schrodinger.infra.phase

Module phase

Phase C++ wrappers

Classes

[hide private]

SwigPyIterator
Proxy of C++ swig::SwigPyIterator class.

SwigIntVector
Proxy of C++ std::vector<(int)> class.

SwigUnsignedIntVector
Proxy of C++ std::vector<(unsigned int)> class.

SwigDoubleVector
Proxy of C++ std::vector<(double)> class.

SwigSizetVector
Proxy of C++ std::vector<(size_t)> class.

SwigStringVector
Proxy of C++ std::vector<(std::string)> class.

SwigVectorIntVector
Proxy of C++ std::vector<(std::vector<(int)>)> class.

SwigVectorDoubleVector
Proxy of C++ std::vector<(std::vector<(double)>)> class.

SwigVectorSizetVector
Proxy of C++ std::vector<(std::vector<(size_t)>)> class.

SwigVectorStringVector
Proxy of C++ std::vector<(std::vector<(std::string)>)> class.

SwigPhpFpTypeVector
Proxy of C++ std::vector<(PhpFpType)> class.

PhpPackedFp
Proxy of C++ PhpPackedFp class.

PhpSite
Proxy of C++ PhpSite class.

SwigVectorPhpSitePhpSite
Proxy of C++ std::vector<(std::pair<(PhpSite,PhpSite)>)> class.

PhpFeaturePattern
Proxy of C++ PhpFeaturePattern class.

PhpFeatureDefinition
Proxy of C++ PhpFeatureDefinition class.

PhpSiteConstraint
Proxy of C++ PhpSiteConstraint class.

PhpSiteMaskData
Proxy of C++ PhpSiteMaskData class.

PhpSiteMaskGroup
Proxy of C++ PhpSiteMaskGroup class.

PhpSiteMask
Proxy of C++ PhpSiteMask class.

PhpFeatureData
Proxy of C++ PhpFeatureData class.

PhpException
Proxy of C++ PhpException class.

PhpIntCoord
Proxy of C++ PhpIntCoord_ class.

PhpAlignCore
Proxy of C++ PhpAlignCore class.

PhpProject
Proxy of C++ PhpProject class.

PhpFastShapePair
Proxy of C++ PhpFastShapePair_ class.

PhpFastShape
Proxy of C++ PhpFastShape class.

PhpComplex
Proxy of C++ PhpComplex class.

PhpDatabaseFp
Proxy of C++ PhpDatabaseFp class.

PhpDeltaHypoSite
Proxy of C++ PhpDeltaHypoSite_ class.

PhpDeltaHypo
Proxy of C++ PhpDeltaHypo class.

PhpSiteWithAtoms
Proxy of C++ PhpSiteWithAtoms class.

PhpDeNovoPharm
Proxy of C++ PhpDeNovoPharm class.

PhpExclVolSphere
Proxy of C++ PhpExclVolSphere_ class.

PhpExclVol
Proxy of C++ PhpExclVol class.

PhpFragPair
Proxy of C++ PhpFragPair_ class.

PhpFeatureFinder
Proxy of C++ PhpFeatureFinder class.

PhpFeatureRules
Proxy of C++ PhpFeatureRules class.

PhpHiClusterPair
Proxy of C++ PhpHiClusterPair_ class.

PhpHiCluster
Proxy of C++ PhpHiCluster class.

PhpAtomClassDescriptions
Proxy of C++ PhpAtomClassDescriptions class.

PhpFeatureClassDescriptions
Proxy of C++ PhpFeatureClassDescriptions class.

PhpQSARModel
Proxy of C++ PhpQSARModel_ class.

PhpVolCoords
Proxy of C++ PhpVolCoords_ class.

PhpQSAR
Proxy of C++ PhpQSAR class.

PhpSiteConstrainer
Proxy of C++ PhpSiteConstrainer class.

PhpHypoAdaptor
Proxy of C++ PhpHypoAdaptor class.

Functions

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_swig_setattr_nondynamic(self, class_type, name, value, static=1)

_swig_setattr(self, class_type, name, value)

_swig_getattr(self, class_type, name)

_swig_repr(self)
repr(x)

_swig_setattr_nondynamic_method(set)

PhpSiteMask_resolveMaskValue(maskValue, groupNumber, minMatch)
PhpSiteMask_resolveMaskValue(int maskValue, size_t & groupNumber, size_t & minMatch)

PhpSiteMask_splitMaskValue(maskValue)
PhpSiteMask_splitMaskValue(int maskValue) -> SwigIntVector

PhpSiteMask_resolveMatchLimits(siteMask, minSites, maxSites)
PhpSiteMask_resolveMatchLimits(SwigIntVector siteMask, size_t & minSites, size_t & maxSites)

PhpSiteMask_getMatchLimits(siteMask)
PhpSiteMask_getMatchLimits(SwigIntVector siteMask) -> SwigIntVector

