdaptor_convertToStatic(PhpHypoAdaptor self)

deleteAttr()

PhpHypoAdaptor_deleteAttr(PhpHypoAdaptor self, std::string const & name)

deleteSite()

PhpHypoAdaptor_deleteSite(PhpHypoAdaptor self, size_t siteIndex)

deleteSiteFast()

PhpHypoAdaptor_deleteSiteFast(PhpHypoAdaptor self, size_t siteIndex)

getAddCtCount()

PhpHypoAdaptor_getAddCtCount(PhpHypoAdaptor self) -> int

getAddCts()

PhpHypoAdaptor_getAddCts(PhpHypoAdaptor self) -> std::vector< MM_Index,std::allocator< MM_Index > >

getCnst()

PhpHypoAdaptor_getCnst(PhpHypoAdaptor self) -> PhpSiteConstrainer

getFd()

PhpHypoAdaptor_getFd(PhpHypoAdaptor self) -> std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getHypoCt()

PhpHypoAdaptor_getHypoCt(PhpHypoAdaptor self) -> MM_Index

getHypoID()

PhpHypoAdaptor_getHypoID(PhpHypoAdaptor self) -> std::string

getHypoSites()

PhpHypoAdaptor_getHypoSites(PhpHypoAdaptor self, bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > >

getIvol()

PhpHypoAdaptor_getIvol(PhpHypoAdaptor self) -> PhpExclVol

getMask()

PhpHypoAdaptor_getMask(PhpHypoAdaptor self) -> PhpSiteMask

getProp()

PhpHypoAdaptor_getProp(PhpHypoAdaptor self, std::string const & propName) -> std::string

getQsar()

PhpHypoAdaptor_getQsar(PhpHypoAdaptor self) -> PhpQSAR

getRad()

PhpHypoAdaptor_getRad(PhpHypoAdaptor self) -> PhpFeatureData

getRefCt()

PhpHypoAdaptor_getRefCt(PhpHypoAdaptor self) -> MM_Index

getRefSites()

PhpHypoAdaptor_getRefSites(PhpHypoAdaptor self, bool wantProj=False, bool append=False) -> std::vector< PhpSite,std::allocator< PhpSite > >

getRules()

PhpHypoAdaptor_getRules(PhpHypoAdaptor self) -> PhpFeatureRules

getSite()

PhpHypoAdaptor_getSite(PhpHypoAdaptor self, size_t siteIndex) -> PhpSite

getSiteByDisplayName()

PhpHypoAdaptor_getSiteByDisplayName(PhpHypoAdaptor self, std::string const & displayName) -> PhpSite

getSiteCount()

PhpHypoAdaptor_getSiteCount(PhpHypoAdaptor self) -> int

getSiteIndexFromDisplayName()

PhpHypoAdaptor_getSiteIndexFromDisplayName(PhpHypoAdaptor self, std::string const & displayName) -> size_t

getSiteTypes()

PhpHypoAdaptor_getSiteTypes(PhpHypoAdaptor self) -> std::string

getSummary()

PhpHypoAdaptor_getSummary(PhpHypoAdaptor self, bool extended=False) -> std::string

getTol()

PhpHypoAdaptor_getTol(PhpHypoAdaptor self) -> PhpDeltaHypo

getXvol()

PhpHypoAdaptor_getXvol(PhpHypoAdaptor self) -> PhpExclVol

hasAddCts()

PhpHypoAdaptor_hasAddCts(PhpHypoAdaptor self) -> bool

hasCnst()

PhpHypoAdaptor_hasCnst(PhpHypoAdaptor self) -> bool

hasIvol()

PhpHypoAdaptor_hasIvol(PhpHypoAdaptor self) -> bool

hasMask()

PhpHypoAdaptor_hasMask(PhpHypoAdaptor self) -> bool

hasQsar()

PhpHypoAdaptor_hasQsar(PhpHypoAdaptor self) -> bool

hasRad()

PhpHypoAdaptor_hasRad(PhpHypoAdaptor self) -> bool

hasRefCt()

PhpHypoAdaptor_hasRefCt(PhpHypoAdaptor self) -> bool

hasRules()

PhpHypoAdaptor_hasRules(PhpHypoAdaptor self) -> bool

hasTol()

PhpHypoAdaptor_hasTol(PhpHypoAdaptor self) -> bool

hasXvol()

PhpHypoAdaptor_hasXvol(PhpHypoAdaptor self) -> bool

merge()

PhpHypoAdaptor_merge(PhpHypoAdaptor self, PhpHypoAdaptor rhs, double tol)

save()

PhpHypoAdaptor_save(PhpHypoAdaptor self, std::string const & hypoID, bool overwrite)

setHypoID()

PhpHypoAdaptor_setHypoID(PhpHypoAdaptor self, std::string const & hypoID)

setRefCtTitle()

PhpHypoAdaptor_setRefCtTitle(PhpHypoAdaptor self, std::string const & title)

transform()

PhpHypoAdaptor_transform(PhpHypoAdaptor self, std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > const & rotation, std::vector< double,std::allocator< double > > const & translation)

updateSite()

PhpHypoAdaptor_updateSite(PhpHypoAdaptor self, size_t siteIndex, PhpSite site)

writeSummary()

PhpHypoAdaptor_writeSummary(PhpHypoAdaptor self, std::ostream & os, bool extended=False)

class schrodinger.infra.phase.PhpHypoOptimizer(hypo: PhpHypoAdaptor, hit_file: std::string const &, active_titles: std::vector< std::string, std::allocator< std::string > > const &, opt_settings: PhpHypoOptimizerSettings)

Bases: object

Proxy of C++ PhpHypoOptimizer class.

thisown

The membership flag

getActiveFitnessOpt()

PhpHypoOptimizer_getActiveFitnessOpt(PhpHypoOptimizer self) -> std::vector< double,std::allocator< double > >

getActiveFitnessStart()

PhpHypoOptimizer_getActiveFitnessStart(PhpHypoOptimizer self) -> std::vector< double,std::allocator< double > >

getDecoyFitnessOpt()

PhpHypoOptimizer_getDecoyFitnessOpt(PhpHypoOptimizer self) -> std::vector< double,std::allocator< double > >

getDecoyFitnessStart()

PhpHypoOptimizer_getDecoyFitnessStart(PhpHypoOptimizer self) -> std::vector< double,std::allocator< double > >

getHypoDrift()

PhpHypoOptimizer_getHypoDrift(PhpHypoOptimizer self) -> double

getHypoOpt()

PhpHypoOptimizer_getHypoOpt(PhpHypoOptimizer self, std::string const new_hypo_id) -> PhpHypoAdaptor

getParamOpt()

PhpHypoOptimizer_getParamOpt(PhpHypoOptimizer self) -> std::vector< double,std::allocator< double > >

class schrodinger.infra.phase.PhpHypoOptimizerSettings

Bases: object

Proxy of C++ PhpHypoOptimizerSettings class.

thisown

The membership flag

max_cycles

PhpHypoOptimizerSettings_max_cycles_get(PhpHypoOptimizerSettings self) -> size_t

max_hypo_drift

PhpHypoOptimizerSettings_max_hypo_drift_get(PhpHypoOptimizerSettings self) -> double

min_hypo_change

PhpHypoOptimizerSettings_min_hypo_change_get(PhpHypoOptimizerSettings self) -> double

align_weight

PhpHypoOptimizerSettings_align_weight_get(PhpHypoOptimizerSettings self) -> double

vector_weight

PhpHypoOptimizerSettings_vector_weight_get(PhpHypoOptimizerSettings self) -> double

verbose

PhpHypoOptimizerSettings_verbose_get(PhpHypoOptimizerSettings self) -> bool

class schrodinger.infra.phase.PhpLicenseGeneric(arg2: int const, arg3: std::string const &)

Bases: object

Proxy of C++ PhpLicenseGeneric class.

thisown

The membership flag

checkLicense()

PhpLicenseGeneric_checkLicense(PhpLicenseGeneric self)

hasLicenseFeature()

PhpLicenseGeneric_hasLicenseFeature(PhpLicenseGeneric self) -> bool

class schrodinger.infra.phase.PhpLicenseElements

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseElements class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseFeature

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseFeature class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicensePartition

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicensePartition class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseScoring

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseScoring class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseDBCreate

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseDBCreate class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseDBSearch

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseDBSearch class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseCoreHopping

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseCoreHopping class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseQSAR

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseQSAR class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseSelectivity

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseSelectivity class.

thisown

The membership flag

class schrodinger.infra.phase.PhpLicenseShapeScreen

Bases: schrodinger.infra.phase.PhpLicenseGeneric

Proxy of C++ PhpLicenseShapeScreen class.

thisown

The membership flag

class schrodinger.infra.phase.PhpMatchOptions(*args)

Bases: object

Proxy of C++ PhpMatchOptions class.

thisown

The membership flag

getAlignCutoff()

PhpMatchOptions_getAlignCutoff(PhpMatchOptions self) -> double

getAlignPenalty()

PhpMatchOptions_getAlignPenalty(PhpMatchOptions self) -> double

getAlignWeight()

PhpMatchOptions_getAlignWeight(PhpMatchOptions self) -> double

getDeltaDist()

PhpMatchOptions_getDeltaDist(PhpMatchOptions self) -> double

getExhaustiveMatching()

PhpMatchOptions_getExhaustiveMatching(PhpMatchOptions self) -> bool

getIncludedVolumeCutoff()

