Package schrodinger :: Package infra :: Module phase

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Module phase

Phase C++ wrappers

Classes

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SwigPyIterator
Proxy of C++ swig::SwigPyIterator class

SwigIntVector
Proxy of C++ std::vector<(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

PhpSite
Proxy of C++ 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

PhpDeltaHypoSite
Proxy of C++ PhpDeltaHypoSite_ class

PhpDeltaHypo
Proxy of C++ PhpDeltaHypo class

PhpExclVolSphere
Proxy of C++ PhpExclVolSphere_ class

PhpExclVol
Proxy of C++ PhpExclVol 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(*args, **kwargs)
PhpSiteMask_resolveMaskValue(int maskValue, size_t & groupNumber, size_t & minMatch)

PhpSiteMask_splitMaskValue(*args, **kwargs)
PhpSiteMask_splitMaskValue(int maskValue) -> SwigIntVector

PhpSiteMask_resolveMatchLimits(*args, **kwargs)
PhpSiteMask_resolveMatchLimits(SwigIntVector siteMask, size_t & minSites, size_t & maxSites)

PhpSiteMask_getMatchLimits(*args, **kwargs)
PhpSiteMask_getMatchLimits(SwigIntVector siteMask) -> SwigIntVector

std::string

getDefaultFdFileBaseName()

std::string

getDefaultFdFilePath()

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

getPhpFunction(*args, **kwargs)
getPhpFunction(std::string const & boostFunction) -> std::string

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

isInVector(*args, **kwargs)
isInVector(SwigIntVector values, int value) -> bool

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

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

Variables

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_newclass = 1

cvar = <Swig global variables>

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)

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'

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_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_FRAG_CTS = 's_phasehypo_FragCts'

PHASE_FRAG_MAP = 's_phasehypo_FragMap'

PHASE_FRAG_SITES = 's_phasehypo_FragSites'

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

__package__ = 'schrodinger.infra'