schrodinger.infra.phase module¶
Phase C++ wrappers
-
class
schrodinger.infra.phase.
PhpAlignCore
(*args)¶ Bases:
object
Proxy of C++ PhpAlignCore class.
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closeContactFailure
()¶ PhpAlignCore_closeContactFailure(PhpAlignCore self) -> bool
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getAlignedB
()¶ PhpAlignCore_getAlignedB(PhpAlignCore self) -> SwigIntVector
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getMappings
()¶ PhpAlignCore_getMappings(PhpAlignCore self) -> std::vector< PhpCoreMapping,std::allocator< PhpCoreMapping > >
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getNumMappings
()¶ PhpAlignCore_getNumMappings(PhpAlignCore self) -> size_t
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stereoFailure
()¶ PhpAlignCore_stereoFailure(PhpAlignCore self) -> bool
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thisown
¶ The membership flag
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-
class
schrodinger.infra.phase.
PhpAtomClassDescriptions
¶ Bases:
object
Proxy of C++ PhpAtomClassDescriptions class.
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getAtomClassDescription
()¶ PhpAtomClassDescriptions_getAtomClassDescription(PhpAtomClassDescriptions self, std::string const & atomClass) -> std::string
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thisown
¶ The membership flag
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class
schrodinger.infra.phase.
PhpComplex
(*args)¶ Bases:
object
Proxy of C++ PhpComplex class.
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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) -> SwigVectorPhpSitePhpSite
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getErrMesg
()¶ PhpComplex_getErrMesg(PhpComplex self) -> std::string
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getLimits
()¶ PhpComplex_getLimits(PhpComplex self, std::string const & parName) -> SwigDoubleVector
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setDefaultLimits
()¶ PhpComplex_setDefaultLimits(PhpComplex self)
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setLimits
()¶ PhpComplex_setLimits(PhpComplex self, std::string const & parName, double parStrict, double parRelaxed)
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thisown
¶ The membership flag
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class
schrodinger.infra.phase.
PhpConfOptions
(*args)¶ Bases:
object
Proxy of C++ PhpConfOptions class.
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getAppendConfs
()¶ PhpConfOptions_getAppendConfs(PhpConfOptions self) -> bool
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getEnergyWindow
()¶ PhpConfOptions_getEnergyWindow(PhpConfOptions self) -> double
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getForceField
()¶ PhpConfOptions_getForceField(PhpConfOptions self) -> PhpConfForceField
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getMaxConfs
()¶ PhpConfOptions_getMaxConfs(PhpConfOptions self) -> int
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getSamplingMethod
()¶ PhpConfOptions_getSamplingMethod(PhpConfOptions self) -> PhpConfSamplingMethod
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setAppendConfs
()¶ PhpConfOptions_setAppendConfs(PhpConfOptions self, bool append_confs)
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setEnergyWindow
()¶ PhpConfOptions_setEnergyWindow(PhpConfOptions self, double energy_window)
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setForceField
()¶ PhpConfOptions_setForceField(PhpConfOptions self, PhpConfForceField force_field)
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setMaxConfs
()¶ PhpConfOptions_setMaxConfs(PhpConfOptions self, int max_confs)
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setSamplingMethod
()¶ PhpConfOptions_setSamplingMethod(PhpConfOptions self, PhpConfSamplingMethod sampling_method)
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thisown
¶ The membership flag
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class
schrodinger.infra.phase.
PhpDatabaseFp
(dbName)¶ Bases:
object
Proxy of C++ PhpDatabaseFp class.
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static
distEuclidean
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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static
distHamming
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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static
distSoergel
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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getAllIDs
()¶ PhpDatabaseFp_getAllIDs(PhpDatabaseFp self) -> SwigSizetVector
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static
getCommonCount
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → size_t¶
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getCt
()¶ PhpDatabaseFp_getCt(PhpDatabaseFp self, size_t molID) -> MM_Index
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getCts
()¶ PhpDatabaseFp_getCts(PhpDatabaseFp self, SwigSizetVector molIDs) -> SwigIntVector
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getFp
()¶ PhpDatabaseFp_getFp(PhpDatabaseFp self, PhpFpType fpType, size_t molID, bool allowMissing=True) -> SwigUnsignedIntVector
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getFpTypesStored
()¶ PhpDatabaseFp_getFpTypesStored(PhpDatabaseFp self) -> SwigPhpFpTypeVector
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getFps
()¶ PhpDatabaseFp_getFps(PhpDatabaseFp self, PhpFpType fpType, SwigSizetVector molIDs, bool allowMissing=True) -> std::vector< std::vector< unsigned int,std::allocator< unsigned int > >,std::allocator< std::vector< unsigned int,std::allocator< unsigned int > > > >
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isStored
()¶ PhpDatabaseFp_isStored(PhpDatabaseFp self, PhpFpType fpType) -> bool
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static
packFp
(SwigUnsignedIntVector onBits, size_t molID=0) → PhpPackedFp¶
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static
simCosine
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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static
simDice
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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static
simTanimoto
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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thisown
¶ The membership flag
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static
unpackFp
(PhpPackedFp packedFp) → SwigUnsignedIntVector¶
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static
-
schrodinger.infra.phase.
PhpDatabaseFp_distEuclidean
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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schrodinger.infra.phase.
PhpDatabaseFp_distHamming
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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schrodinger.infra.phase.
PhpDatabaseFp_distSoergel
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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schrodinger.infra.phase.
PhpDatabaseFp_getCommonCount
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → size_t¶
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schrodinger.infra.phase.
PhpDatabaseFp_packFp
(SwigUnsignedIntVector onBits, size_t molID=0) → PhpPackedFp¶
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schrodinger.infra.phase.
PhpDatabaseFp_simCosine
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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schrodinger.infra.phase.
PhpDatabaseFp_simDice
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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schrodinger.infra.phase.
PhpDatabaseFp_simTanimoto
(SwigUnsignedIntVector fp1, SwigUnsignedIntVector fp2) → double¶
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schrodinger.infra.phase.
PhpDatabaseFp_unpackFp
(PhpPackedFp packedFp) → SwigUnsignedIntVector¶
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class
schrodinger.infra.phase.
PhpDeNovoPharm
(*args)¶ Bases:
object
Proxy of C++ PhpDeNovoPharm class.
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getCentroid
()¶ PhpDeNovoPharm_getCentroid(PhpDeNovoPharm self) -> SwigDoubleVector
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getCentroidHypo
()¶ PhpDeNovoPharm_getCentroidHypo(PhpDeNovoPharm self, std::string const & hypoID) -> PhpHypoAdaptor
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getLigandHypo
()¶ PhpDeNovoPharm_getLigandHypo(PhpDeNovoPharm self, std::string const & hypoID) -> PhpHypoAdaptor
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getReceptorHypo
()¶ PhpDeNovoPharm_getReceptorHypo(PhpDeNovoPharm self, std::string const & hypoID) -> PhpHypoAdaptor
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getSiteCount
()¶ PhpDeNovoPharm_getSiteCount(PhpDeNovoPharm self) -> int
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getSitePairs
()¶ PhpDeNovoPharm_getSitePairs(PhpDeNovoPharm self) -> SwigVectorPhpSitePhpSite
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thisown
¶ The membership flag
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class
schrodinger.infra.phase.
PhpDeltaHypo
(*args)¶ Bases:
object
Proxy of C++ PhpDeltaHypo class.
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addSiteData
(char siteType, double deltaXYZ)¶ addSiteData(size_t siteNumber, char siteType, double deltaXYZ) PhpDeltaHypo_addSiteData(PhpDeltaHypo self, PhpDeltaHypoSite siteData)
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clear
()¶ PhpDeltaHypo_clear(PhpDeltaHypo self)
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exportToFile
()¶ PhpDeltaHypo_exportToFile(PhpDeltaHypo self, std::string const & fileName)
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exportToStream
()¶ PhpDeltaHypo_exportToStream(PhpDeltaHypo self, std::ostream & outStream)
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getDeltaXYZ
()¶ PhpDeltaHypo_getDeltaXYZ(PhpDeltaHypo self, size_t siteIndex) -> double
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getSiteData
()¶ PhpDeltaHypo_getSiteData(PhpDeltaHypo self, size_t siteIndex) -> PhpDeltaHypoSite
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getSiteNumber
()¶ PhpDeltaHypo_getSiteNumber(PhpDeltaHypo self, size_t siteIndex) -> size_t
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getSiteType
()¶ PhpDeltaHypo_getSiteType(PhpDeltaHypo self, size_t siteIndex) -> char
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importFromFile
()¶ PhpDeltaHypo_importFromFile(PhpDeltaHypo self, std::string const & fileName)
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importFromStream
()¶ PhpDeltaHypo_importFromStream(PhpDeltaHypo self, std::istream & inStream)
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numSites
()¶ PhpDeltaHypo_numSites(PhpDeltaHypo self) -> size_t
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thisown
¶ The membership flag
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class
schrodinger.infra.phase.
PhpDeltaHypoSite
¶ Bases:
object
Proxy of C++ PhpDeltaHypoSite_ class.
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deltaXYZ
¶ PhpDeltaHypoSite_deltaXYZ_get(PhpDeltaHypoSite self) -> double
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siteNumber
¶ PhpDeltaHypoSite_siteNumber_get(PhpDeltaHypoSite self) -> size_t
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siteType
¶ PhpDeltaHypoSite_siteType_get(PhpDeltaHypoSite self) -> char
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thisown
¶ The membership flag
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exception
schrodinger.infra.phase.
PhpException
(*args)¶ Bases:
exceptions.Exception
Proxy of C++ PhpException class.
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what
()¶ PhpException_what(PhpException self) -> char const *
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class
schrodinger.infra.phase.
PhpExclVol
(*args)¶ Bases:
object
Proxy of C++ PhpExclVol class.
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addSphere
(double x, double y, double z, double r)¶ PhpExclVol_addSphere(PhpExclVol self, PhpExclVolSphere sphere)
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append
()¶ PhpExclVol_append(PhpExclVol self, PhpExclVol xvol)
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clear
()¶ PhpExclVol_clear(PhpExclVol self)
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exportToFile
()¶ PhpExclVol_exportToFile(PhpExclVol self, std::string const & fileName)
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exportToMMTableFile
()¶ PhpExclVol_exportToMMTableFile(PhpExclVol self, std::string const & fileName)
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exportToStream
()¶ PhpExclVol_exportToStream(PhpExclVol self, std::ostream & outStream)
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filter
()¶ PhpExclVol_filter(PhpExclVol self, MM_Index ct, bool treatHydrogens) -> PhpExclVol
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findViolations
()¶ PhpExclVol_findViolations(PhpExclVol self, MM_Index ctHandle, size_t maxViolations) -> SwigSizetVector
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getSphere
()¶ PhpExclVol_getSphere(PhpExclVol self, size_t sphereIndex) -> PhpExclVolSphere
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getSphereRadius
()¶ PhpExclVol_getSphereRadius(PhpExclVol self, size_t sphereIndex) -> double
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getSphereXYZ
()¶ PhpExclVol_getSphereXYZ(PhpExclVol self, size_t sphereIndex)
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getSpheres
()¶ PhpExclVol_getSpheres(PhpExclVol self) -> std::vector< PhpExclVolSphere,std::allocator< PhpExclVolSphere > >
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getTreatHydrogens
()¶ PhpExclVol_getTreatHydrogens(PhpExclVol self) -> bool
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importFromAnyFile
()¶ PhpExclVol_importFromAnyFile(PhpExclVol self, std::string const & fileName)
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importFromFile
()¶ PhpExclVol_importFromFile(PhpExclVol self, std::string const & fileName)
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importFromMMTableFile
()¶ PhpExclVol_importFromMMTableFile(PhpExclVol self, std::string const & fileName)
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importFromStream
()¶ PhpExclVol_importFromStream(PhpExclVol self, std::istream & inStream)
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numShapes
()¶ PhpExclVol_numShapes(PhpExclVol self) -> size_t
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numSpheres
()¶ PhpExclVol_numSpheres(PhpExclVol self) -> size_t
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removeSphere
()¶ PhpExclVol_removeSphere(PhpExclVol self, size_t sphereIndex)
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setSphereRadius
()¶ PhpExclVol_setSphereRadius(PhpExclVol self, size_t sphereIndex, double r)
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setSphereXYZ
()¶ PhpExclVol_setSphereXYZ(PhpExclVol self, size_t sphereIndex, double x, double y, double z)
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setTreatHydrogens
()¶ PhpExclVol_setTreatHydrogens(PhpExclVol self, bool treatHydrogens)
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thisown
¶ The membership flag
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class
schrodinger.infra.phase.