PhpMatchOptions_getIncludedVolumeCutoff(PhpMatchOptions self) -> double

getIncludedVolumeWeight()

PhpMatchOptions_getIncludedVolumeWeight(PhpMatchOptions self) -> double

getMaxReport()

PhpMatchOptions_getMaxReport(PhpMatchOptions self) -> size_t

getMinSites()

PhpMatchOptions_getMinSites(PhpMatchOptions self) -> size_t

getScoreInPlace()

PhpMatchOptions_getScoreInPlace(PhpMatchOptions self) -> bool

getTimeLimit()

PhpMatchOptions_getTimeLimit(PhpMatchOptions self) -> double

getVectorCutoff()

PhpMatchOptions_getVectorCutoff(PhpMatchOptions self) -> double

getVectorWeight()

PhpMatchOptions_getVectorWeight(PhpMatchOptions self) -> double

getVolumeCutoff()

PhpMatchOptions_getVolumeCutoff(PhpMatchOptions self) -> double

getVolumeWeight()

PhpMatchOptions_getVolumeWeight(PhpMatchOptions self) -> double

getUseAtomTypes()

PhpMatchOptions_getUseAtomTypes(PhpMatchOptions self) -> bool

getUseHardAlignCutoff()

PhpMatchOptions_getUseHardAlignCutoff(PhpMatchOptions self) -> bool

setAlignCutoff()

PhpMatchOptions_setAlignCutoff(PhpMatchOptions self, double align_cutoff)

setAlignPenalty()

PhpMatchOptions_setAlignPenalty(PhpMatchOptions self, double align_penalty)

setAlignWeight()

PhpMatchOptions_setAlignWeight(PhpMatchOptions self, double align_weight)

setDeltaDist()

PhpMatchOptions_setDeltaDist(PhpMatchOptions self, double delta_dist)

setExhaustiveMatching()

PhpMatchOptions_setExhaustiveMatching(PhpMatchOptions self, bool exhaustive)

setIncludedVolumeCutoff()

PhpMatchOptions_setIncludedVolumeCutoff(PhpMatchOptions self, double ivol_cutoff)

setIncludedVolumeWeight()

PhpMatchOptions_setIncludedVolumeWeight(PhpMatchOptions self, double ivol_weight)

setMaxReport()

PhpMatchOptions_setMaxReport(PhpMatchOptions self, size_t max_report)

setMinSites()

PhpMatchOptions_setMinSites(PhpMatchOptions self, size_t min_sites)

setScoreInPlace()

PhpMatchOptions_setScoreInPlace(PhpMatchOptions self, bool score_in_place)

setTimeLimit()

PhpMatchOptions_setTimeLimit(PhpMatchOptions self, double time_limit)

setVectorCutoff()

PhpMatchOptions_setVectorCutoff(PhpMatchOptions self, double vector_cutoff)

setVectorWeight()

PhpMatchOptions_setVectorWeight(PhpMatchOptions self, double vector_weight)

setVolumeCutoff()

PhpMatchOptions_setVolumeCutoff(PhpMatchOptions self, double volume_cutoff)

setVolumeWeight()

PhpMatchOptions_setVolumeWeight(PhpMatchOptions self, double volume_weight)

setUseAtomTypes()

PhpMatchOptions_setUseAtomTypes(PhpMatchOptions self, bool use_atom_types)

setUseHardAlignCutoff()

PhpMatchOptions_setUseHardAlignCutoff(PhpMatchOptions self, bool use_hard_cutoff)

class schrodinger.infra.phase.PhpMMconfAdaptor

Bases: object

Proxy of C++ PhpMMconfAdaptor class.

thisown

The membership flag

setOptions()

PhpMMconfAdaptor_setOptions(PhpMMconfAdaptor self, PhpConfOptions conf_options)

generateConformers(MM_Index ct, double max_range=1.0e6) → std::vector< MM_Index,std::allocator< MM_Index > >

PhpMMconfAdaptor_generateConformers(PhpMMconfAdaptor self, MM_Index ct, std::vector< int,std::allocator< int > > const & frozen_atoms, double max_range=1.0e6) -> std::vector< MM_Index,std::allocator< MM_Index > >

numConformations()

PhpMMconfAdaptor_numConformations(PhpMMconfAdaptor self) -> int

getConformationHandle()

PhpMMconfAdaptor_getConformationHandle(PhpMMconfAdaptor self, int arg3) -> int

writeFile()

PhpMMconfAdaptor_writeFile(PhpMMconfAdaptor self, std::string const & arg3)

execute()

PhpMMconfAdaptor_execute(PhpMMconfAdaptor self, int ctHandle)

setFrozenAtoms()

PhpMMconfAdaptor_setFrozenAtoms(PhpMMconfAdaptor self, std::vector< int,std::allocator< int > > const & atoms)

setMaxConformations()

PhpMMconfAdaptor_setMaxConformations(PhpMMconfAdaptor self, int arg3)

setNumConfsPerRotBond()

PhpMMconfAdaptor_setNumConfsPerRotBond(PhpMMconfAdaptor self, int arg3)

setSamplingMethod()

PhpMMconfAdaptor_setSamplingMethod(PhpMMconfAdaptor self, int arg3)

setRelativeEnergy()

PhpMMconfAdaptor_setRelativeEnergy(PhpMMconfAdaptor self, double arg3)

setAmideSamplingMethod()

PhpMMconfAdaptor_setAmideSamplingMethod(PhpMMconfAdaptor self, int arg3)

setVerbosity()

PhpMMconfAdaptor_setVerbosity(PhpMMconfAdaptor self, int verbosity)

setEnableOptimization()

PhpMMconfAdaptor_setEnableOptimization(PhpMMconfAdaptor self, bool arg3)

getEnableOptimization()

PhpMMconfAdaptor_getEnableOptimization(PhpMMconfAdaptor self) -> bool

setForceField()

PhpMMconfAdaptor_setForceField(PhpMMconfAdaptor self, std::string const & force_field_name)

getForceField()

PhpMMconfAdaptor_getForceField(PhpMMconfAdaptor self) -> std::string

setUseNDDOForCharges()

PhpMMconfAdaptor_setUseNDDOForCharges(PhpMMconfAdaptor self, bool use_nddo)

getUseNDDOForCharges()

PhpMMconfAdaptor_getUseNDDOForCharges(PhpMMconfAdaptor self) -> bool

class schrodinger.infra.phase.PhpOpenRingFinder(ct: MM_Index, atom_subset: std::vector< size_t, std::allocator< size_t > > const &)

Bases: object

Proxy of C++ PhpOpenRingFinder class.

thisown

The membership flag

getOpenRingAtoms()

PhpOpenRingFinder_getOpenRingAtoms(PhpOpenRingFinder self, size_t ring_index, bool subset_only=False) -> std::vector< size_t,std::allocator< size_t > >

getOpenRingCount()

PhpOpenRingFinder_getOpenRingCount(PhpOpenRingFinder self) -> size_t

class schrodinger.infra.phase.PhpOptionsParser(*args)

Bases: object

Proxy of C++ PhpOptionsParser class.

thisown

The membership flag

getArgs()

PhpOptionsParser_getArgs(PhpOptionsParser self) -> std::vector< std::string,std::allocator< std::string > >

getFlags()

PhpOptionsParser_getFlags(PhpOptionsParser self) -> std::vector< std::string,std::allocator< std::string > >

getPairs()

PhpOptionsParser_getPairs(PhpOptionsParser self) -> std::vector< std::pair< std::string,std::string >,std::allocator< std::pair< std::string,std::string > > >

getPosArgs()

PhpOptionsParser_getPosArgs(PhpOptionsParser self) -> std::vector< std::string,std::allocator< std::string > >

getProgramName()

PhpOptionsParser_getProgramName(PhpOptionsParser self) -> std::string

getValidFlags()

PhpOptionsParser_getValidFlags(PhpOptionsParser self) -> std::vector< std::string,std::allocator< std::string > >

getValidPairs()

PhpOptionsParser_getValidPairs(PhpOptionsParser self) -> std::vector< std::pair< std::string,std::string >,std::allocator< std::pair< std::string,std::string > > >

getValueForKey()

PhpOptionsParser_getValueForKey(PhpOptionsParser self, std::string const & key) -> std::string

hasFlag()

PhpOptionsParser_hasFlag(PhpOptionsParser self, std::string const & flag) -> bool

helpRequested()

PhpOptionsParser_helpRequested(PhpOptionsParser self) -> bool

class schrodinger.infra.phase.PhpPackedFp(*args)

Bases: object

Proxy of C++ PhpPackedFp class.

thisown

The membership flag

molID

PhpPackedFp_molID_get(PhpPackedFp self) -> size_t

bits

PhpPackedFp_bits_get(PhpPackedFp self) -> std::string const &

lenOrig

PhpPackedFp_lenOrig_get(PhpPackedFp self) -> size_t

class schrodinger.infra.phase.PhpProject

Bases: object

Proxy of C++ PhpProject class.

thisown

The membership flag

addLigands(std::string const & projectName, std::string const & inFile, PhpFileReadMode readMode, std::string const & titleProp, std::string const & actProp, std::string const & jobName, bool save)

PhpProject_addLigands(PhpProject self, std::string const & projectName, std::string const & sourceProjectName, std::vector< int,std::allocator< int > > const & ligandIDs, std::string const & actProp, std::string const & jobName, bool save)

afterStep()

PhpProject_afterStep(PhpProject self, std::string const & proposedStep) -> bool

alignLigands()