PhpDatabaseFp_distEuclidean(fp1, fp2)
PhpDatabaseFp_distEuclidean(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> double

PhpDatabaseFp_distHamming(fp1, fp2)
PhpDatabaseFp_distHamming(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> double

PhpDatabaseFp_distSoergel(fp1, fp2)
PhpDatabaseFp_distSoergel(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> double

PhpDatabaseFp_getCommonCount(fp1, fp2)
PhpDatabaseFp_getCommonCount(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> size_t

PhpDatabaseFp_packFp(onBits, molID=0)
PhpDatabaseFp_packFp(SwigUnsignedIntVector onBits, size_t molID=0) -> PhpPackedFp

PhpDatabaseFp_simCosine(fp1, fp2)
PhpDatabaseFp_simCosine(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> double

PhpDatabaseFp_simDice(fp1, fp2)
PhpDatabaseFp_simDice(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> double

PhpDatabaseFp_simTanimoto(fp1, fp2)
PhpDatabaseFp_simTanimoto(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) -> double

PhpDatabaseFp_unpackFp(packedFp)
PhpDatabaseFp_unpackFp(PhpPackedFp packedFp) -> SwigUnsignedIntVector

addStaticDummyAtom(staticFrag, fragType, xyz, bondedTo=0)
addStaticDummyAtom(MM_Index staticFrag, std::string const & fragType, SwigDoubleVector xyz, int bondedTo=0)

checkStaticFrag(*args, **kwargs)
checkStaticFrag(std::string const & fragType, size_t npoints, std::string mesg)

coordsMatch(ct, atom, coords, tol)
coordsMatch(MM_Index ct, int atom, SwigDoubleVector coords, double tol) -> bool

createLocateSite(bf)
createLocateSite(PhpBaseFeature const & bf) -> PhpLocateSitePoint *

createStaticFrag(staticSite)
createStaticFrag(PhpSite staticSite) -> MM_Index

createStaticMol(*args, **kwargs)
createStaticMol(std::vector< PhpSite,std::allocator< PhpSite > > const & sites, MM_Index ctStart) -> MM_Index

createStaticSite(*args)
createStaticSite(std::string const & fragType, SwigVectorDoubleVector xyz) -> PhpSite createStaticSite(PhpSite site) -> PhpSite

deleteAllAtoms(ct)
deleteAllAtoms(MM_Index ct)

findFirstQSite(sites)
findFirstQSite(std::vector< PhpSite,std::allocator< PhpSite > > const & sites) -> size_t

generateLcsMapFromBaseFeatures(features)
generateLcsMapFromBaseFeatures(std::vector< PhpBaseFeature,std::allocator< PhpBaseFeature > > const & features) -> PhpLcsMap

generateSitesFromBaseFeatures(features, atoms)
generateSitesFromBaseFeatures(std::vector< PhpBaseFeature,std::allocator< PhpBaseFeature > > const & features, std::vector< PhpAtom,std::allocator< PhpAtom > > const & atoms) -> std::vector< PhpSite,std::allocator< PhpSite > >

getFragAtoms(ct, site, tol)
getFragAtoms(MM_Index ct, PhpSite site, double tol) -> SwigIntVector

getFragAtomID(fragType, atomIndex)
getFragAtomID(std::string const & fragType, size_t atomIndex) -> std::string

getListOfBondedAtoms(ct, atom)
getListOfBondedAtoms(MM_Index ct, size_t atom) -> SwigSizetVector

getNonQCount(features)
getNonQCount(std::vector< PhpBaseFeature,std::allocator< PhpBaseFeature > > const & features) -> int

initMMlibs()

getCtTitle(ctHandle)
getCtTitle(MM_Index ctHandle) -> std::string

std::string

getDefaultFdFileBaseName()

std::string

getDefaultFdFilePath()

getLongLine(istr, s)
getLongLine(std::istream & istr, std::string & s) -> std::istream &

getPhpFunction(boostFunction)
getPhpFunction(std::string const & boostFunction) -> std::string

getTopoDistanceMatrix(*args)
getTopoDistanceMatrix(MM_Index ctHandle) -> SwigVectorIntVector getTopoDistanceMatrix(MM_Index ctHandle, SwigVectorIntVector brokenBonds) -> SwigVectorIntVector

isInVector(values, value)
isInVector(SwigIntVector values, int value) -> bool

printVectorValues(*args, **kwargs)
printVectorValues(SwigIntVector values, std::string sep, std::string lastSep) -> std::string

tokenizeDelimitedString(*args, **kwargs)
tokenizeDelimitedString(std::string const & s, char sep, bool trim=False) -> SwigStringVector

conformerBlockPositions(*args, **kwargs)
conformerBlockPositions(std::string const & structure_file, std::string title_property, bool use_titles=False, bool use_stereo=True, bool use_annotations=False) -> SwigSizetVector

