Package schrodinger :: Package infra :: Module phase :: Class PhpProject

Class PhpProject

object --+
         |
        PhpProject

Proxy of C++ PhpProject class

Instance Methods

[hide private]

__repr__(self)
repr(x)

__init__(self)
__init__(PhpProject self) -> PhpProject

__swig_destroy__(...)
delete_PhpProject(PhpProject self)

addLigands(...)
PhpProject_addLigands(PhpProject self, std::string const & projectName, std::string const & inFile, bool connect, ...

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, ...

assignActives(...)
PhpProject_assignActives(PhpProject self, double minAct)

assignDefaultGroups(...)
PhpProject_assignDefaultGroups(PhpProject self)

assignGroups(...)
PhpProject_assignGroups(PhpProject self, SwigStringVector titles) -> std::vector< std::vector< int,std::allocator< int > >,std::allocator< std::vector< int,std::allocator< int > > > >

assignInactives(...)
PhpProject_assignInactives(PhpProject self, double maxAct)

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

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

buildQsarModel(...)
PhpProject_buildQsarModel(PhpProject self, std::string const & inFile, std::string const & actProp, std::string const & qsarSetProp, ...

closeProject(...)
PhpProject_closeProject(PhpProject self)

combineFragmentCts(...)
PhpProject_combineFragmentCts(PhpProject self, SwigIntVector fragments) -> MM_Index

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

commitMasterData(...)
PhpProject_commitMasterData(PhpProject self, bool writeFirst=False)

copyFile(...)
PhpProject_copyFile(PhpProject self, std::string const & baseName, std::string const & fromDir, std::string const & toDir, ...

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

getConformerCount(...)
PhpProject_getConformerCount(PhpProject self, int ligandID) -> int

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

getConformers(...)
PhpProject_getConformers(PhpProject self, int ligandID) -> SwigIntVector

getDbID(...)
PhpProject_getDbID(PhpProject self, int ligandID) -> int

getDefaultFdFile(...)
PhpProject_getDefaultFdFile(PhpProject self) -> std::string

getDefaultFeatureFreq(...)
PhpProject_getDefaultFeatureFreq(PhpProject self) -> PhpFeatureData

getDefaultFeatureRadii(...)
PhpProject_getDefaultFeatureRadii(PhpProject self) -> PhpFeatureData

getDefaultFeatureTol(...)
PhpProject_getDefaultFeatureTol(PhpProject self) -> PhpFeatureData

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

getFdFile(...)
PhpProject_getFdFile(PhpProject self) -> std::string

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

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

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

int

getGroupCount()
PhpProject_getGroupCount(PhpProject self, SwigIntVector ligandIDs) -> int

getHypoAlignments(...)
PhpProject_getHypoAlignments(PhpProject self, std::string const & hypoID, bool wantMisses=False) -> SwigIntVector

getHypoIDs(...)
PhpProject_getHypoIDs(PhpProject self, bool fullPath=False) -> SwigStringVector

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

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

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

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, ...

getMatchedSitesStrings(...)
PhpProject_getMatchedSitesStrings(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, ...

getMolSites(...)
PhpProject_getMolSites(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, ...

getMolSitesStrings(...)
PhpProject_getMolSitesStrings(PhpProject self, MM_Index ctHandle, std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > > const & fd, ...

getMustMatch(...)
PhpProject_getMustMatch(PhpProject self, int ligandID) -> bool

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

getQsarHypoIDs(...)
PhpProject_getQsarHypoIDs(PhpProject self, bool fullPath=False) -> SwigStringVector

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

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 const & qsar, std::string const & qsarClass) -> std::string

getQsarModelClasses(...)
PhpProject_getQsarModelClasses(PhpProject self, PhpQSAR const & qsar) -> SwigStringVector

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

getQsarModelCoeff(...)
getQsarModelCoeff(PhpQSAR const & qsar, int numFactors, bool combineClasses=False) -> SwigDoubleVector...

getQsarModelCoeffRange(...)
getQsarModelCoeffRange(PhpQSAR const & qsar, int numFactors, bool combineClasses=False) -> SwigDoubleVector...