PhpProject_alignLigands(PhpProject self, std::vector< int,std::allocator< int > > const & ligandIDs, std::string const & hypoID, double deltaDist=2.0, int minSites=3, double siteWeight=1.0, double vectorWeight=1.0, double volumeWeight=1.0) -> std::vector< MM_Index,std::allocator< MM_Index > >

assignActives()

PhpProject_assignActives(PhpProject self, double minAct)

assignDefaultGroups()

PhpProject_assignDefaultGroups(PhpProject self)

assignGroups()

PhpProject_assignGroups(PhpProject self, std::vector< std::string,std::allocator< std::string > > const & titles) -> std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

assignInactives()

PhpProject_assignInactives(PhpProject self, double maxAct)

assignQsarSet()

PhpProject_assignQsarSet(PhpProject self, int numTrain, int seed=0, bool usePharmSet=False, bool sortByActivity=False)

beforeStep()

PhpProject_beforeStep(PhpProject self, std::string const & proposedStep) -> bool

buildQsarModel()

PhpProject_buildQsarModel(PhpProject self, std::string const & inFile, std::string const & actProp, std::string const & qsarSetProp, std::string const & trainValue, std::string const & testValue, std::string const & modelStyle, std::string const & pharmFile, std::string const & radFile, int maxFactors, double dgrid, int ncv, double tmin, std::string const & prefix) -> std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

closeProject()

PhpProject_closeProject(PhpProject self)

compareFeatureDef()

PhpProject_compareFeatureDef(PhpProject self, std::string const & fdFile1, std::string const & fdFile2) -> int

commitMasterData()

PhpProject_commitMasterData(PhpProject self, bool writeFirst=False)

copyFile()

PhpProject_copyFile(PhpProject self, std::string const & baseName, std::string const & fromDir, std::string const & toDir, bool mustExist=False)

createSites()

PhpProject_createSites(PhpProject self, std::string const & jobName, bool save)

deleteHypotheses()

PhpProject_deleteHypotheses(PhpProject self, std::vector< std::string,std::allocator< std::string > > const & hypoIDs)

deleteLigands()

PhpProject_deleteLigands(PhpProject self, std::vector< int,std::allocator< int > > const & ligandIDs)

deleteQsarModels()

PhpProject_deleteQsarModels(PhpProject self, std::vector< std::string,std::allocator< std::string > > const & hypoIDs)

expActivity()

PhpProject_expActivity(PhpProject self)

generateConfs()

PhpProject_generateConfs(PhpProject self, PhpConfOptions confOptions, std::string const & jobName, bool save)

getAbsolutePath()

PhpProject_getAbsolutePath(PhpProject self, std::string const & path) -> std::string

getActivity()

PhpProject_getActivity(PhpProject self, int ligandID, double missingValue=0.0) -> double

getActivityMissing()

PhpProject_getActivityMissing(PhpProject self, int ligandID) -> bool

getBindingModes()

PhpProject_getBindingModes(PhpProject self, int numModes, std::vector< std::string,std::allocator< std::string > > const & hypoIDs) -> std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

getConformerCount()

PhpProject_getConformerCount(PhpProject self, int ligandID) -> int

getConformer()

PhpProject_getConformer(PhpProject self, int ligandID, int confIndex) -> MM_Index

getConformers()

PhpProject_getConformers(PhpProject self, int ligandID) -> std::vector< MM_Index,std::allocator< MM_Index > >

getDbID()

PhpProject_getDbID(PhpProject self, int ligandID) -> int

getDefaultFdFile()

PhpProject_getDefaultFdFile(PhpProject self) -> std::string

getDefaultFeatureDef()

PhpProject_getDefaultFeatureDef(PhpProject self) -> std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getDefaultFeatureEquiv()

PhpProject_getDefaultFeatureEquiv(PhpProject self) -> std::vector< std::string,std::allocator< std::string > >

getDefaultFeatureFreq()

PhpProject_getDefaultFeatureFreq(PhpProject self) -> PhpFeatureData

getDefaultFeatureRadii()

PhpProject_getDefaultFeatureRadii(PhpProject self) -> PhpFeatureData

getDefaultFeatureTol()

PhpProject_getDefaultFeatureTol(PhpProject self) -> PhpFeatureData

getDefaultSiteMasks()

PhpProject_getDefaultSiteMasks(PhpProject self) -> std::vector< PhpSiteMask,std::allocator< PhpSiteMask > >

getEnergyProp()

PhpProject_getEnergyProp(PhpProject self) -> std::string

getFdFile()

PhpProject_getFdFile(PhpProject self) -> std::string

getFeatureDefFromProj()

PhpProject_getFeatureDefFromProj(PhpProject self) -> std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getFeatureDef()

PhpProject_getFeatureDef(PhpProject self, std::string const & fdFile) -> std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getFeatureEquiv()

PhpProject_getFeatureEquiv(PhpProject self) -> std::vector< std::string,std::allocator< std::string > >

getFeatureFreq()

PhpProject_getFeatureFreq(PhpProject self) -> PhpFeatureData

getFeatureRadii()

PhpProject_getFeatureRadii(PhpProject self) -> PhpFeatureData

getFeatureTol()

PhpProject_getFeatureTol(PhpProject self) -> PhpFeatureData

getGroup()

PhpProject_getGroup(PhpProject self, int ligandID) -> int

getGroupCount() → int

PhpProject_getGroupCount(PhpProject self, std::vector< int,std::allocator< int > > const & ligandIDs) -> int

getHypo()

PhpProject_getHypo(PhpProject self, std::string const & hypoID, bool qsar=False) -> PhpHypoAdaptor

getHypoAlignments()

PhpProject_getHypoAlignments(PhpProject self, std::string const & hypoID, bool wantMisses=False) -> std::vector< MM_Index,std::allocator< MM_Index > >

getHypoFmt()

PhpProject_getHypoFmt(PhpProject self) -> std::string

getHypoIDs()

PhpProject_getHypoIDs(PhpProject self, bool fullPath=False) -> std::vector< std::string,std::allocator< std::string > >

getHypoMatches()

PhpProject_getHypoMatches(PhpProject self, std::string const & hypoID, bool wantMisses=False) -> std::vector< std::vector< std::string,std::allocator< std::string > >,std::allocator< std::vector< std::string,std::allocator< std::string > > > >

getHypoScores()

PhpProject_getHypoScores(PhpProject self, std::string const & hypoID) -> std::vector< std::string,std::allocator< std::string > >

getHypoSites()

PhpProject_getHypoSites(PhpProject self, std::string const & hypoID, bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > >

getHypoSitesStrings()

PhpProject_getHypoSitesStrings(PhpProject self, std::string const & hypoID, bool wantProj=False) -> std::vector< std::vector< std::string,std::allocator< std::string > >,std::allocator< std::vector< std::string,std::allocator< std::string > > > >

getInFileType()

PhpProject_getInFileType(PhpProject self, std::string const & fileName) -> std::string

getInactiveAlignments()

PhpProject_getInactiveAlignments(PhpProject self, std::string const & hypoID, bool allowMissing=False) -> std::vector< MM_Index,std::allocator< MM_Index > >

getLigand()

PhpProject_getLigand(PhpProject self, int ligandID) -> PhpLigand

getLigandCount()

PhpProject_getLigandCount(PhpProject self, std::string const & category) -> int

getLigandIDs()

PhpProject_getLigandIDs(PhpProject self, std::string const & category) -> std::vector< int,std::allocator< int > >

getMatchedSites()

PhpProject_getMatchedSites(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > >

getMatchedSitesStrings()

PhpProject_getMatchedSitesStrings(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, bool wantProj=False) -> std::vector< std::vector< std::string,std::allocator< std::string > >,std::allocator< std::vector< std::string,std::allocator< std::string > > > >

getMolSites()

PhpProject_getMolSites(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > >

getMolSitesAtoms()

PhpProject_getMolSitesAtoms(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, int offset=1) -> std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

getMolSitesStrings()

PhpProject_getMolSitesStrings(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, bool wantProj=False) -> std::vector< std::vector< std::string,std::allocator< std::string > >,std::allocator< std::vector< std::string,std::allocator< std::string > > > >

getMustMatch()

PhpProject_getMustMatch(PhpProject self, int ligandID) -> bool

getPatternMatches()

PhpProject_getPatternMatches(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd) -> std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

getPharmSet()

PhpProject_getPharmSet(PhpProject self, int ligandID) -> std::string

getProjectPath()

PhpProject_getProjectPath(PhpProject self, bool orig=False) -> std::string

getQsarAlignments()

PhpProject_getQsarAlignments(PhpProject self, std::string const & hypoID) -> std::vector< MM_Index,std::allocator< MM_Index > >

getQsarHypoIDs()

PhpProject_getQsarHypoIDs(PhpProject self, bool fullPath=False) -> std::vector< std::string,std::allocator< std::string > >

getQsarCount()

PhpProject_getQsarCount(PhpProject self, std::string const & category) -> int

getQsarIDs()

PhpProject_getQsarIDs(PhpProject self, std::string const & category) -> std::vector< int,std::allocator< int > >

getQsarModel()

PhpProject_getQsarModel(PhpProject self, std::string const & qsarFile, bool fromProject=False) -> PhpQSAR

getQsarModelClassDescription()

PhpProject_getQsarModelClassDescription(PhpProject self, PhpQSAR qsar, std::string const & qsarClass) -> std::string

getQsarModelClasses()

PhpProject_getQsarModelClasses(PhpProject self, PhpQSAR qsar) -> std::vector< std::string,std::allocator< std::string > >

getQsarModelClassFraction()