PhpExclVolSphere
¶ Bases:
object
Proxy of C++ PhpExclVolSphere_ class.
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r
¶ PhpExclVolSphere_r_get(PhpExclVolSphere self) -> double
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thisown
¶ The membership flag
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x
¶ PhpExclVolSphere_x_get(PhpExclVolSphere self) -> double
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y
¶ PhpExclVolSphere_y_get(PhpExclVolSphere self) -> double
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z
¶ PhpExclVolSphere_z_get(PhpExclVolSphere self) -> double
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class
schrodinger.infra.phase.
PhpFastShape
(*args)¶ Bases:
object
Proxy of C++ PhpFastShape class.
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alignCt
()¶ PhpFastShape_alignCt(PhpFastShape self, MM_Index ctHandle, double const [3] trans, double const [3][3] rot)
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alignCtPy
()¶ PhpFastShape_alignCtPy(PhpFastShape self, MM_Index ctHandle, SwigDoubleVector simTrans)
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computeShapeSim
(SwigVectorDoubleVector xyz, SwigDoubleVector r, bool first, bool inplace, double & sim, double [3] trans, double [3][3] rot)¶ computeShapeSim(SwigVectorDoubleVector xyz, SwigDoubleVector r, SwigIntVector stype, bool first, bool inplace, double & sim, double [3] trans, double [3][3] rot) computeShapeSim(MM_Index ctHandle, bool first, bool inplace, double & sim, double [3] trans, double [3][3] rot) PhpFastShape_computeShapeSim(PhpFastShape self, std::vector< PhpSite,std::allocator< PhpSite > > const & sites, PhpLcsMap const & lcsMap, bool first, bool inplace, double & sim, double [3] trans, double [3][3] rot)
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computeShapeSimPy
()¶ PhpFastShape_computeShapeSimPy(PhpFastShape self, MM_Index ctHandle, bool first, bool inplace) -> SwigDoubleVector
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setDebug
()¶ PhpFastShape_setDebug(PhpFastShape self, bool debug)
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFastShapePair
¶ Bases:
object
Proxy of C++ PhpFastShapePair_ class.
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a
¶ PhpFastShapePair_a_get(PhpFastShapePair self) -> double
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b
¶ PhpFastShapePair_b_get(PhpFastShapePair self) -> double
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c
¶ PhpFastShapePair_c_get(PhpFastShapePair self) -> double
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i1
¶ PhpFastShapePair_i1_get(PhpFastShapePair self) -> size_t
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i2
¶ PhpFastShapePair_i2_get(PhpFastShapePair self) -> size_t
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFeatureClassDescriptions
¶ Bases:
object
Proxy of C++ PhpFeatureClassDescriptions class.
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getFeatureClassDescription
()¶ PhpFeatureClassDescriptions_getFeatureClassDescription(PhpFeatureClassDescriptions self, std::string const & featureClass) -> std::string
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFeatureData
(*args)¶ Bases:
object
Proxy of C++ PhpFeatureData class.
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clear
()¶ PhpFeatureData_clear(PhpFeatureData self)
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exportToFile
()¶ PhpFeatureData_exportToFile(PhpFeatureData self, char const * fileName)
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exportToStream
()¶ PhpFeatureData_exportToStream(PhpFeatureData self, std::ostream & outStream)
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getDataColumn
()¶ PhpFeatureData_getDataColumn(PhpFeatureData self, std::string const & variant, size_t dataColumn=0) -> SwigDoubleVector
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getDataRow
()¶ PhpFeatureData_getDataRow(PhpFeatureData self, char featureType) -> SwigDoubleVector
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getDataValue
()¶ PhpFeatureData_getDataValue(PhpFeatureData self, char featureType) -> double
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importFromFile
()¶ PhpFeatureData_importFromFile(PhpFeatureData self, char const * fileName)
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importFromStream
()¶ PhpFeatureData_importFromStream(PhpFeatureData self, std::istream & inStream)
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numDataColumns
()¶ PhpFeatureData_numDataColumns(PhpFeatureData self) -> size_t
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setDataRow
()¶ PhpFeatureData_setDataRow(PhpFeatureData self, char featureType, SwigDoubleVector dataRow)
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setDataValue
()¶ PhpFeatureData_setDataValue(PhpFeatureData self, char featureType, double dataValue)
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setDefaultDataRow
()¶ PhpFeatureData_setDefaultDataRow(PhpFeatureData self, SwigDoubleVector dataRow)
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setDefaultDataValue
()¶ PhpFeatureData_setDefaultDataValue(PhpFeatureData self, double dataValue)
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFeatureDefinition
(*args)¶ Bases:
object
Proxy of C++ PhpFeatureDefinition class.
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addStaticFragmentPatterns
()¶ PhpFeatureDefinition_addStaticFragmentPatterns(PhpFeatureDefinition self)
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clear
()¶ PhpFeatureDefinition_clear(PhpFeatureDefinition self)
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getAllExcludes
()¶ PhpFeatureDefinition_getAllExcludes(PhpFeatureDefinition self) -> std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > >
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getAllIncludes
()¶ PhpFeatureDefinition_getAllIncludes(PhpFeatureDefinition self) -> std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > >
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getExcludePattern
()¶ PhpFeatureDefinition_getExcludePattern(PhpFeatureDefinition self, size_t a_i) -> PhpFeaturePattern
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getExtendDistance
()¶ PhpFeatureDefinition_getExtendDistance(PhpFeatureDefinition self) -> double
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getFeatureComment
()¶ PhpFeatureDefinition_getFeatureComment(PhpFeatureDefinition self) -> std::string
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getFeatureName
()¶ PhpFeatureDefinition_getFeatureName(PhpFeatureDefinition self) -> std::string
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getFeatureNumber
()¶ PhpFeatureDefinition_getFeatureNumber(PhpFeatureDefinition self) -> size_t
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getFeatureType
()¶ PhpFeatureDefinition_getFeatureType(PhpFeatureDefinition self) -> char
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getIncludePattern
()¶ PhpFeatureDefinition_getIncludePattern(PhpFeatureDefinition self, size_t a_i) -> PhpFeaturePattern
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getNumExcludes
()¶ PhpFeatureDefinition_getNumExcludes(PhpFeatureDefinition self) -> size_t
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getNumIncludes
()¶ PhpFeatureDefinition_getNumIncludes(PhpFeatureDefinition self) -> size_t
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getProjectedType
()¶ PhpFeatureDefinition_getProjectedType(PhpFeatureDefinition self) -> bool
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getSasOptions
()¶ PhpFeatureDefinition_getSasOptions(PhpFeatureDefinition self) -> PhpSASOptions
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setAllExcludes
()¶ PhpFeatureDefinition_setAllExcludes(PhpFeatureDefinition self, std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > > & rhs)
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setAllIncludes
()¶ PhpFeatureDefinition_setAllIncludes(PhpFeatureDefinition self, std::vector< PhpFeaturePattern,std::allocator< PhpFeaturePattern > > & rhs)
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setExcludePattern
()¶ PhpFeatureDefinition_setExcludePattern(PhpFeatureDefinition self, PhpFeaturePattern rhs)
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setExtendDistance
()¶ PhpFeatureDefinition_setExtendDistance(PhpFeatureDefinition self, double const a_d)
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setFeatureComment
()¶ PhpFeatureDefinition_setFeatureComment(PhpFeatureDefinition self, std::string const a_comment)
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setFeatureName
()¶ PhpFeatureDefinition_setFeatureName(PhpFeatureDefinition self, std::string const & a_name)
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setFeatureNumber
()¶ PhpFeatureDefinition_setFeatureNumber(PhpFeatureDefinition self, size_t a_i)
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setFeatureType
()¶ PhpFeatureDefinition_setFeatureType(PhpFeatureDefinition self, char a_type)
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setIncludePattern
()¶ PhpFeatureDefinition_setIncludePattern(PhpFeatureDefinition self, PhpFeaturePattern rhs)
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setProjectedTypeOff
()¶ PhpFeatureDefinition_setProjectedTypeOff(PhpFeatureDefinition self)
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setProjectedTypeOn
()¶ PhpFeatureDefinition_setProjectedTypeOn(PhpFeatureDefinition self)
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setSasOptions
()¶ PhpFeatureDefinition_setSasOptions(PhpFeatureDefinition self, PhpSASOptions const & a_sas)
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFeatureFinder
(*args)¶ Bases:
object
Proxy of C++ PhpFeatureFinder class.
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execute
()¶ PhpFeatureFinder_execute(PhpFeatureFinder self)
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getAllFeatures
()¶ PhpFeatureFinder_getAllFeatures(PhpFeatureFinder self) -> std::vector< PhpBaseFeature,std::allocator< PhpBaseFeature > >
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setCTSource
()¶ PhpFeatureFinder_setCTSource(PhpFeatureFinder self, int a_ct)
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setFeatureDefinitions
()¶ PhpFeatureFinder_setFeatureDefinitions(PhpFeatureFinder self, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & a_fd)
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFeaturePattern
(*args)¶ Bases:
object
Proxy of C++ PhpFeaturePattern class.
-
getAtomList
()¶ PhpFeaturePattern_getAtomList(PhpFeaturePattern self) -> SwigSizetVector
-
getEditStatus
()¶ PhpFeaturePattern_getEditStatus(PhpFeaturePattern self) -> bool
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getExtendDistance
()¶ PhpFeaturePattern_getExtendDistance(PhpFeaturePattern self) -> double
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getGeometry
()¶ PhpFeaturePattern_getGeometry(PhpFeaturePattern self) -> std::string
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getPattern
()¶ PhpFeaturePattern_getPattern(PhpFeaturePattern self) -> std::string
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getPatternID
()¶ PhpFeaturePattern_getPatternID(PhpFeaturePattern self) -> int
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getPattyHandle
()¶ PhpFeaturePattern_getPattyHandle(PhpFeaturePattern self) -> int
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getProjectedType
()¶ PhpFeaturePattern_getProjectedType(PhpFeaturePattern self) -> int
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getSummary
()¶ PhpFeaturePattern_getSummary(PhpFeaturePattern self) -> std::string
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getType
()¶ PhpFeaturePattern_getType(PhpFeaturePattern self) -> int
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getTypeSimilarity
()¶ PhpFeaturePattern_getTypeSimilarity(PhpFeaturePattern self) -> int
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getUsedStatus
()¶ PhpFeaturePattern_getUsedStatus(PhpFeaturePattern self) -> bool
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setAtomList
()¶ PhpFeaturePattern_setAtomList(PhpFeaturePattern self, SwigSizetVector rhs)
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setEditOff
()¶ PhpFeaturePattern_setEditOff(PhpFeaturePattern self)
-
setEditOn
()¶ PhpFeaturePattern_setEditOn(PhpFeaturePattern self)
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setExtendDistance
()¶ PhpFeaturePattern_setExtendDistance(PhpFeaturePattern self, double const a_d)
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setGeometry
()¶ PhpFeaturePattern_setGeometry(PhpFeaturePattern self, std::string const & a_geometry)
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setPattern
()¶ PhpFeaturePattern_setPattern(PhpFeaturePattern self, std::string const & a_pattern)
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setPatternID
()¶ PhpFeaturePattern_setPatternID(PhpFeaturePattern self, int a_patternID)
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setPattyHandle
()¶ PhpFeaturePattern_setPattyHandle(PhpFeaturePattern self, int const a_handle)
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setProjectedType
()¶ PhpFeaturePattern_setProjectedType(PhpFeaturePattern self, int a_type)
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setType
()¶ PhpFeaturePattern_setType(PhpFeaturePattern self, int a_type)
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setTypeSimilarity
()¶ PhpFeaturePattern_setTypeSimilarity(PhpFeaturePattern self, int a_typeSimilarity)
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setUsedOff
()¶ PhpFeaturePattern_setUsedOff(PhpFeaturePattern self)
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setUsedOn
()¶ PhpFeaturePattern_setUsedOn(PhpFeaturePattern self)
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thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFeatureRules
(*args)¶ Bases:
object
Proxy of C++ PhpFeatureRules class.
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addRule
()¶ PhpFeatureRules_addRule(PhpFeatureRules self, size_t siteNumber, std::string const & permitted, std::string const & prohibited)
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clear
()¶ PhpFeatureRules_clear(PhpFeatureRules self)
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containsVariant
()¶ PhpFeatureRules_containsVariant(PhpFeatureRules self, std::string const & variant) -> bool
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exportToFile
()¶ PhpFeatureRules_exportToFile(PhpFeatureRules self, std::string const & ruleFile)
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exportToStream
()¶ PhpFeatureRules_exportToStream(PhpFeatureRules self, std::ostream & ruleStream)
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getPermittedFeatures
() → SwigStringVector¶ PhpFeatureRules_getPermittedFeatures(PhpFeatureRules self, size_t siteIndex) -> std::string
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getProhibitedFeatures
() → SwigStringVector¶ 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
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpFragPair
¶ Bases:
object
Proxy of C++ PhpFragPair_ class.
