schrodinger.application.phase.hypothesis module

Module for reading and writing Phase hypotheses.

class schrodinger.application.phase.hypothesis.PhaseHypothesis(*args)

Bases: phase.PhpHypoAdaptor

__init__(*args)

Initializes a Phase hypothesis from phase.PhpHypoAdaptor

title

Returns the hypothesis ID as the title

Returns:hypothesis ID title
Return type:str
property

Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct. When adding a value into the property dictionary, the phase.PhpHypoAdaptor addProp interface is used.

getSiteNumber(site)

Determines site number for the given feature site by comparing its name with names of all the current ‘reference’ sites.

Parameters:site (phase.PhpSite) – feature site object
Returns:site number of the current feature in the hypothesis
Return type:int or None
addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters:equiv_pairs (list) – list of equivalency feauture types
write(filename)

Writes the hypothesis to disk in the single file *.phypo format

Parameters:filename – hypothesis filename to write to
Type:str
visibleXvol()

Returns if the excluded volume visibility property is enabled.

visibleRefCt()

Returns if the reference ligand visibility property is enabled.

visibleTol()

Returns if the tolerances visibility property is enabled.

visiblePropLabels()

Returns if the property labels should be shown.

manageXvolIsOpen()

Returns True if manage excluded volumes panel for this hypothesis is open.

acquire()

acquires ownership of the pointer

addAttr(std::string const & fileName, bool hydrogens=False)

addAttr(std::string const & fileName)

addCnst(PhpSiteConstrainer cnst)
addCt(MM_Index ctHandle, std::string const & role)
addIvol(PhpExclVol ivol)
addMask(PhpSiteMask mask)
addProp(std::string const & propName, std::string const & propValue)

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

addQsar(PhpQSAR qsar)
addRad(PhpFeatureData rad)
addRules(PhpFeatureRules rules)
addSite(PhpSite site)
addTol(PhpDeltaHypo tol)
addTolByType(PhpFeatureData tol)
addXvol(PhpExclVol xvol, bool hydrogens=False)

addXvol(PhpExclVol xvol)

append()

appends another ‘this’ object

buildAllAttr(bool alwaysBuild=False)

buildAllAttr()

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

convertToStatic()

deleteAttr(std::string const & attr_name)
deleteProp(std::string const & propName)
deleteSite(size_t siteIndex)
deleteSiteFast(size_t siteIndex)
disown()

releases ownership of the pointer

getAddCtCount() → int
getAddCts() → std::vector< MM_Index,std::allocator< MM_Index > >
getCnst() → PhpSiteConstrainer
getFd() → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
getHypoCt() → MM_Index
getHypoID() → std::string
getHypoSites(bool wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getHypoSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getIvol() → PhpExclVol
getMask() → PhpSiteMask
getProp(std::string const & propName) → std::string
getQsar() → PhpQSAR
getRad() → PhpFeatureData
getRefCt() → MM_Index
getRefSites(bool wantProj=False, bool append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRefSites(bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > > getRefSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getRules() → PhpFeatureRules
getSite(size_t siteIndex) → PhpSite
getSiteByDisplayName(std::string const & displayName) → PhpSite
getSiteCount() → int
getSiteIndexFromDisplayName(std::string const & displayName) → size_t
getSiteTypes() → std::string
getSummary(bool extended=False, std::string header) → std::string

getSummary(bool extended=False) -> std::string getSummary() -> std::string

getTol() → PhpDeltaHypo
getXvol() → PhpExclVol
hasAddCts() → bool
hasCnst() → bool
hasIvol() → bool
hasMask() → bool
hasProp(std::string const & propName) → bool
hasQsar() → bool
hasRad() → bool
hasRefCt() → bool
hasRules() → bool
hasTol() → bool
hasXvol() → bool
isStatic() → bool
merge(PhpHypoAdaptor rhs, double tol)

merge(PhpHypoAdaptor rhs)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

save(std::string const & hypoID, bool overwrite)
setHypoID(std::string const & hypoID)
setRefCtTitle(std::string const & title)
this
thisown
transform(std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & rotation, std::vector< double, std::allocator< double > > const & translation)
updateSite(size_t siteIndex, PhpSite site)
writeSummary(std::ostream & os, bool extended=False, std::string header)

writeSummary(std::ostream & os, bool extended=False) writeSummary(std::ostream & os)

class schrodinger.application.phase.hypothesis.PhaseHypothesisStandard(hypo_ID, standard_sites, reference_ligand, feature_defintions=None)

Bases: schrodinger.application.phase.hypothesis.PhaseHypothesis

Phase hypothesis created from standard sites found in the given reference ligand. Phase default feature defintions are used if not supplied.