PhpProject_getQsarModelClassFraction(PhpProject self, PhpQSAR qsar, std::string const & qsarClass, int numFactors) -> double

getQsarModelCoeff(PhpQSAR qsar, int numFactors, bool combineClasses=False) → std::vector< double,std::allocator< double > >

getQsarModelCoeff(PhpQSAR qsar, int numFactors, std::string const & qsarClass) -> std::vector< double,std::allocator< double > > PhpProject_getQsarModelCoeff(PhpProject self, PhpQSAR qsar, int numFactors, std::vector< std::string,std::allocator< std::string > > const & qsarClasses, bool combineClasses=False) -> std::vector< double,std::allocator< double > >

getQsarModelCoeffRange(PhpQSAR qsar, int numFactors, bool combineClasses=False) → std::vector< double,std::allocator< double > >

getQsarModelCoeffRange(PhpQSAR qsar, int numFactors, std::string const & qsarClass) -> std::vector< double,std::allocator< double > > PhpProject_getQsarModelCoeffRange(PhpProject self, PhpQSAR qsar, int numFactors, std::vector< std::string,std::allocator< std::string > > const & qsarClasses, bool combineClasses=False) -> std::vector< double,std::allocator< double > >

getQsarModelFactorCount()

PhpProject_getQsarModelFactorCount(PhpProject self, PhpQSAR qsar) -> int

getQsarModelGridLimits()

PhpProject_getQsarModelGridLimits(PhpProject self, PhpQSAR qsar) -> std::vector< double,std::allocator< double > >

getQsarModelGridSpacing()

PhpProject_getQsarModelGridSpacing(PhpProject self, PhpQSAR qsar) -> double

getQsarModelRegF()

PhpProject_getQsarModelRegF(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelRegP()

PhpProject_getQsarModelRegP(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelRegRsqr()

PhpProject_getQsarModelRegRsqr(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelRegRsqrCv()

PhpProject_getQsarModelRegRsqrCv(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelRegRsqrScramble()

PhpProject_getQsarModelRegRsqrScramble(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelRegSD()

PhpProject_getQsarModelRegSD(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelRegStability()

PhpProject_getQsarModelRegStability(PhpProject self, PhpQSAR qsar, int numFactors) -> double

getQsarModelStyle()

PhpProject_getQsarModelStyle(PhpProject self, PhpQSAR qsar) -> std::string

getQsarModelVolBitCount(PhpQSAR qsar) → int

getQsarModelVolBitCount(PhpQSAR qsar, std::string const & qsarClass) -> int PhpProject_getQsarModelVolBitCount(PhpProject self, PhpQSAR qsar, std::vector< std::string,std::allocator< std::string > > const & qsarClasses) -> int

getQsarModelVolClasses()

PhpProject_getQsarModelVolClasses(PhpProject self, PhpQSAR qsar) -> std::vector< std::string,std::allocator< std::string > >

getQsarModelVolCoords(PhpQSAR qsar) → std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getQsarModelVolCoords(PhpQSAR qsar, std::string const & qsarClass) -> std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > PhpProject_getQsarModelVolCoords(PhpProject self, PhpQSAR qsar, std::vector< std::string,std::allocator< std::string > > const & qsarClasses) -> std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getQsarModelVolOnBits(PhpQSAR qsar, MM_Index ctHandle) → std::vector< int,std::allocator< int > >

getQsarModelVolOnBits(PhpQSAR qsar, MM_Index ctHandle, std::string const & qsarClass) -> std::vector< int,std::allocator< int > > PhpProject_getQsarModelVolOnBits(PhpProject self, PhpQSAR qsar, MM_Index ctHandle, std::vector< std::string,std::allocator< std::string > > const & qsarClasses) -> std::vector< int,std::allocator< int > >

getQsarProps()

PhpProject_getQsarProps(PhpProject self, MM_Index & ctHandle) -> std::vector< std::string,std::allocator< std::string > >

getQsarSet()

PhpProject_getQsarSet(PhpProject self, int ligandID) -> std::string

getQsarStats()

PhpProject_getQsarStats(PhpProject self, std::string const & hypoID) -> std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

getRuntimeName()

PhpProject_getRuntimeName(PhpProject self, std::string const & fileName) -> std::string

getSiteMappings()

PhpProject_getSiteMappings(PhpProject self, PhpSite site, std::vector< PhpSite,std::allocator< PhpSite > > const & pool, int maxMap=1, double tol=0.001, bool matchType=True, bool matchNumber=False) -> std::vector< int,std::allocator< int > >

getSitesConformer()

PhpProject_getSitesConformer(PhpProject self, int ligandID, int confIndex) -> std::vector< PhpSite,std::allocator< PhpSite > >

getSitesConformers()

PhpProject_getSitesConformers(PhpProject self, int ligandID) -> std::vector< std::vector< PhpSite,std::allocator< PhpSite > >,std::allocator< std::vector< PhpSite,std::allocator< PhpSite > > > >

getSiteMasks()

PhpProject_getSiteMasks(PhpProject self, bool ignoreDiffs=False) -> std::vector< PhpSiteMask,std::allocator< PhpSiteMask > >

getSlash()

PhpProject_getSlash(PhpProject self) -> std::string

getStep()

PhpProject_getStep(PhpProject self) -> std::string

getTitle()

PhpProject_getTitle(PhpProject self, int ligandID) -> std::string

haveMasterDiffs()

PhpProject_haveMasterDiffs(PhpProject self, bool ignoreQsar=False) -> bool

isValidArchiveName()

PhpProject_isValidArchiveName(PhpProject self, std::string const & projectArchive) -> bool

isValidProjectName()

PhpProject_isValidProjectName(PhpProject self, std::string const & projectName) -> bool

logActivity()

PhpProject_logActivity(PhpProject self)

mapSites()

PhpProject_mapSites(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, std::vector< PhpSite,std::allocator< PhpSite > > * sites, std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > > * atoms, bool wantProj=False)

needSyncFeatureDef()

PhpProject_needSyncFeatureDef(PhpProject self) -> bool

newProject(std::string const & projectName, std::string const & inFile, std::string const & fdFile, PhpFileReadMode readMode, std::string const & titleProp, std::string const & actProp, std::string const & jobName, bool save, std::string hypoFmt, std::string energyProp)

PhpProject_newProject(PhpProject self, std::string const & projectName, std::string const & sourceProjectName, std::vector< int,std::allocator< int > > const & ligandIDs, std::string const & fdFile, std::string const & actProp, std::string const & jobName, bool save, std::string hypoFmt, std::string energyProp)

normalizeFeatureEquiv()

PhpProject_normalizeFeatureEquiv(PhpProject self, std::vector< std::string,std::allocator< std::string > > const & featureEquiv) -> std::vector< std::string,std::allocator< std::string > >

openProject()

PhpProject_openProject(PhpProject self, std::string const & projectName, bool checkMaster=False)

restoreMasterData()

PhpProject_restoreMasterData(PhpProject self)

reviseDatabase()

PhpProject_reviseDatabase(PhpProject self, std::string const & jobName, std::string const & reviseOptions, bool save)

sampleActives()

PhpProject_sampleActives(PhpProject self, int sampleSize, bool includeNone=False)

saveFeatureDef()

PhpProject_saveFeatureDef(PhpProject self, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd)

saveFeatureDefToFile()

PhpProject_saveFeatureDefToFile(PhpProject self, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, std::string const & fdFile)

saveFeatureEquiv()

PhpProject_saveFeatureEquiv(PhpProject self, std::vector< std::string,std::allocator< std::string > > const & featureEquiv)

saveFeatureFreq()

PhpProject_saveFeatureFreq(PhpProject self, PhpFeatureData featureFreq)

saveFeatureRadii()

PhpProject_saveFeatureRadii(PhpProject self, PhpFeatureData featureRadii)

saveFeatureTol()

PhpProject_saveFeatureTol(PhpProject self, PhpFeatureData featureTol)

saveFind()

PhpProject_saveFind(PhpProject self, std::string const & jobName)

saveMasterData()

PhpProject_saveMasterData(PhpProject self)

saveQsar()

PhpProject_saveQsar(PhpProject self, std::string const & jobName)

saveSiteMasks()

PhpProject_saveSiteMasks(PhpProject self, std::vector< PhpSiteMask,std::allocator< PhpSiteMask > > const & siteMasks)

scaleActivity()

PhpProject_scaleActivity(PhpProject self, double scale)

setActivity()

PhpProject_setActivity(PhpProject self, int ligandID, double activity)

setActivityMissing()

PhpProject_setActivityMissing(PhpProject self, int ligandID)

setGroup()

PhpProject_setGroup(PhpProject self, int ligandID, int group)

setMustMatch()

PhpProject_setMustMatch(PhpProject self, int ligandID, bool mustMatch)

setPharmSet()

PhpProject_setPharmSet(PhpProject self, int ligandID, std::string const & pharmSet)

setQsarSet()

PhpProject_setQsarSet(PhpProject self, int ligandID, std::string const & qsarSet)

setupFind()

PhpProject_setupFind(PhpProject self, std::string const & directory) -> std::string

setupQsar()

PhpProject_setupQsar(PhpProject self, std::string const & directory) -> std::string

siteToStrings()

PhpProject_siteToStrings(PhpProject self, PhpSite site) -> std::vector< std::string,std::allocator< std::string > >

syncFeatureDef()

PhpProject_syncFeatureDef(PhpProject self)

testQsarModel()