-
fragType
¶ PhpFragPair_fragType_get(PhpFragPair self) -> std::string const &
-
projType
¶ PhpFragPair_projType_get(PhpFragPair self) -> int
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpHiCluster
(*args)¶ Bases:
object
Proxy of C++ PhpHiCluster class.
-
clear
()¶ PhpHiCluster_clear(PhpHiCluster self)
-
clearClusters
()¶ PhpHiCluster_clearClusters(PhpHiCluster self)
-
createClusters
()¶ PhpHiCluster_createClusters(PhpHiCluster self)
-
getClusterCutPoints
()¶ PhpHiCluster_getClusterCutPoints(PhpHiCluster self, size_t numClusters) -> SwigSizetVector
-
getClusterSizes
()¶ PhpHiCluster_getClusterSizes(PhpHiCluster self, size_t numClusters) -> SwigSizetVector
-
getClusters
()¶ PhpHiCluster_getClusters(PhpHiCluster self, size_t numClusters) -> SwigVectorSizetVector
-
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, SwigVectorDoubleVector dmatrix)
-
setLinkageType
()¶ PhpHiCluster_setLinkageType(PhpHiCluster self, int const linkageType)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpHiClusterPair
¶ Bases:
object
Proxy of C++ PhpHiClusterPair_ class.
-
cluster1
¶ PhpHiClusterPair_cluster1_get(PhpHiClusterPair self) -> SwigSizetVector
-
cluster2
¶ PhpHiClusterPair_cluster2_get(PhpHiClusterPair self) -> SwigSizetVector
-
d12
¶ PhpHiClusterPair_d12_get(PhpHiClusterPair self) -> double
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpHypoAdaptor
(*args)¶ Bases:
object
Proxy of C++ PhpHypoAdaptor class.
-
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) -> SwigIntVector
-
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)
-
thisown
¶ The membership flag
-
transform
()¶ PhpHypoAdaptor_transform(PhpHypoAdaptor self, SwigVectorDoubleVector rotation, SwigDoubleVector 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.
PhpIntCoord
¶ Bases:
object
Proxy of C++ PhpIntCoord_ class.
-
atoms
¶ PhpIntCoord_atoms_get(PhpIntCoord self) -> SwigSizetVector
-
coords
¶ PhpIntCoord_coords_get(PhpIntCoord self) -> SwigDoubleVector
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpMatchOptions
(*args)¶ Bases:
object
Proxy of C++ PhpMatchOptions class.
-
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
-
getUseAtomTypes
()¶ PhpMatchOptions_getUseAtomTypes(PhpMatchOptions self) -> bool
-
getUseHardAlignCutoff
()¶ PhpMatchOptions_getUseHardAlignCutoff(PhpMatchOptions self) -> bool
-
getVectorCutoff
()¶ PhpMatchOptions_getVectorCutoff(PhpMatchOptions self) -> double
-
getVectorWeight
()¶ PhpMatchOptions_getVectorWeight(PhpMatchOptions self) -> double
-
getVolumeCutoff
()¶ PhpMatchOptions_getVolumeCutoff(PhpMatchOptions self) -> double
-
getVolumeWeight
()¶ PhpMatchOptions_getVolumeWeight(PhpMatchOptions self) -> double
-
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)
-
setUseAtomTypes
()¶ PhpMatchOptions_setUseAtomTypes(PhpMatchOptions self, bool use_atom_types)
-
setUseHardAlignCutoff
()¶ PhpMatchOptions_setUseHardAlignCutoff(PhpMatchOptions self, bool use_hard_cutoff)
-
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)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpPackedFp
(*args)¶ Bases:
object
Proxy of C++ PhpPackedFp class.
-
bits
¶ PhpPackedFp_bits_get(PhpPackedFp self) -> std::string const &
-
lenOrig
¶ PhpPackedFp_lenOrig_get(PhpPackedFp self) -> size_t
-
molID
¶ PhpPackedFp_molID_get(PhpPackedFp self) -> size_t
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpProject
¶ Bases:
object
Proxy of C++ PhpProject class.
-
addLigands
(std::string const & projectName, std::string const & inFile, bool connect, bool stereo, 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, SwigIntVector 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, SwigIntVector ligandIDs, std::string const & hypoID, double deltaDist=2.0, int minSites=3, double siteWeight=1.0, double vectorWeight=1.0, double volumeWeight=1.0) -> SwigIntVector
-
assignActives
()¶ PhpProject_assignActives(PhpProject self, double minAct)
-
assignDefaultGroups
()¶ PhpProject_assignDefaultGroups(PhpProject self)
-
assignGroups
()¶ PhpProject_assignGroups(PhpProject self, SwigStringVector titles) -> SwigVectorIntVector
-
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) -> SwigVectorDoubleVector
-
closeProject
()¶ PhpProject_closeProject(PhpProject self)
-
commitMasterData
()¶ PhpProject_commitMasterData(PhpProject self, bool writeFirst=False)
-
compareFeatureDef
()¶ PhpProject_compareFeatureDef(PhpProject self, std::string const & fdFile1, std::string const & fdFile2) -> int
-
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, SwigStringVector hypoIDs)
-
deleteLigands
()¶ PhpProject_deleteLigands(PhpProject self, SwigIntVector ligandIDs)
-
deleteQsarModels
()¶ PhpProject_deleteQsarModels(PhpProject self, SwigStringVector hypoIDs)
-
expActivity
()¶ PhpProject_expActivity(PhpProject self)
-
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, SwigStringVector hypoIDs) -> SwigVectorIntVector
-
getConformer
()¶ PhpProject_getConformer(PhpProject self, int ligandID, int confIndex) -> MM_Index
-
getConformerCount
()¶ PhpProject_getConformerCount(PhpProject self, int ligandID) -> int
-
getConformers
()¶ PhpProject_getConformers(PhpProject self, int ligandID) -> SwigIntVector
-
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) -> SwigStringVector
-
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
-
getFeatureDef
()¶ PhpProject_getFeatureDef(PhpProject self, std::string const & fdFile) -> std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
-
getFeatureDefFromProj
()¶ PhpProject_getFeatureDefFromProj(PhpProject self) -> std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
-
getFeatureEquiv
()¶ PhpProject_getFeatureEquiv(PhpProject self) -> SwigStringVector
-
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, SwigIntVector 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) -> SwigIntVector
-
getHypoFmt
()¶ PhpProject_getHypoFmt(PhpProject self) -> std::string
-
getHypoIDs
()¶ PhpProject_getHypoIDs(PhpProject self, bool fullPath=False) -> SwigStringVector
-
getHypoMatches
()¶ PhpProject_getHypoMatches(PhpProject self, std::string const & hypoID, bool wantMisses=False) -> SwigVectorStringVector
-
getHypoScores
()¶ PhpProject_getHypoScores(PhpProject self, std::string const & hypoID) -> SwigStringVector
-
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) -> SwigVectorStringVector
-
getInFileType
()¶ PhpProject_getInFileType(PhpProject self, std::string const & fileName) -> std::string
-
getInactiveAlignments
()¶ PhpProject_getInactiveAlignments(PhpProject self, std::string const & hypoID, bool allowMissing=False) -> SwigIntVector
-
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) -> SwigIntVector
-
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) -> SwigVectorStringVector
-
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) -> SwigVectorIntVector
-
getMolSitesStrings
()¶ PhpProject_getMolSitesStrings(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, bool wantProj=False) -> SwigVectorStringVector
-
getMustMatch
()¶ PhpProject_getMustMatch(PhpProject self, int ligandID) -> bool
-
getPatternMatches
()¶ PhpProject_getPatternMatches(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd) -> SwigVectorIntVector
-
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) -> SwigIntVector
-
getQsarCount
()¶ PhpProject_getQsarCount(PhpProject self, std::string const & category) -> int
-
getQsarHypoIDs
()¶ PhpProject_getQsarHypoIDs(PhpProject self, bool fullPath=False) -> SwigStringVector
-
getQsarIDs
()¶ PhpProject_getQsarIDs(PhpProject self, std::string const & category) -> SwigIntVector
-
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
-
getQsarModelClassFraction
()¶ PhpProject_getQsarModelClassFraction(PhpProject self, PhpQSAR qsar, std::string const & qsarClass, int numFactors) -> double
-
getQsarModelClasses
()¶ PhpProject_getQsarModelClasses(PhpProject self, PhpQSAR qsar) -> SwigStringVector
-
getQsarModelCoeff
(PhpQSAR qsar, int numFactors, bool combineClasses=False) → SwigDoubleVector¶ getQsarModelCoeff(PhpQSAR qsar, int numFactors, std::string const & qsarClass) -> SwigDoubleVector PhpProject_getQsarModelCoeff(PhpProject self, PhpQSAR qsar, int numFactors, SwigStringVector qsarClasses, bool combineClasses=False) -> SwigDoubleVector
-
getQsarModelCoeffRange
(PhpQSAR qsar, int numFactors, bool combineClasses=False) → SwigDoubleVector¶ getQsarModelCoeffRange(PhpQSAR qsar, int numFactors, std::string const & qsarClass) -> SwigDoubleVector PhpProject_getQsarModelCoeffRange(PhpProject self, PhpQSAR qsar, int numFactors, SwigStringVector qsarClasses, bool combineClasses=False) -> SwigDoubleVector
-
getQsarModelFactorCount
()¶ PhpProject_getQsarModelFactorCount(PhpProject self, PhpQSAR qsar) -> int
-
getQsarModelGridLimits
()¶ PhpProject_getQsarModelGridLimits(PhpProject self, PhpQSAR qsar) -> SwigDoubleVector
-
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, SwigStringVector qsarClasses) -> int
-
getQsarModelVolClasses
()¶ PhpProject_getQsarModelVolClasses(PhpProject self, PhpQSAR qsar) -> SwigStringVector
-
getQsarModelVolCoords
(PhpQSAR qsar) → SwigVectorDoubleVector¶ getQsarModelVolCoords(PhpQSAR qsar, std::string const & qsarClass) -> SwigVectorDoubleVector PhpProject_getQsarModelVolCoords(PhpProject self, PhpQSAR qsar, SwigStringVector qsarClasses) -> SwigVectorDoubleVector
-
getQsarModelVolOnBits
(PhpQSAR qsar, MM_Index ctHandle) → SwigIntVector¶ getQsarModelVolOnBits(PhpQSAR qsar, MM_Index ctHandle, std::string const & qsarClass) -> SwigIntVector PhpProject_getQsarModelVolOnBits(PhpProject self, PhpQSAR qsar, MM_Index ctHandle, SwigStringVector qsarClasses) -> SwigIntVector
-
getQsarProps
()¶ PhpProject_getQsarProps(PhpProject self, MM_Index & ctHandle) -> SwigStringVector
-
getQsarSet
()¶ PhpProject_getQsarSet(PhpProject self, int ligandID) -> std::string
-
getQsarStats
()¶ PhpProject_getQsarStats(PhpProject self, std::string const & hypoID) -> SwigVectorDoubleVector
-
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) -> SwigIntVector
-
getSiteMasks
()¶ PhpProject_getSiteMasks(PhpProject self, bool ignoreDiffs=False) -> std::vector< PhpSiteMask,std::allocator< PhpSiteMask > >
-
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 > > > >
-
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, SwigVectorIntVector atoms, bool wantProj=False)
-
needSyncFeatureDef
()¶ PhpProject_needSyncFeatureDef(PhpProject self) -> bool
-
newProject
(std::string const & projectName, std::string const & inFile, std::string const & fdFile, bool connect, bool stereo, 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, SwigIntVector 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, SwigStringVector featureEquiv) -> SwigStringVector
-
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, SwigStringVector 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) -> SwigStringVector
-
syncFeatureDef
()¶ PhpProject_syncFeatureDef(PhpProject self)
-
testQsarModel
()¶ PhpProject_testQsarModel(PhpProject self, PhpQSAR qsar, std::string const & inFile, std::string const & actProp, std::string const & prefix) -> SwigVectorDoubleVector
-
thisown
¶ The membership flag
-
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
-
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)
-
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.
PhpQSAR
(*args)¶ Bases:
object
Proxy of C++ PhpQSAR class.