__init__(hypo_ID, standard_sites, reference_ligand, feature_defintions=None)
Parameters:
  • hypo_ID (str) – hypothesis ID
  • standard_sites (list of phase.PhpSite) – sites found in the reference structure
  • reference_ligand (structure.Structure) – hypothesis reference ligand
  • feature_defintions (list of phase.PhpFeatureDefinition) – feature definitions used in the hypothesis
acquire()

acquires ownership of the pointer

addAttr(std::string const & fileName, bool hydrogens=False)

addAttr(std::string const & fileName)

addCnst(PhpSiteConstrainer cnst)
addCt(MM_Index ctHandle, std::string const & role)
addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters:equiv_pairs (list) – list of equivalency feauture types
addIvol(PhpExclVol ivol)
addMask(PhpSiteMask mask)
addProp(std::string const & propName, std::string const & propValue)

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

addQsar(PhpQSAR qsar)
addRad(PhpFeatureData rad)
addRules(PhpFeatureRules rules)
addSite(PhpSite site)
addTol(PhpDeltaHypo tol)
addTolByType(PhpFeatureData tol)
addXvol(PhpExclVol xvol, bool hydrogens=False)

addXvol(PhpExclVol xvol)

append()

appends another ‘this’ object

buildAllAttr(bool alwaysBuild=False)

buildAllAttr()

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

convertToStatic()

deleteAttr(std::string const & attr_name)
deleteProp(std::string const & propName)
deleteSite(size_t siteIndex)
deleteSiteFast(size_t siteIndex)
disown()

releases ownership of the pointer

getAddCtCount() → int
getAddCts() → std::vector< MM_Index,std::allocator< MM_Index > >
getCnst() → PhpSiteConstrainer
getFd() → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
getHypoCt() → MM_Index
getHypoID() → std::string
getHypoSites(bool wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getHypoSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getIvol() → PhpExclVol
getMask() → PhpSiteMask
getProp(std::string const & propName) → std::string
getQsar() → PhpQSAR
getRad() → PhpFeatureData
getRefCt() → MM_Index
getRefSites(bool wantProj=False, bool append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRefSites(bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > > getRefSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getRules() → PhpFeatureRules
getSite(size_t siteIndex) → PhpSite
getSiteByDisplayName(std::string const & displayName) → PhpSite
getSiteCount() → int
getSiteIndexFromDisplayName(std::string const & displayName) → size_t
getSiteNumber(site)

Determines site number for the given feature site by comparing its name with names of all the current ‘reference’ sites.

Parameters:site (phase.PhpSite) – feature site object
Returns:site number of the current feature in the hypothesis
Return type:int or None
getSiteTypes() → std::string
getSummary(bool extended=False, std::string header) → std::string

getSummary(bool extended=False) -> std::string getSummary() -> std::string

getTol() → PhpDeltaHypo
getXvol() → PhpExclVol
hasAddCts() → bool
hasCnst() → bool
hasIvol() → bool
hasMask() → bool
hasProp(std::string const & propName) → bool
hasQsar() → bool
hasRad() → bool
hasRefCt() → bool
hasRules() → bool
hasTol() → bool
hasXvol() → bool
isStatic() → bool
manageXvolIsOpen()

Returns True if manage excluded volumes panel for this hypothesis is open.

merge(PhpHypoAdaptor rhs, double tol)

merge(PhpHypoAdaptor rhs)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property

Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct. When adding a value into the property dictionary, the phase.PhpHypoAdaptor addProp interface is used.

save(std::string const & hypoID, bool overwrite)
setHypoID(std::string const & hypoID)
setRefCtTitle(std::string const & title)
this
thisown
title