PhpProject_testQsarModel(PhpProject self, PhpQSAR qsar, std::string const & inFile, std::string const & actProp, std::string const & prefix) -> std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

writeHypoFiles()

PhpProject_writeHypoFiles(PhpProject self, std::string const & hypoID, MM_Index refCt, std::vector< PhpSite,std::allocator< PhpSite > > const & hypoSites, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd)

unzipArchive()

PhpProject_unzipArchive(PhpProject self, std::string const & directory, std::string const & archive)

unzipProject()

PhpProject_unzipProject(PhpProject self, std::string const & directory, std::string const & projectArchive) -> std::string

writeSummary()

PhpProject_writeSummary(PhpProject self, std::ostream & os)

zipDirectory()

PhpProject_zipDirectory(PhpProject self, std::string const & directory, std::string const & archive)

zipProject()

PhpProject_zipProject(PhpProject self, std::string const & directory, std::string const & projectName, bool create=True) -> std::string

class schrodinger.infra.phase.PhpQSARModel

Bases: object

Proxy of C++ PhpQSARModel_ class.

thisown

The membership flag

featureRadii

PhpQSARModel_featureRadii_get(PhpQSARModel self) -> PhpFeatureData

gridSpacing

PhpQSARModel_gridSpacing_get(PhpQSARModel self) -> double

xmin

PhpQSARModel_xmin_get(PhpQSARModel self) -> double

xmax

PhpQSARModel_xmax_get(PhpQSARModel self) -> double

ymin

PhpQSARModel_ymin_get(PhpQSARModel self) -> double

ymax

PhpQSARModel_ymax_get(PhpQSARModel self) -> double

zmin

PhpQSARModel_zmin_get(PhpQSARModel self) -> double

zmax

PhpQSARModel_zmax_get(PhpQSARModel self) -> double

atomClasses

PhpQSARModel_atomClasses_get(PhpQSARModel self) -> std::vector< std::string,std::allocator< std::string > > *

volumeNames

PhpQSARModel_volumeNames_get(PhpQSARModel self) -> std::vector< std::string,std::allocator< std::string > > *

numBitsByClass

PhpQSARModel_numBitsByClass_get(PhpQSARModel self) -> std::map< std::string,size_t,std::less< std::string >,std::allocator< std::pair< std::string const,size_t > > > *

pls

PhpQSARModel_pls_get(PhpQSARModel self) -> PhpPLS

rsqrScramble

PhpQSARModel_rsqrScramble_get(PhpQSARModel self) -> std::vector< double,std::allocator< double > > *

classFractions

PhpQSARModel_classFractions_get(PhpQSARModel self) -> std::map< std::string,std::vector< double,std::allocator< double > >,std::less< std::string >,std::allocator< std::pair< std::string const,std::vector< double,std::allocator< double > > > > > *

class schrodinger.infra.phase.PhpVolCoords

Bases: object

Proxy of C++ PhpVolCoords_ class.

thisown

The membership flag

x

PhpVolCoords_x_get(PhpVolCoords self) -> double

y

PhpVolCoords_y_get(PhpVolCoords self) -> double

z

PhpVolCoords_z_get(PhpVolCoords self) -> double

class schrodinger.infra.phase.PhpQSAR(*args)

Bases: object

Proxy of C++ PhpQSAR class.

thisown

The membership flag

clear()

PhpQSAR_clear(PhpQSAR self)

clearDataSet()

PhpQSAR_clearDataSet(PhpQSAR self)

clearModel()

PhpQSAR_clearModel(PhpQSAR self)

computeRCorr()

PhpQSAR_computeRCorr(PhpQSAR self, std::vector< double,std::allocator< double > > const & x, std::vector< double,std::allocator< double > > const & y) -> double

computeStats()

PhpQSAR_computeStats(PhpQSAR self, std::vector< double,std::allocator< double > > const & yobs, std::vector< double,std::allocator< double > > const & ypred, double & varObs, double & varPred, double & rmsErr, double & qsqr, double & rcorr)

createModel(std::vector< PhpMolModel, std::allocator< PhpMolModel > > const & molecules, std::vector< double, std::allocator< double > > const & activities, std::vector< size_t, std::allocator< size_t > > const & trainList, double gridSpacing, double dbuff, size_t maxFactors) → int

PhpQSAR_createModel(PhpQSAR self, std::vector< size_t,std::allocator< size_t > > const & trainList, double gridSpacing, double dbuff, size_t maxFactors) -> int

crossValidateModel(size_t n, size_t randSeed, std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > & yhatLNO, std::vector< double, std::allocator< double > > & rsqrYobs, std::vector< double, std::allocator< double > > & rsqrYhat) → int

crossValidateModel(size_t n, size_t randSeed, std::vector< double,std::allocator< double > > & rsqrYobs, std::vector< double,std::allocator< double > > & rsqrYhat) -> int PhpQSAR_crossValidateModel(PhpQSAR self, size_t n, size_t randSeed) -> int

duplexDataSet(size_t numTotal, size_t numTrain, size_t & randomSeed, std::vector< size_t, std::allocator< size_t > > & trainList, std::vector< size_t, std::allocator< size_t > > & predList)

PhpQSAR_duplexDataSet(PhpQSAR self, size_t numTrain, size_t & randomSeed, std::vector< double,std::allocator< double > > const & activities, std::vector< size_t,std::allocator< size_t > > & trainList, std::vector< size_t,std::allocator< size_t > > & predList)

exportModel()

PhpQSAR_exportModel(PhpQSAR self, std::string const & modelFile) -> int

exportModelToStream()

PhpQSAR_exportModelToStream(PhpQSAR self, std::ostream & modelStream)

getActivities()

PhpQSAR_getActivities(PhpQSAR self) -> std::vector< double,std::allocator< double > >

getAtomClasses()

PhpQSAR_getAtomClasses(PhpQSAR self) -> std::vector< std::string,std::allocator< std::string > >

getAtomClassDescription()

PhpQSAR_getAtomClassDescription(PhpQSAR self, std::string const & atomClass) -> std::string

getClassFraction()

PhpQSAR_getClassFraction(PhpQSAR self, std::string const & atomClass, size_t numFactors) -> double

getModel()

PhpQSAR_getModel(PhpQSAR self) -> PhpQSARModel

getModelType()

PhpQSAR_getModelType(PhpQSAR self) -> std::string

getMoleculeType()

PhpQSAR_getMoleculeType(PhpQSAR self) -> std::string

getMolecules()

PhpQSAR_getMolecules(PhpQSAR self) -> std::vector< PhpMolModel,std::allocator< PhpMolModel > >

getMolModel()

PhpQSAR_getMolModel(PhpQSAR self, MM_Index ctHandle) -> PhpMolModel

getOnBits()

PhpQSAR_getOnBits(PhpQSAR self, std::vector< size_t,std::allocator< size_t > > const & bits) -> std::vector< size_t,std::allocator< size_t > >

getRegF()

PhpQSAR_getRegF(PhpQSAR self, size_t numFactors) -> double

getRegP()

PhpQSAR_getRegP(PhpQSAR self, size_t numFactors) -> double

getRegRsqr()

PhpQSAR_getRegRsqr(PhpQSAR self, size_t numFactors) -> double

getRegRsqrCv()

PhpQSAR_getRegRsqrCv(PhpQSAR self, size_t numFactors) -> double

getRegRsqrScramble()

PhpQSAR_getRegRsqrScramble(PhpQSAR self, size_t numFactors) -> double

getRegSD()

PhpQSAR_getRegSD(PhpQSAR self, size_t numFactors) -> double

getRegStability()

PhpQSAR_getRegStability(PhpQSAR self, size_t numFactors) -> double

getTestRCorr()

PhpQSAR_getTestRCorr(PhpQSAR self, size_t numFactors) -> double

getTitles()

PhpQSAR_getTitles(PhpQSAR self) -> std::vector< std::string,std::allocator< std::string > >

getTvalue()

PhpQSAR_getTvalue(PhpQSAR self, double p, size_t ndf) -> double

getVectSubset()

PhpQSAR_getVectSubset(PhpQSAR self, std::vector< double,std::allocator< double > > const & v, std::vector< size_t,std::allocator< size_t > > const & subset) -> std::vector< double,std::allocator< double > >

getVolAtomClasses()

PhpQSAR_getVolAtomClasses(PhpQSAR self) -> std::vector< std::string,std::allocator< std::string > >

getVolCoords() → std::vector< PhpVolCoords,std::allocator< PhpVolCoords > >

getVolCoords(std::string const & atomClass) -> std::vector< PhpVolCoords,std::allocator< PhpVolCoords > > PhpQSAR_getVolCoords(PhpQSAR self, std::vector< std::string,std::allocator< std::string > > const & atomClasses) -> std::vector< PhpVolCoords,std::allocator< PhpVolCoords > >

getVolOccBits(PhpMolModel const & molModel) → std::vector< size_t,std::allocator< size_t > >

getVolOccBits(size_t imol) -> std::vector< size_t,std::allocator< size_t > > getVolOccBits(PhpMolModel const & molModel, std::string const & atomClass) -> std::vector< size_t,std::allocator< size_t > > getVolOccBits(size_t imol, std::string const & atomClass) -> std::vector< size_t,std::allocator< size_t > > getVolOccBits(PhpMolModel const & molModel, std::vector< std::string,std::allocator< std::string > > const & atomClasses) -> std::vector< size_t,std::allocator< size_t > > PhpQSAR_getVolOccBits(PhpQSAR self, size_t imol, std::vector< std::string,std::allocator< std::string > > const & atomClasses) -> std::vector< size_t,std::allocator< size_t > >

getVolRegCoeffs(size_t numFactors, bool combineAtomClasses=False) → std::vector< double,std::allocator< double > >

getVolRegCoeffs(size_t numFactors, std::string const & atomClass) -> std::vector< double,std::allocator< double > > PhpQSAR_getVolRegCoeffs(PhpQSAR self, size_t numFactors, std::vector< std::string,std::allocator< std::string > > const & atomClasses, bool combineAtomClasses=False) -> std::vector< double,std::allocator< double > >

importActivities(char const * actFile) → int

PhpQSAR_importActivities(PhpQSAR self, std::vector< double,std::allocator< double > > const & activities)

importModel(std::string const & modelFile) → int

PhpQSAR_importModel(PhpQSAR self, std::istream & modelStream) -> int

importMolecules(char const * maeFile) → int

PhpQSAR_importMolecules(PhpQSAR self, std::vector< MM_Index,std::allocator< MM_Index > > const & ctHandles)

importMoleculesAndActivities()