-
clear
()¶ PhpQSAR_clear(PhpQSAR self)
-
clearDataSet
()¶ PhpQSAR_clearDataSet(PhpQSAR self)
-
clearModel
()¶ PhpQSAR_clearModel(PhpQSAR self)
-
computeRCorr
()¶ PhpQSAR_computeRCorr(PhpQSAR self, SwigDoubleVector x, SwigDoubleVector y) -> double
-
computeStats
()¶ PhpQSAR_computeStats(PhpQSAR self, SwigDoubleVector yobs, SwigDoubleVector ypred, double & varObs, double & varPred, double & rmsErr, double & qsqr, double & rcorr)
-
createModel
(std::vector< PhpMolModel, std::allocator< PhpMolModel > > const & molecules, SwigDoubleVector activities, SwigSizetVector trainList, double gridSpacing, double dbuff, size_t maxFactors) → int¶ PhpQSAR_createModel(PhpQSAR self, SwigSizetVector trainList, double gridSpacing, double dbuff, size_t maxFactors) -> int
-
crossValidateModel
(size_t n, size_t randSeed, SwigVectorDoubleVector yhatLNO, SwigDoubleVector rsqrYobs, SwigDoubleVector rsqrYhat) → int¶ crossValidateModel(size_t n, size_t randSeed, SwigDoubleVector rsqrYobs, SwigDoubleVector rsqrYhat) -> int PhpQSAR_crossValidateModel(PhpQSAR self, size_t n, size_t randSeed) -> int
-
duplexDataSet
(size_t numTotal, size_t numTrain, size_t & randomSeed, SwigSizetVector trainList, SwigSizetVector predList)¶ PhpQSAR_duplexDataSet(PhpQSAR self, size_t numTrain, size_t & randomSeed, SwigDoubleVector activities, SwigSizetVector trainList, SwigSizetVector predList)
-
exportModel
()¶ PhpQSAR_exportModel(PhpQSAR self, std::string const & modelFile) -> int
-
exportModelToStream
()¶ PhpQSAR_exportModelToStream(PhpQSAR self, std::ostream & modelStream)
-
getActivities
()¶ PhpQSAR_getActivities(PhpQSAR self) -> SwigDoubleVector
-
getAtomClassDescription
()¶ PhpQSAR_getAtomClassDescription(PhpQSAR self, std::string const & atomClass) -> std::string
-
getAtomClasses
()¶ PhpQSAR_getAtomClasses(PhpQSAR self) -> SwigStringVector
-
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 > >
-
getOnBits
()¶ PhpQSAR_getOnBits(PhpQSAR self, SwigSizetVector bits) -> SwigSizetVector
-
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) -> SwigStringVector
-
getTvalue
()¶ PhpQSAR_getTvalue(PhpQSAR self, double p, size_t ndf) -> double
-
getVectSubset
()¶ PhpQSAR_getVectSubset(PhpQSAR self, SwigDoubleVector v, SwigSizetVector subset) -> SwigDoubleVector
-
getVolAtomClasses
()¶ PhpQSAR_getVolAtomClasses(PhpQSAR self) -> SwigStringVector
-
getVolCoords
() → std::vector< PhpVolCoords,std::allocator< PhpVolCoords > >¶ getVolCoords(std::string const & atomClass) -> std::vector< PhpVolCoords,std::allocator< PhpVolCoords > > PhpQSAR_getVolCoords(PhpQSAR self, SwigStringVector atomClasses) -> std::vector< PhpVolCoords,std::allocator< PhpVolCoords > >
-
getVolOccBits
(PhpMolModel const & molModel) → SwigSizetVector¶ getVolOccBits(size_t imol) -> SwigSizetVector getVolOccBits(PhpMolModel const & molModel, std::string const & atomClass) -> SwigSizetVector getVolOccBits(size_t imol, std::string const & atomClass) -> SwigSizetVector getVolOccBits(PhpMolModel const & molModel, SwigStringVector atomClasses) -> SwigSizetVector PhpQSAR_getVolOccBits(PhpQSAR self, size_t imol, SwigStringVector atomClasses) -> SwigSizetVector
-
getVolRegCoeffs
(size_t numFactors, bool combineAtomClasses=False) → SwigDoubleVector¶ getVolRegCoeffs(size_t numFactors, std::string const & atomClass) -> SwigDoubleVector PhpQSAR_getVolRegCoeffs(PhpQSAR self, size_t numFactors, SwigStringVector atomClasses, bool combineAtomClasses=False) -> SwigDoubleVector
-
importActivities
(char const * actFile) → int¶ PhpQSAR_importActivities(PhpQSAR self, SwigDoubleVector activities)
-
importModel
(std::string const & modelFile) → int¶ PhpQSAR_importModel(PhpQSAR self, std::istream & modelStream) -> int
-
importMolecules
(char const * maeFile) → int¶ PhpQSAR_importMolecules(PhpQSAR self, SwigIntVector 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, SwigStringVector atomClasses) -> size_t
-
printDelimitedActivities
()¶ PhpQSAR_printDelimitedActivities(PhpQSAR self, std::ostream & outStream, SwigSizetVector observations, SwigStringVector qsarSet, std::string const & delim, bool printHeaders=True)
-
printDelimitedBits
()¶ PhpQSAR_printDelimitedBits(PhpQSAR self, std::ostream & outStream, SwigSizetVector observations, SwigStringVector 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, SwigDoubleVector activities, SwigSizetVector predList, bool trainingSet=False)¶ PhpQSAR_printPred(PhpQSAR self, std::ostream & outStream, SwigSizetVector predList, bool trainingSet=False)
-
printVolOccBits
(std::ostream & outStream, std::vector< PhpMolModel, std::allocator< PhpMolModel > > const & molecules, SwigSizetVector molList)¶ printVolOccBits(std::ostream & outStream, SwigSizetVector 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, SwigDoubleVector activities, SwigSizetVector predList, size_t numFactors, SwigDoubleVector predActivities, double & rmsErr, double & qsqr)¶ testModel(SwigSizetVector predList, size_t numFactors, SwigDoubleVector predActivities, double & rmsErr, double & qsqr) testModel(std::vector< PhpMolModel,std::allocator< PhpMolModel > > const & molecules, std::vector< PhpMolVolume,std::allocator< PhpMolVolume > > & molVolumes, SwigDoubleVector activities, SwigSizetVector predList, size_t numFactors, bool restorePatterns, SwigDoubleVector predActivities, double & rmsErr, double & qsqr) testModel(std::vector< PhpMolModel,std::allocator< PhpMolModel > > const & molecules, SwigDoubleVector activities, SwigSizetVector predList, size_t numFactors1, size_t numFactors2, SwigVectorDoubleVector predActivities, SwigDoubleVector rmsErr, SwigDoubleVector qsqr) PhpQSAR_testModel(PhpQSAR self, SwigSizetVector predList, size_t numFactors1, size_t numFactors2, SwigVectorDoubleVector predActivities, SwigDoubleVector rmsErr, SwigDoubleVector qsqr)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpQSARModel
¶ Bases:
object
Proxy of C++ PhpQSARModel_ class.
-
atomClasses
¶ PhpQSARModel_atomClasses_get(PhpQSARModel self) -> SwigStringVector
-
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 > > > > > *
-
featureRadii
¶ PhpQSARModel_featureRadii_get(PhpQSARModel self) -> PhpFeatureData
-
gridSpacing
¶ PhpQSARModel_gridSpacing_get(PhpQSARModel self) -> double
-
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) -> SwigDoubleVector
-
thisown
¶ The membership flag
-
volumeNames
¶ PhpQSARModel_volumeNames_get(PhpQSARModel self) -> SwigStringVector
-
xmax
¶ PhpQSARModel_xmax_get(PhpQSARModel self) -> double
-
xmin
¶ PhpQSARModel_xmin_get(PhpQSARModel self) -> double
-
ymax
¶ PhpQSARModel_ymax_get(PhpQSARModel self) -> double
-
ymin
¶ PhpQSARModel_ymin_get(PhpQSARModel self) -> double
-
zmax
¶ PhpQSARModel_zmax_get(PhpQSARModel self) -> double
-
zmin
¶ PhpQSARModel_zmin_get(PhpQSARModel self) -> double
-
-
class
schrodinger.infra.phase.
PhpScreener
(hypo, mode)¶ Bases:
object
Proxy of C++ PhpScreener class.
-
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) -> SwigIntVector
-
setConfOptions
()¶ PhpScreener_setConfOptions(PhpScreener self, PhpConfOptions conf_options)
-
setMatchOptions
()¶ PhpScreener_setMatchOptions(PhpScreener self, PhpMatchOptions match_options)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpSite
(*args)¶ Bases:
object
Proxy of C++ PhpSite class.
-
SiteStatusOff
= 1¶
-
SiteStatusOn
= 0¶
-
calculateSimilarity
()¶ PhpSite_calculateSimilarity(PhpSite self, PhpSite rhs) -> double
-
distance
()¶ PhpSite_distance(PhpSite self, PhpSite rhs) -> double
-
getCoordinates
()¶ PhpSite_getCoordinates(PhpSite self) -> SwigDoubleVector
-
getDisplayName
()¶ PhpSite_getDisplayName(PhpSite self) -> std::string
-
getFragType
()¶ PhpSite_getFragType(PhpSite self) -> std::string
-
getMaskValue
()¶ PhpSite_getMaskValue(PhpSite self) -> int
-
getPermitted
()¶ PhpSite_getPermitted(PhpSite self) -> std::string
-
getProhibited
()¶ PhpSite_getProhibited(PhpSite self) -> std::string
-
getProjCoords
()¶ PhpSite_getProjCoords(PhpSite self) -> SwigVectorDoubleVector
-
getProjectedOnly
()¶ PhpSite_getProjectedOnly(PhpSite self) -> bool
-
getRad
()¶ PhpSite_getRad(PhpSite self) -> double
-
getSiteDescription
()¶ PhpSite_getSiteDescription(PhpSite self) -> std::string
-
getSiteName
()¶ PhpSite_getSiteName(PhpSite self, int offset=1) -> std::string
-
getSiteNumber
()¶ PhpSite_getSiteNumber(PhpSite self) -> size_t
-
getSiteSimilarity
()¶ PhpSite_getSiteSimilarity(PhpSite self) -> int
-
getSiteStatus
()¶ PhpSite_getSiteStatus(PhpSite self) -> int
-
getSiteType
()¶ PhpSite_getSiteType(PhpSite self) -> std::string
-
getSiteTypeChar
()¶ PhpSite_getSiteTypeChar(PhpSite self) -> char
-
getTol
()¶ PhpSite_getTol(PhpSite self) -> double
-
getXCoord
()¶ PhpSite_getXCoord(PhpSite self) -> double
-
getXP
()¶ PhpSite_getXP(PhpSite self) -> double
-
getYCoord
()¶ PhpSite_getYCoord(PhpSite self) -> double
-
getZCoord
()¶ PhpSite_getZCoord(PhpSite self) -> double
-
hasXP
()¶ PhpSite_hasXP(PhpSite self) -> bool
-
setCoordinates
()¶ PhpSite_setCoordinates(PhpSite self, double a_x, double a_y, double a_z)
-
setDefaults
()¶ PhpSite_setDefaults(PhpSite self)
-
setFragType
()¶ PhpSite_setFragType(PhpSite self, std::string const & fragType)
-
setMaskValue
()¶ PhpSite_setMaskValue(PhpSite self, int mask)
-
setPermitted
()¶ PhpSite_setPermitted(PhpSite self, std::string const & permitted)
-
setProhibited
()¶ PhpSite_setProhibited(PhpSite self, std::string const & prohibited)
-
setProjCoords
()¶ PhpSite_setProjCoords(PhpSite self, SwigVectorDoubleVector projCoords)
-
setProjectedOnly
()¶ PhpSite_setProjectedOnly(PhpSite self, bool const a_status)
-
setRad
()¶ PhpSite_setRad(PhpSite self, double rad)
-
setSiteNumber
()¶ PhpSite_setSiteNumber(PhpSite self, size_t const a_number)
-
setSiteSimilarity
()¶ PhpSite_setSiteSimilarity(PhpSite self, int const a_type)
-
setSiteStatusOff
()¶ PhpSite_setSiteStatusOff(PhpSite self)
-
setSiteStatusOn
()¶ PhpSite_setSiteStatusOn(PhpSite self)
-
setSiteType
()¶ PhpSite_setSiteType(PhpSite self, std::string const & a_type)
-
setSiteTypeChar
()¶ PhpSite_setSiteTypeChar(PhpSite self, char const a_char)
-
setStatus
()¶ PhpSite_setStatus(PhpSite self, int a_status)
-
setTol
()¶ PhpSite_setTol(PhpSite self, double tol)
-
setXCoord
()¶ PhpSite_setXCoord(PhpSite self, double a_x)
-
setXP
()¶ PhpSite_setXP(PhpSite self, double xp, bool defined=True)
-
setYCoord
()¶ PhpSite_setYCoord(PhpSite self, double a_y)
-
setZCoord
()¶ PhpSite_setZCoord(PhpSite self, double a_z)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpSiteConstrainer
(*args)¶ Bases:
object
Proxy of C++ PhpSiteConstrainer class.