Returns the hypothesis ID as the title

Returns:hypothesis ID title
Return type:str
transform(std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & rotation, std::vector< double, std::allocator< double > > const & translation)
updateSite(size_t siteIndex, PhpSite site)
visiblePropLabels()

Returns if the property labels should be shown.

visibleRefCt()

Returns if the reference ligand visibility property is enabled.

visibleTol()

Returns if the tolerances visibility property is enabled.

visibleXvol()

Returns if the excluded volume visibility property is enabled.

write(filename)

Writes the hypothesis to disk in the single file *.phypo format

Parameters:filename – hypothesis filename to write to
Type:str
writeSummary(std::ostream & os, bool extended=False, std::string header)

writeSummary(std::ostream & os, bool extended=False) writeSummary(std::ostream & os)

class schrodinger.application.phase.hypothesis.PhaseHypothesisStatic(hypo_ID, static_sites, feature_defintions=None)

Bases: schrodinger.application.phase.hypothesis.PhaseHypothesis

Phase hypothesis created from sites which will all be converted into static fragment sites. Phase default feature defintions are used if not supplied.

__init__(hypo_ID, static_sites, feature_defintions=None)
Parameters:
  • hypo_ID (str) – hypothesis ID
  • static_sites (list of phase.PhpSite) – sites which will be converted to static fragments
  • feature_defintions (list of phase.PhpFeatureDefinition) – feature definitions used in the hypothesis
acquire()

acquires ownership of the pointer

addAttr(std::string const & fileName, bool hydrogens=False)

addAttr(std::string const & fileName)

addCnst(PhpSiteConstrainer cnst)
addCt(MM_Index ctHandle, std::string const & role)
addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters:equiv_pairs (list) – list of equivalency feauture types
addIvol(PhpExclVol ivol)
addMask(PhpSiteMask mask)
addProp(std::string const & propName, std::string const & propValue)

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

addQsar(PhpQSAR qsar)
addRad(PhpFeatureData rad)
addRules(PhpFeatureRules rules)
addSite(PhpSite site)
addTol(PhpDeltaHypo tol)
addTolByType(PhpFeatureData tol)
addXvol(PhpExclVol xvol, bool hydrogens=False)

addXvol(PhpExclVol xvol)

append()

appends another ‘this’ object

buildAllAttr(bool alwaysBuild=False)

buildAllAttr()

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

convertToStatic()

deleteAttr(std::string const & attr_name)
deleteProp(std::string const & propName)
deleteSite(size_t siteIndex)
deleteSiteFast(size_t siteIndex)
disown()

releases ownership of the pointer

getAddCtCount() → int
getAddCts() → std::vector< MM_Index,std::allocator< MM_Index > >
getCnst() → PhpSiteConstrainer
getFd() → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
getHypoCt() → MM_Index
getHypoID() → std::string
getHypoSites(bool wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getHypoSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getIvol() → PhpExclVol
getMask() → PhpSiteMask
getProp(std::string const & propName) → std::string
getQsar() → PhpQSAR
getRad() → PhpFeatureData
getRefCt() → MM_Index
getRefSites(bool wantProj=False, bool append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRefSites(bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > > getRefSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getRules() → PhpFeatureRules
getSite(size_t siteIndex) → PhpSite
getSiteByDisplayName(std::string const & displayName) → PhpSite
getSiteCount() → int
getSiteIndexFromDisplayName(std::string const & displayName) → size_t
getSiteNumber(site)

Determines site number for the given feature site by comparing its name with names of all the current ‘reference’ sites.

Parameters:site (phase.PhpSite) – feature site object
Returns:site number of the current feature in the hypothesis
Return type:int or None
getSiteTypes() → std::string
getSummary(bool extended=False, std::string header) → std::string

getSummary(bool extended=False) -> std::string getSummary() -> std::string

getTol() → PhpDeltaHypo
getXvol() → PhpExclVol
hasAddCts() → bool
hasCnst() → bool
hasIvol() → bool
hasMask() → bool
hasProp(std::string const & propName) → bool
hasQsar() → bool
hasRad() → bool
hasRefCt() → bool
hasRules() → bool
hasTol() → bool
hasXvol() → bool
isStatic() → bool
manageXvolIsOpen()