PhpQSAR_importMoleculesAndActivities(PhpQSAR self, char const * maeFile, char const * activityProperty, double missingActivity=0.0) -> int

importPharm(char const * pharmFile, char const * featureRadiusFile=None) → int

PhpQSAR_importPharm(PhpQSAR self, std::vector< std::vector< PhpSite,std::allocator< PhpSite > >,std::allocator< std::vector< PhpSite,std::allocator< PhpSite > > > > const & pharmVect) -> int

numActivities()

PhpQSAR_numActivities(PhpQSAR self) -> size_t

numMolecules()

PhpQSAR_numMolecules(PhpQSAR self) -> size_t

numPLSFactors()

PhpQSAR_numPLSFactors(PhpQSAR self) -> size_t

numVolBits() → size_t

numVolBits(std::string const & atomClass) -> size_t PhpQSAR_numVolBits(PhpQSAR self, std::vector< std::string,std::allocator< std::string > > const & atomClasses) -> size_t

printDelimitedActivities()

PhpQSAR_printDelimitedActivities(PhpQSAR self, std::ostream & outStream, std::vector< size_t,std::allocator< size_t > > const & observations, std::vector< std::string,std::allocator< std::string > > const & qsarSet, std::string const & delim, bool printHeaders=True)

printDelimitedBits()

PhpQSAR_printDelimitedBits(PhpQSAR self, std::ostream & outStream, std::vector< size_t,std::allocator< size_t > > const & observations, std::vector< std::string,std::allocator< std::string > > const & qsarSet, std::string const & delim, bool printHeaders=True)

printModel()

PhpQSAR_printModel(PhpQSAR self, std::ostream & outStream, bool printVolumeBits=True)

printPred(std::ostream & outStream, std::vector< PhpMolModel, std::allocator< PhpMolModel > > const & molecules, std::vector< double, std::allocator< double > > const & activities, std::vector< size_t, std::allocator< size_t > > const & predList, bool trainingSet=False)

PhpQSAR_printPred(PhpQSAR self, std::ostream & outStream, std::vector< size_t,std::allocator< size_t > > const & predList, bool trainingSet=False)

printVolOccBits(std::ostream & outStream, std::vector< PhpMolModel, std::allocator< PhpMolModel > > const & molecules, std::vector< size_t, std::allocator< size_t > > const & molList)

printVolOccBits(std::ostream & outStream, std::vector< size_t,std::allocator< size_t > > const & molList) PhpQSAR_printVolOccBits(PhpQSAR self, std::ostream & outStream)

setTvalueFilterOff()

PhpQSAR_setTvalueFilterOff(PhpQSAR self)

setTvalueFilterOn()

PhpQSAR_setTvalueFilterOn(PhpQSAR self, double tmin, size_t n, size_t seed)

testModel(std::vector< PhpMolModel, std::allocator< PhpMolModel > > const & molecules, std::vector< double, std::allocator< double > > const & activities, std::vector< size_t, std::allocator< size_t > > const & predList, size_t numFactors, std::vector< double, std::allocator< double > > & predActivities, double & rmsErr, double & qsqr)

testModel(std::vector< size_t,std::allocator< size_t > > const & predList, size_t numFactors, std::vector< double,std::allocator< double > > & predActivities, double & rmsErr, double & qsqr) testModel(std::vector< PhpMolModel,std::allocator< PhpMolModel > > const & molecules, std::vector< PhpMolVolume,std::allocator< PhpMolVolume > > & molVolumes, std::vector< double,std::allocator< double > > const & activities, std::vector< size_t,std::allocator< size_t > > const & predList, size_t numFactors, bool restorePatterns, std::vector< double,std::allocator< double > > & predActivities, double & rmsErr, double & qsqr) testModel(std::vector< PhpMolModel,std::allocator< PhpMolModel > > const & molecules, std::vector< double,std::allocator< double > > const & activities, std::vector< size_t,std::allocator< size_t > > const & predList, size_t numFactors1, size_t numFactors2, std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > & predActivities, std::vector< double,std::allocator< double > > & rmsErr, std::vector< double,std::allocator< double > > & qsqr) PhpQSAR_testModel(PhpQSAR self, std::vector< size_t,std::allocator< size_t > > const & predList, size_t numFactors1, size_t numFactors2, std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > & predActivities, std::vector< double,std::allocator< double > > & rmsErr, std::vector< double,std::allocator< double > > & qsqr)

class schrodinger.infra.phase.PhpAtomClassDescriptions

Bases: object

Proxy of C++ PhpAtomClassDescriptions class.

thisown

The membership flag

getAtomClassDescription()

PhpAtomClassDescriptions_getAtomClassDescription(PhpAtomClassDescriptions self, std::string const & atomClass) -> std::string

class schrodinger.infra.phase.PhpFeatureClassDescriptions

Bases: object

Proxy of C++ PhpFeatureClassDescriptions class.

thisown

The membership flag

getFeatureClassDescription()

PhpFeatureClassDescriptions_getFeatureClassDescription(PhpFeatureClassDescriptions self, std::string const & featureClass) -> std::string

class schrodinger.infra.phase.PhpScreener(hypo: PhpHypoAdaptor, mode: PhpScreenMode)

Bases: object

Proxy of C++ PhpScreener class.

thisown

The membership flag

getConfCount()

PhpScreener_getConfCount(PhpScreener self) -> int

getConfOptions()

PhpScreener_getConfOptions(PhpScreener self) -> PhpConfOptions

getMatchCount()

PhpScreener_getMatchCount(PhpScreener self) -> int

getMatchOptions()

PhpScreener_getMatchOptions(PhpScreener self) -> PhpMatchOptions

screen()

PhpScreener_screen(PhpScreener self, PhpStructureBus structure, bool refine=False) -> std::vector< MM_Index,std::allocator< MM_Index > >

setConfOptions()

PhpScreener_setConfOptions(PhpScreener self, PhpConfOptions conf_options)

setMatchOptions()

PhpScreener_setMatchOptions(PhpScreener self, PhpMatchOptions match_options)

schrodinger.infra.phase.find_index_matches(std::string const & db_name, PhpHypoAdaptor hypo, size_t min_sites, double delta_dist) → std::vector< size_t,std::allocator< size_t > >

find_index_matches(std::string const & db_name, PhpHypoAdaptor hypo, size_t min_sites, double delta_dist, std::vector< size_t,std::allocator< size_t > > const & subset) -> std::vector< size_t,std::allocator< size_t > >

schrodinger.infra.phase.get_alt_index_name(std::string const & db_name, PhpHypoAdaptor hypo) → std::string

schrodinger.infra.phase.get_database_ids(std::string const & db_name, std::string const preferred_subset) → std::vector< size_t,std::allocator< size_t > >

schrodinger.infra.phase.has_alt_index(std::string const & db_name, PhpHypoAdaptor hypo) → bool

schrodinger.infra.phase.is_phase_database(std::string const & db_name) → bool

schrodinger.infra.phase.read_phase_subset(std::string const & subset_file) → std::vector< size_t,std::allocator< size_t > >

schrodinger.infra.phase.same_feature_definitions(std::string const & db_name, PhpHypoAdaptor hypo) → bool

schrodinger.infra.phase.write_phase_subset(std::string const & subset_file, std::vector< size_t, std::allocator< size_t > > const & mol_ids)

class schrodinger.infra.phase.PhpSite(*args)

Bases: object

Proxy of C++ PhpSite class.

thisown

The membership flag

setXCoord()

PhpSite_setXCoord(PhpSite self, double a_x)

getXCoord()

PhpSite_getXCoord(PhpSite self) -> double

setYCoord()

PhpSite_setYCoord(PhpSite self, double a_y)

getYCoord()

PhpSite_getYCoord(PhpSite self) -> double

setZCoord()

PhpSite_setZCoord(PhpSite self, double a_z)

getZCoord()

PhpSite_getZCoord(PhpSite self) -> double

setCoordinates()

PhpSite_setCoordinates(PhpSite self, double a_x, double a_y, double a_z)

getCoordinates()

PhpSite_getCoordinates(PhpSite self) -> std::vector< double,std::allocator< double > >

setSiteType()

PhpSite_setSiteType(PhpSite self, std::string const & a_type)

setSiteTypeChar()

PhpSite_setSiteTypeChar(PhpSite self, char const a_char)

getSiteType()

PhpSite_getSiteType(PhpSite self) -> std::string

getSiteTypeChar()