-
addConstraint
()¶ PhpSiteConstrainer_addConstraint(PhpSiteConstrainer self, PhpSiteConstraint constraint)
-
clear
()¶ PhpSiteConstrainer_clear(PhpSiteConstrainer self)
-
exportConstraints
(std::string const & outFile)¶ PhpSiteConstrainer_exportConstraints(PhpSiteConstrainer self, std::ostream & outStream)
-
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
-
getConstraints
() → std::vector< PhpSiteConstraint,std::allocator< PhpSiteConstraint > >¶ PhpSiteConstrainer_getConstraints(PhpSiteConstrainer self, size_t numSites) -> std::vector< PhpSiteConstraint,std::allocator< PhpSiteConstraint > >
-
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, SwigSizetVector refSiteIndices, PhpLigand const & matchedLigand, size_t matchedConfIndex, SwigSizetVector 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, SwigSizetVector matchedSiteIndices, std::string & reason) -> bool
-
printConstraint
()¶ PhpSiteConstrainer_printConstraint(PhpSiteConstrainer self, PhpSiteConstraint constraint, std::ostream & outStream)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpSiteConstraint
(*args)¶ Bases:
object
Proxy of C++ PhpSiteConstraint class.
-
getSiteIndices
()¶ PhpSiteConstraint_getSiteIndices(PhpSiteConstraint self) -> SwigIntVector
-
getSiteTypes
()¶ PhpSiteConstraint_getSiteTypes(PhpSiteConstraint self) -> std::string
-
getTol
()¶ PhpSiteConstraint_getTol(PhpSiteConstraint self) -> double
-
getValue
()¶ PhpSiteConstraint_getValue(PhpSiteConstraint self) -> double
-
setConstraint
()¶ PhpSiteConstraint_setConstraint(PhpSiteConstraint self, SwigIntVector u_siteIndices, std::string const & u_siteTypes, double u_value, double u_tol)
-
siteIndices
¶ PhpSiteConstraint_siteIndices_get(PhpSiteConstraint self) -> SwigSizetVector
-
siteTypes
¶ PhpSiteConstraint_siteTypes_get(PhpSiteConstraint self) -> std::string const &
-
thisown
¶ The membership flag
-
tol
¶ PhpSiteConstraint_tol_get(PhpSiteConstraint self) -> double
-
value
¶ PhpSiteConstraint_value_get(PhpSiteConstraint self) -> double
-
-
class
schrodinger.infra.phase.
PhpSiteMask
(*args)¶ Bases:
object
Proxy of C++ PhpSiteMask class.
-
addSiteMaskData
(size_t siteNumber, char siteType, int maskValue)¶ PhpSiteMask_addSiteMaskData(PhpSiteMask self, PhpSiteMaskData siteMaskData)
-
addSiteMaskGroup
(SwigSizetVector 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)
-
static
getMatchLimits
(SwigIntVector siteMask) → SwigIntVector¶
-
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) -> SwigIntVector
-
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
resolveMatchLimits
(SwigIntVector siteMask, size_t & minSites, size_t & maxSites)¶
-
static
splitMaskValue
(int maskValue) → SwigIntVector¶
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpSiteMaskData
(*args)¶ Bases:
object
Proxy of C++ PhpSiteMaskData class.
-
getMaskValue
()¶ PhpSiteMaskData_getMaskValue(PhpSiteMaskData self) -> int
-
getSiteNumber
()¶ PhpSiteMaskData_getSiteNumber(PhpSiteMaskData self) -> int
-
getSiteType
()¶ PhpSiteMaskData_getSiteType(PhpSiteMaskData self) -> char
-
maskValue
¶ PhpSiteMaskData_maskValue_get(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
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpSiteMaskGroup
(*args)¶ Bases:
object
Proxy of C++ PhpSiteMaskGroup class.
-
getGroupNumber
()¶ PhpSiteMaskGroup_getGroupNumber(PhpSiteMaskGroup self) -> int
-
getMinMatch
()¶ PhpSiteMaskGroup_getMinMatch(PhpSiteMaskGroup self) -> int
-
getSiteIndices
()¶ PhpSiteMaskGroup_getSiteIndices(PhpSiteMaskGroup self) -> SwigIntVector
-
groupNumber
¶ PhpSiteMaskGroup_groupNumber_get(PhpSiteMaskGroup self) -> size_t
-
minMatch
¶ PhpSiteMaskGroup_minMatch_get(PhpSiteMaskGroup self) -> size_t
-
setGroup
()¶ PhpSiteMaskGroup_setGroup(PhpSiteMaskGroup self, SwigIntVector u_siteIndices, int u_minMatch, int u_groupNumber)
-
siteIndices
¶ PhpSiteMaskGroup_siteIndices_get(PhpSiteMaskGroup self) -> SwigSizetVector
-
thisown
¶ The membership flag
-
-
schrodinger.infra.phase.
PhpSiteMask_getMatchLimits
(SwigIntVector siteMask) → SwigIntVector¶
-
schrodinger.infra.phase.
PhpSiteMask_resolveMaskValue
(int maskValue, size_t & groupNumber, size_t & minMatch)¶
-
schrodinger.infra.phase.
PhpSiteMask_resolveMatchLimits
(SwigIntVector siteMask, size_t & minSites, size_t & maxSites)¶
-
schrodinger.infra.phase.
PhpSiteMask_splitMaskValue
(int maskValue) → SwigIntVector¶
-
class
schrodinger.infra.phase.
PhpSiteWithAtoms
¶ Bases:
object
Proxy of C++ PhpSiteWithAtoms class.
-
atoms
¶ PhpSiteWithAtoms_atoms_get(PhpSiteWithAtoms self) -> std::set< int >
-
site
¶ PhpSiteWithAtoms_site_get(PhpSiteWithAtoms self) -> PhpSite
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpStructureBus
(*args)¶ Bases:
object
Proxy of C++ PhpStructureBus class.
-
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) -> SwigIntVector
-
getCtVectorCopy
()¶ PhpStructureBus_getCtVectorCopy(PhpStructureBus self) -> SwigIntVector
-
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
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
PhpStructureReader
(*args)¶ Bases:
object
Proxy of C++ PhpStructureReader class.
-
next
()¶ PhpStructureReader_next(PhpStructureReader self) -> PhpStructureBus
-
thisown
¶ The membership flag
-
-
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.
SwigDoubleVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(double)> class.
-
append
()¶ SwigDoubleVector_append(SwigDoubleVector self, std::vector< double >::value_type const & x)
-
assign
()¶ SwigDoubleVector_assign(SwigDoubleVector self, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
-
back
()¶ SwigDoubleVector_back(SwigDoubleVector self) -> std::vector< double >::value_type const &
-
begin
()¶ SwigDoubleVector_begin(SwigDoubleVector self) -> std::vector< double >::iterator
-
capacity
()¶ SwigDoubleVector_capacity(SwigDoubleVector self) -> std::vector< double >::size_type
-
clear
()¶ SwigDoubleVector_clear(SwigDoubleVector self)
-
empty
()¶ SwigDoubleVector_empty(SwigDoubleVector self) -> bool
-
end
()¶ SwigDoubleVector_end(SwigDoubleVector self) -> std::vector< double >::iterator
-
erase
(std::vector< double >::iterator pos) → std::vector< double >::iterator¶ SwigDoubleVector_erase(SwigDoubleVector self, std::vector< double >::iterator first, std::vector< double >::iterator last) -> std::vector< double >::iterator
-
front
()¶ SwigDoubleVector_front(SwigDoubleVector self) -> std::vector< double >::value_type const &
-
get_allocator
()¶ SwigDoubleVector_get_allocator(SwigDoubleVector self) -> std::vector< double >::allocator_type
-
insert
(std::vector< double >::iterator pos, std::vector< double >::value_type const & x) → std::vector< double >::iterator¶ SwigDoubleVector_insert(SwigDoubleVector self, std::vector< double >::iterator pos, std::vector< double >::size_type n, std::vector< double >::value_type const & x)
-
iterator
()¶ SwigDoubleVector_iterator(SwigDoubleVector self) -> SwigPyIterator
-
pop
()¶ SwigDoubleVector_pop(SwigDoubleVector self) -> std::vector< double >::value_type
-
pop_back
()¶ SwigDoubleVector_pop_back(SwigDoubleVector self)
-
push_back
()¶ SwigDoubleVector_push_back(SwigDoubleVector self, std::vector< double >::value_type const & x)
-
rbegin
()¶ SwigDoubleVector_rbegin(SwigDoubleVector self) -> std::vector< double >::reverse_iterator
-
rend
()¶ SwigDoubleVector_rend(SwigDoubleVector self) -> std::vector< double >::reverse_iterator
-
reserve
()¶ SwigDoubleVector_reserve(SwigDoubleVector self, std::vector< double >::size_type n)
-
resize
(std::vector< double >::size_type new_size)¶ SwigDoubleVector_resize(SwigDoubleVector self, std::vector< double >::size_type new_size, std::vector< double >::value_type const & x)
-
size
()¶ SwigDoubleVector_size(SwigDoubleVector self) -> std::vector< double >::size_type
-
swap
()¶ SwigDoubleVector_swap(SwigDoubleVector self, SwigDoubleVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigIntVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(int)> class.
-
append
()¶ SwigIntVector_append(SwigIntVector self, std::vector< int >::value_type const & x)
-
assign
()¶ SwigIntVector_assign(SwigIntVector self, std::vector< int >::size_type n, std::vector< int >::value_type const & x)
-
back
()¶ SwigIntVector_back(SwigIntVector self) -> std::vector< int >::value_type const &
-
begin
()¶ SwigIntVector_begin(SwigIntVector self) -> std::vector< int >::iterator
-
capacity
()¶ SwigIntVector_capacity(SwigIntVector self) -> std::vector< int >::size_type
-
clear
()¶ SwigIntVector_clear(SwigIntVector self)
-
empty
()¶ SwigIntVector_empty(SwigIntVector self) -> bool
-
end
()¶ SwigIntVector_end(SwigIntVector self) -> std::vector< int >::iterator
-
erase
(std::vector< int >::iterator pos) → std::vector< int >::iterator¶ SwigIntVector_erase(SwigIntVector self, std::vector< int >::iterator first, std::vector< int >::iterator last) -> std::vector< int >::iterator
-
front
()¶ SwigIntVector_front(SwigIntVector self) -> std::vector< int >::value_type const &
-
get_allocator
()¶ SwigIntVector_get_allocator(SwigIntVector self) -> std::vector< int >::allocator_type
-
insert
(std::vector< int >::iterator pos, std::vector< int >::value_type const & x) → std::vector< int >::iterator¶ SwigIntVector_insert(SwigIntVector self, std::vector< int >::iterator pos, std::vector< int >::size_type n, std::vector< int >::value_type const & x)
-
iterator
()¶ SwigIntVector_iterator(SwigIntVector self) -> SwigPyIterator
-
pop
()¶ SwigIntVector_pop(SwigIntVector self) -> std::vector< int >::value_type
-
pop_back
()¶ SwigIntVector_pop_back(SwigIntVector self)
-
push_back
()¶ SwigIntVector_push_back(SwigIntVector self, std::vector< int >::value_type const & x)
-
rbegin
()¶ SwigIntVector_rbegin(SwigIntVector self) -> std::vector< int >::reverse_iterator
-
rend
()¶ SwigIntVector_rend(SwigIntVector self) -> std::vector< int >::reverse_iterator
-
reserve
()¶ SwigIntVector_reserve(SwigIntVector self, std::vector< int >::size_type n)
-
resize
(std::vector< int >::size_type new_size)¶ SwigIntVector_resize(SwigIntVector self, std::vector< int >::size_type new_size, std::vector< int >::value_type const & x)
-
size
()¶ SwigIntVector_size(SwigIntVector self) -> std::vector< int >::size_type
-
swap
()¶ SwigIntVector_swap(SwigIntVector self, SwigIntVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigPhpFpTypeVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(PhpFpType)> class.