getQsarModelFactorCount(...)
PhpProject_getQsarModelFactorCount(PhpProject self, PhpQSAR const & qsar) -> int

getQsarModelGridLimits(...)
PhpProject_getQsarModelGridLimits(PhpProject self, PhpQSAR const & qsar) -> SwigDoubleVector

getQsarModelGridSpacing(...)
PhpProject_getQsarModelGridSpacing(PhpProject self, PhpQSAR const & qsar) -> double

getQsarModelRegF(...)
PhpProject_getQsarModelRegF(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelRegP(...)
PhpProject_getQsarModelRegP(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelRegRsqr(...)
PhpProject_getQsarModelRegRsqr(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelRegRsqrCv(...)
PhpProject_getQsarModelRegRsqrCv(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelRegRsqrScramble(...)
PhpProject_getQsarModelRegRsqrScramble(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelRegSD(...)
PhpProject_getQsarModelRegSD(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelRegStability(...)
PhpProject_getQsarModelRegStability(PhpProject self, PhpQSAR const & qsar, int numFactors) -> double

getQsarModelStyle(...)
PhpProject_getQsarModelStyle(PhpProject self, PhpQSAR const & qsar) -> std::string

getQsarModelVolBitCount(...)
getQsarModelVolBitCount(PhpQSAR const & qsar) -> int getQsarModelVolBitCount(PhpQSAR const & qsar, std::string const & qsarClass) -> int PhpProject_getQsarModelVolBitCount(PhpProject self, PhpQSAR const & qsar, SwigStringVector qsarClasses) -> int

getQsarModelVolClasses(...)
PhpProject_getQsarModelVolClasses(PhpProject self, PhpQSAR const & qsar) -> SwigStringVector

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

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

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

getSiteFragment(...)
PhpProject_getSiteFragment(PhpProject self, std::string const & siteType, SwigDoubleVector xyz1, SwigDoubleVector xyz2) -> MM_Index

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

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

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

getSlash(...)
PhpProject_getSlash(PhpProject self) -> std::string

getStep(...)
PhpProject_getStep(PhpProject self) -> std::string

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

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

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

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

logActivity(...)
PhpProject_logActivity(PhpProject self)

needSyncFeatureDef(...)
PhpProject_needSyncFeatureDef(PhpProject self) -> bool

newProject(...)
PhpProject_newProject(PhpProject self, std::string const & projectName, std::string const & inFile, std::string const & fdFile, ...

openProject(...)
PhpProject_openProject(PhpProject self, std::string const & projectName)

restoreMasterData(...)
PhpProject_restoreMasterData(PhpProject self)

reviseDatabase(...)
PhpProject_reviseDatabase(PhpProject self, std::string const & jobName, std::string const & reviseOptions, ...

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

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

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 const & qsar, std::string const & inFile, std::string const & actProp, ...

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

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

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, ...

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

thisown
The membership flag

Inherited from object: __class__

Method Details

[hide private]

repr(self)
(Representation operator)

repr(x)

Overrides: object.__repr__: (inherited documentation)

init(self)
(Constructor)

__init__(PhpProject self) -> PhpProject

Overrides: object.__init__

addLigands(...)


PhpProject_addLigands(PhpProject self, 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)

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, bool useSiteMask=True) -> SwigIntVector

buildQsarModel(...)


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

copyFile(...)


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

getMatchedSites(...)


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

getMatchedSitesStrings(...)


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

getMolSites(...)


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

getMolSitesStrings(...)


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

getQsarModelCoeff(...)


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

getQsarModelCoeffRange(...)


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

newProject(...)


PhpProject_newProject(PhpProject self, 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)

reviseDatabase(...)


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

testQsarModel(...)


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

writeHypoFiles(...)


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

zipProject(...)


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

Property Details

[hide private]

thisown

The membership flag

Get Method:: unreachable(x)
Set Method:: unreachable(x, v)

Class PhpProject

__repr__(self) (Representation operator)

__init__(self) (Constructor)

addLigands(...)

alignLigands(...)

buildQsarModel(...)

copyFile(...)

getMatchedSites(...)

getMatchedSitesStrings(...)

getMolSites(...)

getMolSitesStrings(...)

getQsarModelCoeff(...)

getQsarModelCoeffRange(...)

newProject(...)

reviseDatabase(...)

testQsarModel(...)

writeHypoFiles(...)

zipProject(...)

thisown

repr(self)
(Representation operator)

init(self)
(Constructor)