PhpSite_getSiteTypeChar(PhpSite self) -> char

setSiteNumber()

PhpSite_setSiteNumber(PhpSite self, size_t const a_number)

getSiteNumber()

PhpSite_getSiteNumber(PhpSite self) -> size_t

getSiteName()

PhpSite_getSiteName(PhpSite self, int offset=1) -> std::string

getDisplayName()

PhpSite_getDisplayName(PhpSite self) -> std::string

getSiteDescription()

PhpSite_getSiteDescription(PhpSite self) -> std::string

setSiteSimilarity()

PhpSite_setSiteSimilarity(PhpSite self, int const a_type)

getSiteSimilarity()

PhpSite_getSiteSimilarity(PhpSite self) -> int

calculateSimilarity()

PhpSite_calculateSimilarity(PhpSite self, PhpSite rhs) -> double

SiteStatusOn = 0

SiteStatusOff = 1

setStatus()

PhpSite_setStatus(PhpSite self, int a_status)

setSiteStatusOn()

PhpSite_setSiteStatusOn(PhpSite self)

setSiteStatusOff()

PhpSite_setSiteStatusOff(PhpSite self)

getSiteStatus()

PhpSite_getSiteStatus(PhpSite self) -> int

setProjectedOnly()

PhpSite_setProjectedOnly(PhpSite self, bool const a_status)

getProjectedOnly()

PhpSite_getProjectedOnly(PhpSite self) -> bool

distance()

PhpSite_distance(PhpSite self, PhpSite rhs) -> double

setFragType()

PhpSite_setFragType(PhpSite self, std::string const & fragType)

getFragType()

PhpSite_getFragType(PhpSite self) -> std::string

setMaskValue()

PhpSite_setMaskValue(PhpSite self, int mask)

getMaskValue()

PhpSite_getMaskValue(PhpSite self) -> int

setPermitted()

PhpSite_setPermitted(PhpSite self, std::string const & permitted)

getPermitted()

PhpSite_getPermitted(PhpSite self) -> std::string

setProhibited()

PhpSite_setProhibited(PhpSite self, std::string const & prohibited)

getProhibited()

PhpSite_getProhibited(PhpSite self) -> std::string

setProjCoords()

PhpSite_setProjCoords(PhpSite self, std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > > const & projCoords)

getProjCoords()

PhpSite_getProjCoords(PhpSite self) -> std::vector< std::vector< double,std::allocator< double > >,std::allocator< std::vector< double,std::allocator< double > > > >

setRad()

PhpSite_setRad(PhpSite self, double rad)

getRad()

PhpSite_getRad(PhpSite self) -> double

setTol()

PhpSite_setTol(PhpSite self, double tol)

getTol()

PhpSite_getTol(PhpSite self) -> double

setXP()

PhpSite_setXP(PhpSite self, double xp, bool defined=True)

getXP()

PhpSite_getXP(PhpSite self) -> double

hasXP()

PhpSite_hasXP(PhpSite self) -> bool

setDefaults()

PhpSite_setDefaults(PhpSite self)

class schrodinger.infra.phase.PhpSiteConstrainer(*args)

Bases: object

Proxy of C++ PhpSiteConstrainer class.

thisown

The membership flag

addConstraint()

PhpSiteConstrainer_addConstraint(PhpSiteConstrainer self, PhpSiteConstraint constraint)

clear()

PhpSiteConstrainer_clear(PhpSiteConstrainer self)

exportConstraints(std::string const & outFile)

PhpSiteConstrainer_exportConstraints(PhpSiteConstrainer self, std::ostream & outStream)

getConstraints() → std::vector< PhpSiteConstraint,std::allocator< PhpSiteConstraint > >

PhpSiteConstrainer_getConstraints(PhpSiteConstrainer self, size_t numSites) -> std::vector< PhpSiteConstraint,std::allocator< PhpSiteConstraint > >

getConstraint()

PhpSiteConstrainer_getConstraint(PhpSiteConstrainer self, size_t i, size_t numSites) -> PhpSiteConstraint

getConstraintValue()

PhpSiteConstrainer_getConstraintValue(PhpSiteConstrainer self, std::vector< PhpSite,std::allocator< PhpSite > > const & sites) -> double

hasProjectedSites()

PhpSiteConstrainer_hasProjectedSites(PhpSiteConstrainer self) -> bool

importConstraints(std::string const & inFile)

PhpSiteConstrainer_importConstraints(PhpSiteConstrainer self, std::istream & inStream)

numConstraints() → size_t

PhpSiteConstrainer_numConstraints(PhpSiteConstrainer self, size_t numSites) -> size_t

passes(std::vector< PhpSite, std::allocator< PhpSite > > const & sites, PhpSiteConstraint constraint) → bool

passes(std::vector< PhpSite,std::allocator< PhpSite > > const & hypoSites, std::string & reason) -> bool passes(std::vector< PhpSite,std::allocator< PhpSite > > const & hypoSites, PhpLigand const & refLigand, size_t refConfIndex, std::string & reason) -> bool passes(PhpLigand const & refLigand, size_t refConfIndex, std::vector< size_t,std::allocator< size_t > > const & refSiteIndices, PhpLigand const & matchedLigand, size_t matchedConfIndex, std::vector< size_t,std::allocator< size_t > > const & matchedSiteIndices, std::vector< PhpSite,std::allocator< PhpSite > > & refSitesNeeded, std::string & reason) -> bool PhpSiteConstrainer_passes(PhpSiteConstrainer self, std::vector< PhpSite,std::allocator< PhpSite > > const & hypoSites, bool checkHypoSites, PhpLigand const & matchedLigand, size_t matchedConfIndex, std::vector< size_t,std::allocator< size_t > > const & matchedSiteIndices, std::string & reason) -> bool

printConstraint()

PhpSiteConstrainer_printConstraint(PhpSiteConstrainer self, PhpSiteConstraint constraint, std::ostream & outStream)

class schrodinger.infra.phase.PhpSiteConstraint(*args)

Bases: object

Proxy of C++ PhpSiteConstraint class.

thisown

The membership flag

getSiteIndices()

PhpSiteConstraint_getSiteIndices(PhpSiteConstraint self) -> std::vector< int,std::allocator< int > >

getSiteTypes()

PhpSiteConstraint_getSiteTypes(PhpSiteConstraint self) -> std::string

getValue()

PhpSiteConstraint_getValue(PhpSiteConstraint self) -> double

getTol()

PhpSiteConstraint_getTol(PhpSiteConstraint self) -> double

setConstraint()

PhpSiteConstraint_setConstraint(PhpSiteConstraint self, std::vector< int,std::allocator< int > > const & u_siteIndices, std::string const & u_siteTypes, double u_value, double u_tol)

siteIndices

PhpSiteConstraint_siteIndices_get(PhpSiteConstraint self) -> std::vector< size_t,std::allocator< size_t > > *

siteTypes

PhpSiteConstraint_siteTypes_get(PhpSiteConstraint self) -> std::string const &

value

PhpSiteConstraint_value_get(PhpSiteConstraint self) -> double

tol

PhpSiteConstraint_tol_get(PhpSiteConstraint self) -> double

class schrodinger.infra.phase.PhpSiteMask(*args)

Bases: object

Proxy of C++ PhpSiteMask class.

thisown

The membership flag

addSiteMaskData(size_t siteNumber, char siteType, int maskValue)

PhpSiteMask_addSiteMaskData(PhpSiteMask self, PhpSiteMaskData siteMaskData)

addSiteMaskGroup(std::vector< size_t, std::allocator< size_t > > const & siteIndices, size_t minMatch)

PhpSiteMask_addSiteMaskGroup(PhpSiteMask self, PhpSiteMaskGroup group)

clear()

PhpSiteMask_clear(PhpSiteMask self)

clearSiteMaskGroups()

PhpSiteMask_clearSiteMaskGroups(PhpSiteMask self)

exportToFile()

PhpSiteMask_exportToFile(PhpSiteMask self, std::string const & fileName)

exportToStream()

PhpSiteMask_exportToStream(PhpSiteMask self, std::ostream & outStream)

getSiteMaskData()

PhpSiteMask_getSiteMaskData(PhpSiteMask self, size_t siteIndex) -> PhpSiteMaskData

getSiteMaskGroups()

PhpSiteMask_getSiteMaskGroups(PhpSiteMask self) -> std::vector< PhpSiteMaskGroup,std::allocator< PhpSiteMaskGroup > >

getSiteMaskValue()

PhpSiteMask_getSiteMaskValue(PhpSiteMask self, size_t siteIndex) -> int

getSiteMaskVector()

PhpSiteMask_getSiteMaskVector(PhpSiteMask self) -> std::vector< int,std::allocator< int > >

getSiteNumber()

PhpSiteMask_getSiteNumber(PhpSiteMask self, size_t siteIndex) -> size_t

getSiteType()

PhpSiteMask_getSiteType(PhpSiteMask self, size_t siteIndex) -> char

importFromFile()

PhpSiteMask_importFromFile(PhpSiteMask self, std::string const & fileName)

importFromStream()

PhpSiteMask_importFromStream(PhpSiteMask self, std::istream & inStream)

numSites()