-
append
()¶ SwigPhpFpTypeVector_append(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::value_type const & x)
-
assign
()¶ SwigPhpFpTypeVector_assign(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::size_type n, std::vector< enum PhpFpType >::value_type const & x)
-
back
()¶ SwigPhpFpTypeVector_back(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::value_type const &
-
begin
()¶ SwigPhpFpTypeVector_begin(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::iterator
-
capacity
()¶ SwigPhpFpTypeVector_capacity(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::size_type
-
clear
()¶ SwigPhpFpTypeVector_clear(SwigPhpFpTypeVector self)
-
empty
()¶ SwigPhpFpTypeVector_empty(SwigPhpFpTypeVector self) -> bool
-
end
()¶ SwigPhpFpTypeVector_end(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::iterator
-
erase
(std::vector< enum PhpFpType >::iterator pos) → std::vector< enum PhpFpType >::iterator¶ SwigPhpFpTypeVector_erase(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::iterator first, std::vector< enum PhpFpType >::iterator last) -> std::vector< enum PhpFpType >::iterator
-
front
()¶ SwigPhpFpTypeVector_front(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::value_type const &
-
get_allocator
()¶ SwigPhpFpTypeVector_get_allocator(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::allocator_type
-
insert
(std::vector< enum PhpFpType >::iterator pos, std::vector< enum PhpFpType >::value_type const & x) → std::vector< enum PhpFpType >::iterator¶ SwigPhpFpTypeVector_insert(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::iterator pos, std::vector< enum PhpFpType >::size_type n, std::vector< enum PhpFpType >::value_type const & x)
-
iterator
()¶ SwigPhpFpTypeVector_iterator(SwigPhpFpTypeVector self) -> SwigPyIterator
-
pop
()¶ SwigPhpFpTypeVector_pop(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::value_type
-
pop_back
()¶ SwigPhpFpTypeVector_pop_back(SwigPhpFpTypeVector self)
-
push_back
()¶ SwigPhpFpTypeVector_push_back(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::value_type const & x)
-
rbegin
()¶ SwigPhpFpTypeVector_rbegin(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::reverse_iterator
-
rend
()¶ SwigPhpFpTypeVector_rend(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::reverse_iterator
-
reserve
()¶ SwigPhpFpTypeVector_reserve(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::size_type n)
-
resize
(std::vector< enum PhpFpType >::size_type new_size)¶ SwigPhpFpTypeVector_resize(SwigPhpFpTypeVector self, std::vector< enum PhpFpType >::size_type new_size, std::vector< enum PhpFpType >::value_type const & x)
-
size
()¶ SwigPhpFpTypeVector_size(SwigPhpFpTypeVector self) -> std::vector< enum PhpFpType >::size_type
-
swap
()¶ SwigPhpFpTypeVector_swap(SwigPhpFpTypeVector self, SwigPhpFpTypeVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigPhpStructureBusVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(PhpStructureBus)> class.
-
append
()¶ SwigPhpStructureBusVector_append(SwigPhpStructureBusVector self, PhpStructureBus x)
-
assign
()¶ SwigPhpStructureBusVector_assign(SwigPhpStructureBusVector self, std::vector< PhpStructureBus >::size_type n, PhpStructureBus x)
-
back
()¶ SwigPhpStructureBusVector_back(SwigPhpStructureBusVector self) -> PhpStructureBus
-
begin
()¶ SwigPhpStructureBusVector_begin(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::iterator
-
capacity
()¶ SwigPhpStructureBusVector_capacity(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::size_type
-
clear
()¶ SwigPhpStructureBusVector_clear(SwigPhpStructureBusVector self)
-
empty
()¶ SwigPhpStructureBusVector_empty(SwigPhpStructureBusVector self) -> bool
-
end
()¶ SwigPhpStructureBusVector_end(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::iterator
-
erase
(std::vector< PhpStructureBus >::iterator pos) → std::vector< PhpStructureBus >::iterator¶ SwigPhpStructureBusVector_erase(SwigPhpStructureBusVector self, std::vector< PhpStructureBus >::iterator first, std::vector< PhpStructureBus >::iterator last) -> std::vector< PhpStructureBus >::iterator
-
front
()¶ SwigPhpStructureBusVector_front(SwigPhpStructureBusVector self) -> PhpStructureBus
-
get_allocator
()¶ SwigPhpStructureBusVector_get_allocator(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::allocator_type
-
insert
(std::vector< PhpStructureBus >::iterator pos, PhpStructureBus x) → std::vector< PhpStructureBus >::iterator¶ SwigPhpStructureBusVector_insert(SwigPhpStructureBusVector self, std::vector< PhpStructureBus >::iterator pos, std::vector< PhpStructureBus >::size_type n, PhpStructureBus x)
-
iterator
()¶ SwigPhpStructureBusVector_iterator(SwigPhpStructureBusVector self) -> SwigPyIterator
-
pop
()¶ SwigPhpStructureBusVector_pop(SwigPhpStructureBusVector self) -> PhpStructureBus
-
pop_back
()¶ SwigPhpStructureBusVector_pop_back(SwigPhpStructureBusVector self)
-
push_back
()¶ SwigPhpStructureBusVector_push_back(SwigPhpStructureBusVector self, PhpStructureBus x)
-
rbegin
()¶ SwigPhpStructureBusVector_rbegin(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::reverse_iterator
-
rend
()¶ SwigPhpStructureBusVector_rend(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::reverse_iterator
-
reserve
()¶ SwigPhpStructureBusVector_reserve(SwigPhpStructureBusVector self, std::vector< PhpStructureBus >::size_type n)
-
resize
(std::vector< PhpStructureBus >::size_type new_size)¶ SwigPhpStructureBusVector_resize(SwigPhpStructureBusVector self, std::vector< PhpStructureBus >::size_type new_size, PhpStructureBus x)
-
size
()¶ SwigPhpStructureBusVector_size(SwigPhpStructureBusVector self) -> std::vector< PhpStructureBus >::size_type
-
swap
()¶ SwigPhpStructureBusVector_swap(SwigPhpStructureBusVector self, SwigPhpStructureBusVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigPyIterator
(*args, **kwargs)¶ Bases:
object
Proxy of C++ swig::SwigPyIterator class.
-
advance
()¶ SwigPyIterator_advance(SwigPyIterator self, ptrdiff_t n) -> SwigPyIterator
-
copy
()¶ SwigPyIterator_copy(SwigPyIterator self) -> 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
-
incr
()¶ SwigPyIterator_incr(SwigPyIterator self, size_t n=1) -> SwigPyIterator
-
next
()¶ SwigPyIterator_next(SwigPyIterator self) -> PyObject *
-
previous
()¶ SwigPyIterator_previous(SwigPyIterator self) -> PyObject *
-
thisown
¶ The membership flag
-
value
()¶ SwigPyIterator_value(SwigPyIterator self) -> PyObject *
-
-
class
schrodinger.infra.phase.
SwigSizetVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(size_t)> class.
-
append
()¶ SwigSizetVector_append(SwigSizetVector self, std::vector< size_t >::value_type const & x)
-
assign
()¶ SwigSizetVector_assign(SwigSizetVector self, std::vector< size_t >::size_type n, std::vector< size_t >::value_type const & x)
-
back
()¶ SwigSizetVector_back(SwigSizetVector self) -> std::vector< size_t >::value_type const &
-
begin
()¶ SwigSizetVector_begin(SwigSizetVector self) -> std::vector< size_t >::iterator
-
capacity
()¶ SwigSizetVector_capacity(SwigSizetVector self) -> std::vector< size_t >::size_type
-
clear
()¶ SwigSizetVector_clear(SwigSizetVector self)
-
empty
()¶ SwigSizetVector_empty(SwigSizetVector self) -> bool
-
end
()¶ SwigSizetVector_end(SwigSizetVector self) -> std::vector< size_t >::iterator
-
erase
(std::vector< size_t >::iterator pos) → std::vector< size_t >::iterator¶ SwigSizetVector_erase(SwigSizetVector self, std::vector< size_t >::iterator first, std::vector< size_t >::iterator last) -> std::vector< size_t >::iterator
-
front
()¶ SwigSizetVector_front(SwigSizetVector self) -> std::vector< size_t >::value_type const &
-
get_allocator
()¶ SwigSizetVector_get_allocator(SwigSizetVector self) -> std::vector< size_t >::allocator_type
-
insert
(std::vector< size_t >::iterator pos, std::vector< size_t >::value_type const & x) → std::vector< size_t >::iterator¶ SwigSizetVector_insert(SwigSizetVector self, std::vector< size_t >::iterator pos, std::vector< size_t >::size_type n, std::vector< size_t >::value_type const & x)
-
iterator
()¶ SwigSizetVector_iterator(SwigSizetVector self) -> SwigPyIterator
-
pop
()¶ SwigSizetVector_pop(SwigSizetVector self) -> std::vector< size_t >::value_type
-
pop_back
()¶ SwigSizetVector_pop_back(SwigSizetVector self)
-
push_back
()¶ SwigSizetVector_push_back(SwigSizetVector self, std::vector< size_t >::value_type const & x)
-
rbegin
()¶ SwigSizetVector_rbegin(SwigSizetVector self) -> std::vector< size_t >::reverse_iterator
-
rend
()¶ SwigSizetVector_rend(SwigSizetVector self) -> std::vector< size_t >::reverse_iterator
-
reserve
()¶ SwigSizetVector_reserve(SwigSizetVector self, std::vector< size_t >::size_type n)
-
resize
(std::vector< size_t >::size_type new_size)¶ SwigSizetVector_resize(SwigSizetVector self, std::vector< size_t >::size_type new_size, std::vector< size_t >::value_type const & x)
-
size
()¶ SwigSizetVector_size(SwigSizetVector self) -> std::vector< size_t >::size_type
-
swap
()¶ SwigSizetVector_swap(SwigSizetVector self, SwigSizetVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigStringStringMap
(*args)¶ Bases:
object
Proxy of C++ std::map<(std::string,std::string)> class.
-
asdict
()¶ SwigStringStringMap_asdict(SwigStringStringMap self) -> PyObject *
-
begin
()¶ SwigStringStringMap_begin(SwigStringStringMap self) -> std::map< std::string,std::string >::iterator
-
clear
()¶ SwigStringStringMap_clear(SwigStringStringMap self)
-
count
()¶ SwigStringStringMap_count(SwigStringStringMap self, std::map< std::string,std::string >::key_type const & x) -> std::map< std::string,std::string >::size_type
-
empty
()¶ SwigStringStringMap_empty(SwigStringStringMap self) -> bool
-
end
()¶ SwigStringStringMap_end(SwigStringStringMap self) -> std::map< std::string,std::string >::iterator
-
erase
(std::map< std::string, std::string >::key_type const & x) → std::map< std::string,std::string >::size_type¶ erase(std::map< std::string,std::string >::iterator position) SwigStringStringMap_erase(SwigStringStringMap self, std::map< std::string,std::string >::iterator first, std::map< std::string,std::string >::iterator last)
-
find
()¶ SwigStringStringMap_find(SwigStringStringMap self, std::map< std::string,std::string >::key_type const & x) -> std::map< std::string,std::string >::iterator
-
get_allocator
()¶ SwigStringStringMap_get_allocator(SwigStringStringMap self) -> std::map< std::string,std::string >::allocator_type
-
has_key
()¶ SwigStringStringMap_has_key(SwigStringStringMap self, std::map< std::string,std::string >::key_type const & key) -> bool
-
items
()¶ SwigStringStringMap_items(SwigStringStringMap self) -> PyObject *
-
iterator
()¶ SwigStringStringMap_iterator(SwigStringStringMap self) -> SwigPyIterator
-
iteritems
()¶
-
iterkeys
()¶
-
itervalues
()¶
-
key_iterator
()¶ SwigStringStringMap_key_iterator(SwigStringStringMap self) -> SwigPyIterator
-
keys
()¶ SwigStringStringMap_keys(SwigStringStringMap self) -> PyObject *
-
lower_bound
()¶ SwigStringStringMap_lower_bound(SwigStringStringMap self, std::map< std::string,std::string >::key_type const & x) -> std::map< std::string,std::string >::iterator
-
rbegin
()¶ SwigStringStringMap_rbegin(SwigStringStringMap self) -> std::map< std::string,std::string >::reverse_iterator
-
rend
()¶ SwigStringStringMap_rend(SwigStringStringMap self) -> std::map< std::string,std::string >::reverse_iterator
-
size
()¶ SwigStringStringMap_size(SwigStringStringMap self) -> std::map< std::string,std::string >::size_type
-
swap
()¶ SwigStringStringMap_swap(SwigStringStringMap self, SwigStringStringMap v)
-
thisown
¶ The membership flag
-
upper_bound
()¶ SwigStringStringMap_upper_bound(SwigStringStringMap self, std::map< std::string,std::string >::key_type const & x) -> std::map< std::string,std::string >::iterator
-
value_iterator
()¶ SwigStringStringMap_value_iterator(SwigStringStringMap self) -> SwigPyIterator
-
values
()¶ SwigStringStringMap_values(SwigStringStringMap self) -> PyObject *
-
-
class
schrodinger.infra.phase.
SwigStringVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(std::string)> class.
-
append
()¶ SwigStringVector_append(SwigStringVector self, std::vector< std::string >::value_type const & x)
-
assign
()¶ SwigStringVector_assign(SwigStringVector self, std::vector< std::string >::size_type n, std::vector< std::string >::value_type const & x)
-
back
()¶ SwigStringVector_back(SwigStringVector self) -> std::vector< std::string >::value_type const &
-
begin
()¶ SwigStringVector_begin(SwigStringVector self) -> std::vector< std::string >::iterator
-
capacity
()¶ SwigStringVector_capacity(SwigStringVector self) -> std::vector< std::string >::size_type
-
clear
()¶ SwigStringVector_clear(SwigStringVector self)
-
empty
()¶ SwigStringVector_empty(SwigStringVector self) -> bool
-
end
()¶ SwigStringVector_end(SwigStringVector self) -> std::vector< std::string >::iterator
-
erase
(std::vector< std::string >::iterator pos) → std::vector< std::string >::iterator¶ SwigStringVector_erase(SwigStringVector self, std::vector< std::string >::iterator first, std::vector< std::string >::iterator last) -> std::vector< std::string >::iterator
-
front
()¶ SwigStringVector_front(SwigStringVector self) -> std::vector< std::string >::value_type const &
-
get_allocator
()¶ SwigStringVector_get_allocator(SwigStringVector self) -> std::vector< std::string >::allocator_type
-
insert
(std::vector< std::string >::iterator pos, std::vector< std::string >::value_type const & x) → std::vector< std::string >::iterator¶ SwigStringVector_insert(SwigStringVector self, std::vector< std::string >::iterator pos, std::vector< std::string >::size_type n, std::vector< std::string >::value_type const & x)
-
iterator
()¶ SwigStringVector_iterator(SwigStringVector self) -> SwigPyIterator
-
pop
()¶ SwigStringVector_pop(SwigStringVector self) -> std::vector< std::string >::value_type
-
pop_back
()¶ SwigStringVector_pop_back(SwigStringVector self)
-
push_back
()¶ SwigStringVector_push_back(SwigStringVector self, std::vector< std::string >::value_type const & x)
-
rbegin
()¶ SwigStringVector_rbegin(SwigStringVector self) -> std::vector< std::string >::reverse_iterator
-
rend
()¶ SwigStringVector_rend(SwigStringVector self) -> std::vector< std::string >::reverse_iterator
-
reserve
()¶ SwigStringVector_reserve(SwigStringVector self, std::vector< std::string >::size_type n)
-
resize
(std::vector< std::string >::size_type new_size)¶ SwigStringVector_resize(SwigStringVector self, std::vector< std::string >::size_type new_size, std::vector< std::string >::value_type const & x)
-
size
()¶ SwigStringVector_size(SwigStringVector self) -> std::vector< std::string >::size_type
-
swap
()¶ SwigStringVector_swap(SwigStringVector self, SwigStringVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigUnsignedIntVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(unsigned int)> class.
-
append
()¶ SwigUnsignedIntVector_append(SwigUnsignedIntVector self, std::vector< unsigned int >::value_type const & x)
-
assign
()¶ SwigUnsignedIntVector_assign(SwigUnsignedIntVector self, std::vector< unsigned int >::size_type n, std::vector< unsigned int >::value_type const & x)
-
back
()¶ SwigUnsignedIntVector_back(SwigUnsignedIntVector self) -> std::vector< unsigned int >::value_type const &
-
begin
()¶ SwigUnsignedIntVector_begin(SwigUnsignedIntVector self) -> std::vector< unsigned int >::iterator
-
capacity
()¶ SwigUnsignedIntVector_capacity(SwigUnsignedIntVector self) -> std::vector< unsigned int >::size_type
-
clear
()¶ SwigUnsignedIntVector_clear(SwigUnsignedIntVector self)
-
empty
()¶ SwigUnsignedIntVector_empty(SwigUnsignedIntVector self) -> bool
-
end
()¶ SwigUnsignedIntVector_end(SwigUnsignedIntVector self) -> std::vector< unsigned int >::iterator
-
erase
(std::vector< unsigned int >::iterator pos) → std::vector< unsigned int >::iterator¶ SwigUnsignedIntVector_erase(SwigUnsignedIntVector self, std::vector< unsigned int >::iterator first, std::vector< unsigned int >::iterator last) -> std::vector< unsigned int >::iterator
-
front
()¶ SwigUnsignedIntVector_front(SwigUnsignedIntVector self) -> std::vector< unsigned int >::value_type const &
-
get_allocator
()¶ SwigUnsignedIntVector_get_allocator(SwigUnsignedIntVector self) -> std::vector< unsigned int >::allocator_type
-
insert
(std::vector< unsigned int >::iterator pos, std::vector< unsigned int >::value_type const & x) → std::vector< unsigned int >::iterator¶ SwigUnsignedIntVector_insert(SwigUnsignedIntVector self, std::vector< unsigned int >::iterator pos, std::vector< unsigned int >::size_type n, std::vector< unsigned int >::value_type const & x)
-
iterator
()¶ SwigUnsignedIntVector_iterator(SwigUnsignedIntVector self) -> SwigPyIterator
-
pop
()¶ SwigUnsignedIntVector_pop(SwigUnsignedIntVector self) -> std::vector< unsigned int >::value_type
-
pop_back
()¶ SwigUnsignedIntVector_pop_back(SwigUnsignedIntVector self)
-
push_back
()¶ SwigUnsignedIntVector_push_back(SwigUnsignedIntVector self, std::vector< unsigned int >::value_type const & x)
-
rbegin
()¶ SwigUnsignedIntVector_rbegin(SwigUnsignedIntVector self) -> std::vector< unsigned int >::reverse_iterator
-
rend
()¶ SwigUnsignedIntVector_rend(SwigUnsignedIntVector self) -> std::vector< unsigned int >::reverse_iterator
-
reserve
()¶ SwigUnsignedIntVector_reserve(SwigUnsignedIntVector self, std::vector< unsigned int >::size_type n)
-
resize
(std::vector< unsigned int >::size_type new_size)¶ SwigUnsignedIntVector_resize(SwigUnsignedIntVector self, std::vector< unsigned int >::size_type new_size, std::vector< unsigned int >::value_type const & x)
-
size
()¶ SwigUnsignedIntVector_size(SwigUnsignedIntVector self) -> std::vector< unsigned int >::size_type
-
swap
()¶ SwigUnsignedIntVector_swap(SwigUnsignedIntVector self, SwigUnsignedIntVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigVectorDoubleVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(std::vector<(double)>)> class.
-
append
()¶ SwigVectorDoubleVector_append(SwigVectorDoubleVector self, SwigDoubleVector x)
-
assign
()¶ SwigVectorDoubleVector_assign(SwigVectorDoubleVector self, std::vector< std::vector< double > >::size_type n, SwigDoubleVector x)
-
back
()¶ SwigVectorDoubleVector_back(SwigVectorDoubleVector self) -> SwigDoubleVector
-
begin
()¶ SwigVectorDoubleVector_begin(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::iterator
-
capacity
()¶ SwigVectorDoubleVector_capacity(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::size_type
-
clear
()¶ SwigVectorDoubleVector_clear(SwigVectorDoubleVector self)
-
empty
()¶ SwigVectorDoubleVector_empty(SwigVectorDoubleVector self) -> bool
-
end
()¶ SwigVectorDoubleVector_end(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::iterator
-
erase
(std::vector< std::vector< double > >::iterator pos) → std::vector< std::vector< double > >::iterator¶ SwigVectorDoubleVector_erase(SwigVectorDoubleVector self, std::vector< std::vector< double > >::iterator first, std::vector< std::vector< double > >::iterator last) -> std::vector< std::vector< double > >::iterator
-
front
()¶ SwigVectorDoubleVector_front(SwigVectorDoubleVector self) -> SwigDoubleVector
-
get_allocator
()¶ SwigVectorDoubleVector_get_allocator(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::allocator_type
-
insert
(std::vector< std::vector< double > >::iterator pos, SwigDoubleVector x) → std::vector< std::vector< double > >::iterator¶ SwigVectorDoubleVector_insert(SwigVectorDoubleVector self, std::vector< std::vector< double > >::iterator pos, std::vector< std::vector< double > >::size_type n, SwigDoubleVector x)
-
iterator
()¶ SwigVectorDoubleVector_iterator(SwigVectorDoubleVector self) -> SwigPyIterator
-
pop
()¶ SwigVectorDoubleVector_pop(SwigVectorDoubleVector self) -> SwigDoubleVector
-
pop_back
()¶ SwigVectorDoubleVector_pop_back(SwigVectorDoubleVector self)
-
push_back
()¶ SwigVectorDoubleVector_push_back(SwigVectorDoubleVector self, SwigDoubleVector x)
-
rbegin
()¶ SwigVectorDoubleVector_rbegin(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::reverse_iterator
-
rend
()¶ SwigVectorDoubleVector_rend(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::reverse_iterator
-
reserve
()¶ SwigVectorDoubleVector_reserve(SwigVectorDoubleVector self, std::vector< std::vector< double > >::size_type n)
-
resize
(std::vector< std::vector< double > >::size_type new_size)¶ SwigVectorDoubleVector_resize(SwigVectorDoubleVector self, std::vector< std::vector< double > >::size_type new_size, SwigDoubleVector x)
-
size
()¶ SwigVectorDoubleVector_size(SwigVectorDoubleVector self) -> std::vector< std::vector< double > >::size_type
-
swap
()¶ SwigVectorDoubleVector_swap(SwigVectorDoubleVector self, SwigVectorDoubleVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigVectorIntVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(std::vector<(int)>)> class.
-
append
()¶ SwigVectorIntVector_append(SwigVectorIntVector self, SwigIntVector x)
-
assign
()¶ SwigVectorIntVector_assign(SwigVectorIntVector self, std::vector< std::vector< int > >::size_type n, SwigIntVector x)
-
back
()¶ SwigVectorIntVector_back(SwigVectorIntVector self) -> SwigIntVector
-
begin
()¶ SwigVectorIntVector_begin(SwigVectorIntVector self) -> std::vector< std::vector< int > >::iterator
-
capacity
()¶ SwigVectorIntVector_capacity(SwigVectorIntVector self) -> std::vector< std::vector< int > >::size_type
-
clear
()¶ SwigVectorIntVector_clear(SwigVectorIntVector self)
-
empty
()¶ SwigVectorIntVector_empty(SwigVectorIntVector self) -> bool
-
end
()¶ SwigVectorIntVector_end(SwigVectorIntVector self) -> std::vector< std::vector< int > >::iterator
-
erase
(std::vector< std::vector< int > >::iterator pos) → std::vector< std::vector< int > >::iterator¶ SwigVectorIntVector_erase(SwigVectorIntVector self, std::vector< std::vector< int > >::iterator first, std::vector< std::vector< int > >::iterator last) -> std::vector< std::vector< int > >::iterator
-
front
()¶ SwigVectorIntVector_front(SwigVectorIntVector self) -> SwigIntVector
-
get_allocator
()¶ SwigVectorIntVector_get_allocator(SwigVectorIntVector self) -> std::vector< std::vector< int > >::allocator_type
-
insert
(std::vector< std::vector< int > >::iterator pos, SwigIntVector x) → std::vector< std::vector< int > >::iterator¶ SwigVectorIntVector_insert(SwigVectorIntVector self, std::vector< std::vector< int > >::iterator pos, std::vector< std::vector< int > >::size_type n, SwigIntVector x)
-
iterator
()¶ SwigVectorIntVector_iterator(SwigVectorIntVector self) -> SwigPyIterator
-
pop
()¶ SwigVectorIntVector_pop(SwigVectorIntVector self) -> SwigIntVector
-
pop_back
()¶ SwigVectorIntVector_pop_back(SwigVectorIntVector self)
-
push_back
()¶ SwigVectorIntVector_push_back(SwigVectorIntVector self, SwigIntVector x)
-
rbegin
()¶ SwigVectorIntVector_rbegin(SwigVectorIntVector self) -> std::vector< std::vector< int > >::reverse_iterator
-
rend
()¶ SwigVectorIntVector_rend(SwigVectorIntVector self) -> std::vector< std::vector< int > >::reverse_iterator
-
reserve
()¶ SwigVectorIntVector_reserve(SwigVectorIntVector self, std::vector< std::vector< int > >::size_type n)
-
resize
(std::vector< std::vector< int > >::size_type new_size)¶ SwigVectorIntVector_resize(SwigVectorIntVector self, std::vector< std::vector< int > >::size_type new_size, SwigIntVector x)
-
size
()¶ SwigVectorIntVector_size(SwigVectorIntVector self) -> std::vector< std::vector< int > >::size_type
-
swap
()¶ SwigVectorIntVector_swap(SwigVectorIntVector self, SwigVectorIntVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigVectorPhpSitePhpSite
(*args)¶ Bases:
object
Proxy of C++ std::vector<(std::pair<(PhpSite,PhpSite)>)> class.