Variables

[hide private]

FP_TYPE_DENDRITIC = 0
hash(x)

FP_TYPE_FDENDRITIC = 1

FP_TYPE_LINEAR = 2

FP_TYPE_MACCS = 3
hash(x)

FP_TYPE_MOLPRINT2D = 4

FP_TYPE_RADIAL = 5

FP_TYPE_ECFP4 = 6

FP_TYPE_ECFP6 = 7

FP_TYPE_FCFP4 = 8

FP_TYPE_FCFP6 = 9

cvar = <Swig global variables>

FEATURE_TYPE_ACCEPTOR = 'A'

FEATURE_TYPE_DONOR = 'D'

FEATURE_TYPE_HYDROPHOBIC = 'H'

FEATURE_TYPE_NEGATIVE_IONIC = 'N'

FEATURE_TYPE_POSITIVE_IONIC = 'P'

FEATURE_TYPE_PROJECTED = 'Q'

FEATURE_TYPE_AROMATIC = 'R'

FEATURE_TYPE_CUSTOM_X = 'X'

FEATURE_TYPE_CUSTOM_Y = 'Y'

FEATURE_TYPE_CUSTOM_Z = 'Z'

FEATURE_DESCRIPTION = <schrodinger.utils.mmutil.StringStringMa...

PHASE_DEFAULT_MASK = 0
hash(x)

PHASE_DEFAULT_RAD = 2.0

PHASE_DEFAULT_TOL = 2.0

PHASE_DEFAULT_XP = 0.0

PHASE_DEFAULT_EXTENDED_DISTANCE = 1.8

PHASE_HYPO_SCORE = 'r_phase_PhaseHypoScore'

PHASE_LIGAND_GROUP = 'i_phase_Ligand_Group'

PHASE_LIGAND_NAME = 's_phase_Ligand_Name'

PHASE_MUST_MATCH = 'b_phase_Must_Match'

PHASE_PHARM_SET = 's_phase_Pharm_Set'

PHASE_SCREEN_SCORE = 'r_phase_PhaseScreenScore'

PHASE_DCPH_OUTPUT = 'b_phase_Common_Pharmacophore_Output'

HYDROGENS_NONE = 0
hash(x)

HYDROGENS_POLAR = 1

HYDROGENS_ALL = 2

PhpFastShapeHydrogens = (0, 1, 2)

OVERLAP_NORM_MAX = 1

OVERLAP_NORM_MIN = 2

OVERLAP_NORM_REF = 3
hash(x)

OVERLAP_NORM_SCREEN = 4

PhpFastShapeNorm = (1, 2, 3, 4)

PHASE_MAX_FP_MEMORY = 10000

FRAG_TYPE_A0 = 'A0'

FRAG_TYPE_A1 = 'A1'

FRAG_TYPE_A2 = 'A2'

FRAG_TYPE_A3 = 'A3'

FRAG_TYPE_D0 = 'D0'

FRAG_TYPE_D1 = 'D1'

FRAG_TYPE_H = 'H'

FRAG_TYPE_N = 'N'

FRAG_TYPE_P = 'P'

FRAG_TYPE_R2 = 'R2'

FRAG_TYPE_TO_NATOMS = cvar.FRAG_TYPE_TO_NATOMS

PHASE_FRAG_ID_PROP = 's_phasehypo_fragment_id'

PHASE_FRAG_ID_BASE = '_base'

PHASE_FRAG_ID_PROJ = '_proj_'

PROJ_TYPE_ZERO = 0
hash(x)

PROJ_TYPE_STANDARD_MAX = 9

PROJ_TYPE_MAX = 14

PROJ_STANDARD_D = 1

PROJ_STANDARD_A_SP3_1LP = 2

PROJ_STANDARD_A_SP2_1LP = 3
hash(x)

PROJ_STANDARD_A_SP_1LP = 4

PROJ_STANDARD_A_SP3_2LP = 5

PROJ_STANDARD_A_SP2_2LP = 6

PROJ_STANDARD_A_SP3_3LP = 7

PROJ_STANDARD_R = 8

PROJ_STANDARD_A_SP2_3LP = 9

PROJ_FRAG_A0 = 0
hash(x)

PROJ_FRAG_A1 = 10

PROJ_FRAG_A2 = 11

PROJ_FRAG_A3 = 12

PROJ_FRAG_D0 = 0
hash(x)

PROJ_FRAG_D1 = 13

PROJ_FRAG_H = 0
hash(x)

PROJ_FRAG_N = 0
hash(x)

PROJ_FRAG_P = 0
hash(x)

PROJ_FRAG_R2 = 14

DEFAULT_AROMATIC_VECTOR = 'default_aromatic_vector'