PhpSiteMask_numSites(PhpSiteMask self) -> size_t

static resolveMaskValue(int maskValue, size_t & groupNumber, size_t & minMatch)

static splitMaskValue(int maskValue) → std::vector< int,std::allocator< int > >

static resolveMatchLimits(std::vector< int, std::allocator< int > > const & siteMask, size_t & minSites, size_t & maxSites)

static getMatchLimits(std::vector< int, std::allocator< int > > const & siteMask) → std::vector< int,std::allocator< int > >

schrodinger.infra.phase.PhpSiteMask_resolveMaskValue(int maskValue, size_t & groupNumber, size_t & minMatch)

schrodinger.infra.phase.PhpSiteMask_splitMaskValue(int maskValue) → std::vector< int,std::allocator< int > >

schrodinger.infra.phase.PhpSiteMask_resolveMatchLimits(std::vector< int, std::allocator< int > > const & siteMask, size_t & minSites, size_t & maxSites)

schrodinger.infra.phase.PhpSiteMask_getMatchLimits(std::vector< int, std::allocator< int > > const & siteMask) → std::vector< int,std::allocator< int > >

class schrodinger.infra.phase.PhpSiteMaskData(*args)

Bases: object

Proxy of C++ PhpSiteMaskData class.

thisown

The membership flag

getSiteNumber()

PhpSiteMaskData_getSiteNumber(PhpSiteMaskData self) -> int

getSiteType()

PhpSiteMaskData_getSiteType(PhpSiteMaskData self) -> char

getMaskValue()

PhpSiteMaskData_getMaskValue(PhpSiteMaskData self) -> int

setData()

PhpSiteMaskData_setData(PhpSiteMaskData self, int u_siteNumber, char u_site, int u_maskValue)

siteNumber

PhpSiteMaskData_siteNumber_get(PhpSiteMaskData self) -> size_t

siteType

PhpSiteMaskData_siteType_get(PhpSiteMaskData self) -> char

maskValue

PhpSiteMaskData_maskValue_get(PhpSiteMaskData self) -> int

class schrodinger.infra.phase.PhpSiteMaskGroup(*args)

Bases: object

Proxy of C++ PhpSiteMaskGroup class.

thisown

The membership flag

getSiteIndices()

PhpSiteMaskGroup_getSiteIndices(PhpSiteMaskGroup self) -> std::vector< int,std::allocator< int > >

getMinMatch()

PhpSiteMaskGroup_getMinMatch(PhpSiteMaskGroup self) -> int

getGroupNumber()

PhpSiteMaskGroup_getGroupNumber(PhpSiteMaskGroup self) -> int

setGroup()

PhpSiteMaskGroup_setGroup(PhpSiteMaskGroup self, std::vector< int,std::allocator< int > > const & u_siteIndices, int u_minMatch, int u_groupNumber)

siteIndices

PhpSiteMaskGroup_siteIndices_get(PhpSiteMaskGroup self) -> std::vector< size_t,std::allocator< size_t > > *

minMatch

PhpSiteMaskGroup_minMatch_get(PhpSiteMaskGroup self) -> size_t

groupNumber

PhpSiteMaskGroup_groupNumber_get(PhpSiteMaskGroup self) -> size_t

class schrodinger.infra.phase.PhpStructureBus(*args)

Bases: object

Proxy of C++ PhpStructureBus class.

thisown

The membership flag

empty()

PhpStructureBus_empty(PhpStructureBus self) -> bool

getCt()

PhpStructureBus_getCt(PhpStructureBus self) -> MM_Index

getCtCopy()

PhpStructureBus_getCtCopy(PhpStructureBus self) -> MM_Index

getCtVector()

PhpStructureBus_getCtVector(PhpStructureBus self) -> std::vector< MM_Index,std::allocator< MM_Index > >

getCtVectorCopy()

PhpStructureBus_getCtVectorCopy(PhpStructureBus self) -> std::vector< MM_Index,std::allocator< MM_Index > >

getLigand()

PhpStructureBus_getLigand(PhpStructureBus self) -> PhpLigand const &

getLigandCopy()

PhpStructureBus_getLigandCopy(PhpStructureBus self) -> PhpLigand

getRecord()

PhpStructureBus_getRecord(PhpStructureBus self) -> PhpDbStructRecord const &

getRecordCopy()

PhpStructureBus_getRecordCopy(PhpStructureBus self) -> PhpDbStructRecord

getStructureFormat()

PhpStructureBus_getStructureFormat(PhpStructureBus self) -> PhpStructureFormat

class schrodinger.infra.phase.PhpStructureReader(*args)

Bases: object

Proxy of C++ PhpStructureReader class.

thisown

The membership flag

next()

PhpStructureReader_next(PhpStructureReader self) -> PhpStructureBus

class schrodinger.infra.phase.PhpStructureSplitter(struct_files: std::vector< std::string, std::allocator< std::string > >, num_out_files: int, out_file_prefix: std::string const &, verbose: bool = False, update_interval: int = 10000)

Bases: object

Proxy of C++ PhpStructureSplitter class.

thisown

The membership flag

getFileCountIn()

PhpStructureSplitter_getFileCountIn(PhpStructureSplitter self) -> int

getFileCountOut()

PhpStructureSplitter_getFileCountOut(PhpStructureSplitter self) -> int

getFileFormat()

PhpStructureSplitter_getFileFormat(PhpStructureSplitter self) -> PhpFileFormat

getFileNamesIn()

PhpStructureSplitter_getFileNamesIn(PhpStructureSplitter self) -> std::vector< std::string,std::allocator< std::string > >

getFileNamesOut()

PhpStructureSplitter_getFileNamesOut(PhpStructureSplitter self) -> std::vector< std::string,std::allocator< std::string > >

getStructureCountIn()

PhpStructureSplitter_getStructureCountIn(PhpStructureSplitter self) -> int

getStructureCountsIn()

PhpStructureSplitter_getStructureCountsIn(PhpStructureSplitter self) -> std::vector< int,std::allocator< int > >

getStructureCountsOut()

PhpStructureSplitter_getStructureCountsOut(PhpStructureSplitter self) -> std::vector< int,std::allocator< int > >

class schrodinger.infra.phase.PhpSubsetSplitter(*args, **kwargs)

Bases: object

Proxy of C++ PhpSubsetSplitter class.

thisown

The membership flag

getDbCount()

PhpSubsetSplitter_getDbCount(PhpSubsetSplitter self) -> int

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

PhpSubsetSplitter_getDbPaths(PhpSubsetSplitter self, int subjob_number) -> std::vector< std::string,std::allocator< std::string > >

getRecordCount() → int

PhpSubsetSplitter_getRecordCount(PhpSubsetSplitter self, int subjob_number) -> int

getSubjobCount()

PhpSubsetSplitter_getSubjobCount(PhpSubsetSplitter self) -> int

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

PhpSubsetSplitter_getSubsetFiles(PhpSubsetSplitter self, int subjob_number) -> std::vector< std::string,std::allocator< std::string > >

class schrodinger.infra.phase.PhpTextFileReader(file_name: std::string const &, strip_newline: bool = True)

Bases: object

Proxy of C++ PhpTextFileReader class.

thisown

The membership flag

begin()

PhpTextFileReader_begin(PhpTextFileReader self) -> PhpTextFileIterator

end()

PhpTextFileReader_end(PhpTextFileReader self) -> PhpTextFileIterator

getLine()

PhpTextFileReader_getLine(PhpTextFileReader self) -> std::string const &

readNext()

PhpTextFileReader_readNext(PhpTextFileReader self) -> bool

class schrodinger.infra.phase.PhpTextFileIterator(*args)

Bases: object

Proxy of C++ PhpTextFileIterator class.

thisown

The membership flag

class schrodinger.infra.phase.PhpSortCapperDoubleIncreasing(max_size: size_t)

Bases: object

Proxy of C++ PhpSortCapper<(double,std::less<(double)>)> class.

thisown

The membership flag

getMaxSize()

PhpSortCapperDoubleIncreasing_getMaxSize(PhpSortCapperDoubleIncreasing self) -> size_t

getValues()

PhpSortCapperDoubleIncreasing_getValues(PhpSortCapperDoubleIncreasing self) -> std::vector< double,std::allocator< double > >

insert()

PhpSortCapperDoubleIncreasing_insert(PhpSortCapperDoubleIncreasing self, double value) -> bool

size()

PhpSortCapperDoubleIncreasing_size(PhpSortCapperDoubleIncreasing self) -> size_t

class schrodinger.infra.phase.PhpSortCapperDoubleDecreasing(max_size: size_t)

Bases: object

Proxy of C++ PhpSortCapper<(double,std::greater<(double)>)> class.

thisown

The membership flag

getMaxSize()

PhpSortCapperDoubleDecreasing_getMaxSize(PhpSortCapperDoubleDecreasing self) -> size_t

getValues()

PhpSortCapperDoubleDecreasing_getValues(PhpSortCapperDoubleDecreasing self) -> std::vector< double,std::allocator< double > >

insert()

PhpSortCapperDoubleDecreasing_insert(PhpSortCapperDoubleDecreasing self, double value) -> bool

size()

PhpSortCapperDoubleDecreasing_size(PhpSortCapperDoubleDecreasing self) -> size_t

schrodinger.infra.phase.conformerBlockPositions(std::string const & structure_file, std::string title_property, bool use_titles=False, bool use_stereo=True, bool use_annotations=False) → std::vector< size_t,std::allocator< size_t > >

schrodinger.infra.phase.createConfOptions(PhpOptionsParser parser) → PhpConfOptions

createConfOptions(std::vector< std::string,std::allocator< std::string > > const & args) -> PhpConfOptions

schrodinger.infra.phase.extractConfOptionsArgs(PhpConfOptions conf_options) → std::vector< std::string,std::allocator< std::string > >