-
append
()¶ SwigVectorPhpSitePhpSite_append(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::value_type const & x)
-
assign
()¶ SwigVectorPhpSitePhpSite_assign(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::size_type n, std::vector< std::pair< PhpSite,PhpSite > >::value_type const & x)
-
back
()¶ SwigVectorPhpSitePhpSite_back(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::value_type const &
-
begin
()¶ SwigVectorPhpSitePhpSite_begin(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::iterator
-
capacity
()¶ SwigVectorPhpSitePhpSite_capacity(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::size_type
-
clear
()¶ SwigVectorPhpSitePhpSite_clear(SwigVectorPhpSitePhpSite self)
-
empty
()¶ SwigVectorPhpSitePhpSite_empty(SwigVectorPhpSitePhpSite self) -> bool
-
end
()¶ SwigVectorPhpSitePhpSite_end(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::iterator
-
erase
(std::vector< std::pair< PhpSite, PhpSite > >::iterator pos) → std::vector< std::pair< PhpSite,PhpSite > >::iterator¶ SwigVectorPhpSitePhpSite_erase(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::iterator first, std::vector< std::pair< PhpSite,PhpSite > >::iterator last) -> std::vector< std::pair< PhpSite,PhpSite > >::iterator
-
front
()¶ SwigVectorPhpSitePhpSite_front(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::value_type const &
-
get_allocator
()¶ SwigVectorPhpSitePhpSite_get_allocator(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::allocator_type
-
insert
(std::vector< std::pair< PhpSite, PhpSite > >::iterator pos, std::vector< std::pair< PhpSite, PhpSite > >::value_type const & x) → std::vector< std::pair< PhpSite,PhpSite > >::iterator¶ SwigVectorPhpSitePhpSite_insert(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::iterator pos, std::vector< std::pair< PhpSite,PhpSite > >::size_type n, std::vector< std::pair< PhpSite,PhpSite > >::value_type const & x)
-
iterator
()¶ SwigVectorPhpSitePhpSite_iterator(SwigVectorPhpSitePhpSite self) -> SwigPyIterator
-
pop
()¶ SwigVectorPhpSitePhpSite_pop(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::value_type
-
pop_back
()¶ SwigVectorPhpSitePhpSite_pop_back(SwigVectorPhpSitePhpSite self)
-
push_back
()¶ SwigVectorPhpSitePhpSite_push_back(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::value_type const & x)
-
rbegin
()¶ SwigVectorPhpSitePhpSite_rbegin(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::reverse_iterator
-
rend
()¶ SwigVectorPhpSitePhpSite_rend(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::reverse_iterator
-
reserve
()¶ SwigVectorPhpSitePhpSite_reserve(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::size_type n)
-
resize
(std::vector< std::pair< PhpSite, PhpSite > >::size_type new_size)¶ SwigVectorPhpSitePhpSite_resize(SwigVectorPhpSitePhpSite self, std::vector< std::pair< PhpSite,PhpSite > >::size_type new_size, std::vector< std::pair< PhpSite,PhpSite > >::value_type const & x)
-
size
()¶ SwigVectorPhpSitePhpSite_size(SwigVectorPhpSitePhpSite self) -> std::vector< std::pair< PhpSite,PhpSite > >::size_type
-
swap
()¶ SwigVectorPhpSitePhpSite_swap(SwigVectorPhpSitePhpSite self, SwigVectorPhpSitePhpSite v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigVectorSizetVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(std::vector<(size_t)>)> class.
-
append
()¶ SwigVectorSizetVector_append(SwigVectorSizetVector self, SwigSizetVector x)
-
assign
()¶ SwigVectorSizetVector_assign(SwigVectorSizetVector self, std::vector< std::vector< size_t > >::size_type n, SwigSizetVector x)
-
back
()¶ SwigVectorSizetVector_back(SwigVectorSizetVector self) -> SwigSizetVector
-
begin
()¶ SwigVectorSizetVector_begin(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::iterator
-
capacity
()¶ SwigVectorSizetVector_capacity(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::size_type
-
clear
()¶ SwigVectorSizetVector_clear(SwigVectorSizetVector self)
-
empty
()¶ SwigVectorSizetVector_empty(SwigVectorSizetVector self) -> bool
-
end
()¶ SwigVectorSizetVector_end(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::iterator
-
erase
(std::vector< std::vector< size_t > >::iterator pos) → std::vector< std::vector< size_t > >::iterator¶ SwigVectorSizetVector_erase(SwigVectorSizetVector self, std::vector< std::vector< size_t > >::iterator first, std::vector< std::vector< size_t > >::iterator last) -> std::vector< std::vector< size_t > >::iterator
-
front
()¶ SwigVectorSizetVector_front(SwigVectorSizetVector self) -> SwigSizetVector
-
get_allocator
()¶ SwigVectorSizetVector_get_allocator(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::allocator_type
-
insert
(std::vector< std::vector< size_t > >::iterator pos, SwigSizetVector x) → std::vector< std::vector< size_t > >::iterator¶ SwigVectorSizetVector_insert(SwigVectorSizetVector self, std::vector< std::vector< size_t > >::iterator pos, std::vector< std::vector< size_t > >::size_type n, SwigSizetVector x)
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iterator
()¶ SwigVectorSizetVector_iterator(SwigVectorSizetVector self) -> SwigPyIterator
-
pop
()¶ SwigVectorSizetVector_pop(SwigVectorSizetVector self) -> SwigSizetVector
-
pop_back
()¶ SwigVectorSizetVector_pop_back(SwigVectorSizetVector self)
-
push_back
()¶ SwigVectorSizetVector_push_back(SwigVectorSizetVector self, SwigSizetVector x)
-
rbegin
()¶ SwigVectorSizetVector_rbegin(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::reverse_iterator
-
rend
()¶ SwigVectorSizetVector_rend(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::reverse_iterator
-
reserve
()¶ SwigVectorSizetVector_reserve(SwigVectorSizetVector self, std::vector< std::vector< size_t > >::size_type n)
-
resize
(std::vector< std::vector< size_t > >::size_type new_size)¶ SwigVectorSizetVector_resize(SwigVectorSizetVector self, std::vector< std::vector< size_t > >::size_type new_size, SwigSizetVector x)
-
size
()¶ SwigVectorSizetVector_size(SwigVectorSizetVector self) -> std::vector< std::vector< size_t > >::size_type
-
swap
()¶ SwigVectorSizetVector_swap(SwigVectorSizetVector self, SwigVectorSizetVector v)
-
thisown
¶ The membership flag
-
-
class
schrodinger.infra.phase.
SwigVectorStringVector
(*args)¶ Bases:
object
Proxy of C++ std::vector<(std::vector<(std::string)>)> class.
-
append
()¶ SwigVectorStringVector_append(SwigVectorStringVector self, SwigStringVector x)
-
assign
()¶ SwigVectorStringVector_assign(SwigVectorStringVector self, std::vector< std::vector< std::string > >::size_type n, SwigStringVector x)
-
back
()¶ SwigVectorStringVector_back(SwigVectorStringVector self) -> SwigStringVector
-
begin
()¶ SwigVectorStringVector_begin(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::iterator
-
capacity
()¶ SwigVectorStringVector_capacity(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::size_type
-
clear
()¶ SwigVectorStringVector_clear(SwigVectorStringVector self)
-
empty
()¶ SwigVectorStringVector_empty(SwigVectorStringVector self) -> bool
-
end
()¶ SwigVectorStringVector_end(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::iterator
-
erase
(std::vector< std::vector< std::string > >::iterator pos) → std::vector< std::vector< std::string > >::iterator¶ SwigVectorStringVector_erase(SwigVectorStringVector self, std::vector< std::vector< std::string > >::iterator first, std::vector< std::vector< std::string > >::iterator last) -> std::vector< std::vector< std::string > >::iterator
-
front
()¶ SwigVectorStringVector_front(SwigVectorStringVector self) -> SwigStringVector
-
get_allocator
()¶ SwigVectorStringVector_get_allocator(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::allocator_type
-
insert
(std::vector< std::vector< std::string > >::iterator pos, SwigStringVector x) → std::vector< std::vector< std::string > >::iterator¶ SwigVectorStringVector_insert(SwigVectorStringVector self, std::vector< std::vector< std::string > >::iterator pos, std::vector< std::vector< std::string > >::size_type n, SwigStringVector x)
-
iterator
()¶ SwigVectorStringVector_iterator(SwigVectorStringVector self) -> SwigPyIterator
-
pop
()¶ SwigVectorStringVector_pop(SwigVectorStringVector self) -> SwigStringVector
-
pop_back
()¶ SwigVectorStringVector_pop_back(SwigVectorStringVector self)
-
push_back
()¶ SwigVectorStringVector_push_back(SwigVectorStringVector self, SwigStringVector x)
-
rbegin
()¶ SwigVectorStringVector_rbegin(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::reverse_iterator
-
rend
()¶ SwigVectorStringVector_rend(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::reverse_iterator
-
reserve
()¶ SwigVectorStringVector_reserve(SwigVectorStringVector self, std::vector< std::vector< std::string > >::size_type n)
-
resize
(std::vector< std::vector< std::string > >::size_type new_size)¶ SwigVectorStringVector_resize(SwigVectorStringVector self, std::vector< std::vector< std::string > >::size_type new_size, SwigStringVector x)
-
size
()¶ SwigVectorStringVector_size(SwigVectorStringVector self) -> std::vector< std::vector< std::string > >::size_type
-
swap
()¶ SwigVectorStringVector_swap(SwigVectorStringVector self, SwigVectorStringVector v)
-
thisown
¶ The membership flag
-
-
schrodinger.infra.phase.
addStaticDummyAtom
(MM_Index staticFrag, std::string const & fragType, SwigDoubleVector xyz, int bondedTo=0)¶
-
schrodinger.infra.phase.
checkStaticFrag
(std::string const & fragType, size_t npoints, std::string mesg)¶
-
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) → SwigSizetVector¶
-
schrodinger.infra.phase.
coordsMatch
(MM_Index ct, int atom, SwigDoubleVector 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, SwigVectorDoubleVector xyz) → PhpSite¶ createStaticSite(PhpSite site) -> PhpSite
-
schrodinger.infra.phase.
deleteAllAtoms
(MM_Index ct)¶
-
schrodinger.infra.phase.
deleteCtVector
(SwigIntVector cts)¶
-
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.
getCtTitle
(MM_Index ctHandle) → std::string¶
-
schrodinger.infra.phase.
getDefaultFdFileBaseName
() → std::string¶
-
schrodinger.infra.phase.
getDefaultFdFilePath
() → std::string¶
-
schrodinger.infra.phase.
getFragAtomID
(std::string const & fragType, size_t atomIndex) → std::string¶
-
schrodinger.infra.phase.
getFragAtoms
(MM_Index ct, PhpSite site, double tol) → SwigIntVector¶
-
schrodinger.infra.phase.
getListOfBondedAtoms
(MM_Index ct, size_t atom) → SwigSizetVector¶
-
schrodinger.infra.phase.
getLongLine
(std::istream & istr, std::string & s) → std::istream &¶
-
schrodinger.infra.phase.
getNonQCount
(std::vector< PhpBaseFeature, std::allocator< PhpBaseFeature > > const & features) → int¶
-
schrodinger.infra.phase.
getPhpFunction
(std::string const & boostFunction) → std::string¶
-
schrodinger.infra.phase.
getTopoDistanceMatrix
(MM_Index ctHandle) → SwigVectorIntVector¶ getTopoDistanceMatrix(MM_Index ctHandle, SwigVectorIntVector brokenBonds) -> SwigVectorIntVector
-
schrodinger.infra.phase.
initMMlibs
()¶
-
schrodinger.infra.phase.
isInVector
(SwigIntVector values, int value) → bool¶
-
schrodinger.infra.phase.
isNanValue
(double const & value) → bool¶
-
schrodinger.infra.phase.
printVectorValues
(SwigIntVector values, std::string sep, std::string lastSep) → std::string¶
-
schrodinger.infra.phase.
tokenizeDelimitedString
(std::string const & s, char sep, bool trim=False) → SwigStringVector¶