DEFAULT_AROMATIC_SURFACE = 'default_aromatic_surface'

DEFAULT_ALIPHATIC_SURFACE = 'default_aliphatic_surface'

DEFAULT_NEGATIVE_IONIC = 'default_negative_ionic'

DEFAULT_POSITIVE_IONIC = 'default_positive_ionic'

DEFAULT_FRAG_PREFIX = 'default_frag_'

DEFAULT_FRAG_A0 = 'default_frag_a0'

DEFAULT_FRAG_A1 = 'default_frag_a1'

DEFAULT_FRAG_A2 = 'default_frag_a2'

DEFAULT_FRAG_A3 = 'default_frag_a3'

DEFAULT_FRAG_D0 = 'default_frag_d0'

DEFAULT_FRAG_D1 = 'default_frag_d1'

DEFAULT_FRAG_H = 'default_frag_h'

DEFAULT_FRAG_N = 'default_frag_n'

DEFAULT_FRAG_P = 'default_frag_p'

DEFAULT_FRAG_R2 = 'default_frag_r2'

DEFAULT_PATTERNS = ('default_aromatic_vector', 'default_aromat...

PATTERN_TO_FRAG_PAIR = cvar.PATTERN_TO_FRAG_PAIR

PROJ_TYPE_TO_NBONDS = cvar.PROJ_TYPE_TO_NBONDS

PROJ_TYPE_TO_NPROJ = cvar.PROJ_TYPE_TO_NPROJ

PHASE_MAX_HITS_MEMORY = 100000

PhpHiClusterLinkageSingle = 0
hash(x)

PhpHiClusterLinkageAverage = 1

PhpHiClusterLinkageComplete = 2

PhpQSARSuccess = 0
hash(x)

PhpQSARGridError = 1

PhpQSAROutOfMemory = 2

PhpQSARBadActData = 3
hash(x)

PhpQSARFileNotFound = 4

PhpQSARReadError = 5

PhpQSAROutputError = 6

PhpQSARmmlibsError = 7

PhpQSARWrongModelType = 8

PhpQSARBadVolOccBits = 9

PhpQSARNoXVar = 10

PhpQSARUnknownError = 11

PHASE_HYPO_FILE_EXT = '.phypo'

PHASE_ACTIVE_TITLES = 's_phasehypo_ActiveTitles'

PHASE_CONSTRAINTS = 's_phasehypo_Constraints'

PHASE_EXCLUDED_VOLUMES = 's_phasehypo_ExcludedVolumes'

PHASE_FEATURE_DEFINITIONS = 's_phasehypo_FeatureDefinitions'

PHASE_FEATURE_RADII = 's_phasehypo_FeatureRadii'

PHASE_FEATURE_RULES = 's_phasehypo_FeatureRules'

PHASE_HITS_TITLES = 's_phasehypo_HitsTitles'

PHASE_HYPO_ID = 's_phasehypo_HypoID'

PHASE_HYPO_ROLE = 's_phasehypo_HypoRole'

PHASE_INCLUDED_VOLUMES = 's_phasehypo_IncludedVolumes'

PHASE_MATCHING_TOLERANCES = 's_phasehypo_MatchingTolerances'

PHASE_MIN_SITES = 'i_phasehypo_MinSites'

PHASE_QSAR_MODEL = 's_phasehypo_QsarModel'

PHASE_REF_CT = 's_phasehypo_RefCt'

PHASE_RUNNAME = 's_phasehypo_RunName'

PHASE_SITE_MASK = 's_phasehypo_SiteMask'

PHASE_SITE_TYPES = 's_phasehypo_SiteTypes'

PHASE_SITES = 's_phasehypo_Sites'

PHASE_SITES_WITH_PROJ = 's_phasehypo_SitesWithProj'

PHASE_TOTAL_DECOYS = 'i_phasehypo_TotalDecoys'

ROLE_HYPO = 'hypo'

ROLE_REF = 'ref'

ROLE_ACTIVE = 'active'

ROLE_INACTIVE = 'inactive'

ROLE_TRAIN = 'train'

ROLE_TEST = 'test'

PHASE_STRICT_TOL = 0.001

PHASE_LOOSE_TOL = 2.0

PHASE_REDUN_TOL = 0.5

__package__ = 'schrodinger.infra'

Variables Details

[hide private]

FEATURE_DESCRIPTION

Value:

<schrodinger.utils.mmutil.StringStringMap; proxy of <Swig Object of ty
pe 'FeatureStateMap *' at 0x7f2d5b1bb4e0> >

DEFAULT_PATTERNS

Value:

('default_aromatic_vector',
 'default_aromatic_surface',
 'default_aliphatic_surface',
 'default_negative_ionic',
 'default_positive_ionic',
 'default_frag_a0',
 'default_frag_a1',
 'default_frag_a2',
...