Returns True if manage excluded volumes panel for this hypothesis is open.

merge(PhpHypoAdaptor rhs, double tol)

merge(PhpHypoAdaptor rhs)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property

Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct. When adding a value into the property dictionary, the phase.PhpHypoAdaptor addProp interface is used.

save(std::string const & hypoID, bool overwrite)
setHypoID(std::string const & hypoID)
setRefCtTitle(std::string const & title)
this
thisown
title

Returns the hypothesis ID as the title

Returns:hypothesis ID title
Return type:str
transform(std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & rotation, std::vector< double, std::allocator< double > > const & translation)
updateSite(size_t siteIndex, PhpSite site)
visiblePropLabels()

Returns if the property labels should be shown.

visibleRefCt()

Returns if the reference ligand visibility property is enabled.

visibleTol()

Returns if the tolerances visibility property is enabled.

visibleXvol()

Returns if the excluded volume visibility property is enabled.

write(filename)

Writes the hypothesis to disk in the single file *.phypo format

Parameters:filename – hypothesis filename to write to
Type:str
writeSummary(std::ostream & os, bool extended=False, std::string header)

writeSummary(std::ostream & os, bool extended=False) writeSummary(std::ostream & os)

class schrodinger.application.phase.hypothesis.PhaseHypothesisHybrid(hypo_ID, static_sites, standard_sites, reference_ligand, feature_defintions=None)

Bases: schrodinger.application.phase.hypothesis.PhaseHypothesis

Phase hypothesis created from both sites which will all be converted into static fragment sites, as well as standard sites found in the given reference ligand. Phase default feature defintions are used if not supplied.

__init__(hypo_ID, static_sites, standard_sites, reference_ligand, feature_defintions=None)
Parameters:
  • hypo_ID (str) – hypothesis ID
  • static_sites (list of phase.PhpSite) – sites which will be converted to static fragments
  • standard_sites (list of phase.PhpSite) – sites found in the reference structure
  • reference_ligand (structure.Structure or int) – hypothesis reference ligand which can be either structure (preferred) or structure handle
  • feature_defintions (list of phase.PhpFeatureDefinition) – feature definitions used in the hypothesis
acquire()

acquires ownership of the pointer

addAttr(std::string const & fileName, bool hydrogens=False)

addAttr(std::string const & fileName)

addCnst(PhpSiteConstrainer cnst)
addCt(MM_Index ctHandle, std::string const & role)
addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters:equiv_pairs (list) – list of equivalency feauture types
addIvol(PhpExclVol ivol)
addMask(PhpSiteMask mask)
addProp(std::string const & propName, std::string const & propValue)

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

addQsar(PhpQSAR qsar)
addRad(PhpFeatureData rad)
addRules(PhpFeatureRules rules)
addSite(PhpSite site)
addTol(PhpDeltaHypo tol)
addTolByType(PhpFeatureData tol)
addXvol(PhpExclVol xvol, bool hydrogens=False)

addXvol(PhpExclVol xvol)

append()

appends another ‘this’ object

buildAllAttr(bool alwaysBuild=False)

buildAllAttr()

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

convertToStatic()

deleteAttr(std::string const & attr_name)
deleteProp(std::string const & propName)
deleteSite(size_t siteIndex)
deleteSiteFast(size_t siteIndex)
disown()

releases ownership of the pointer

getAddCtCount() → int
getAddCts() → std::vector< MM_Index,std::allocator< MM_Index > >
getCnst() → PhpSiteConstrainer
getFd() → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
getHypoCt() → MM_Index
getHypoID() → std::string
getHypoSites(bool wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getHypoSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getIvol() → PhpExclVol
getMask() → PhpSiteMask
getProp(std::string const & propName) → std::string
getQsar() → PhpQSAR
getRad() → PhpFeatureData
getRefCt() → MM_Index
getRefSites(bool wantProj=False, bool append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRefSites(bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > > getRefSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getRules() → PhpFeatureRules
getSite(size_t siteIndex) → PhpSite
getSiteByDisplayName(std::string const & displayName) → PhpSite
getSiteCount() → int
getSiteIndexFromDisplayName(std::string const & displayName) → size_t
getSiteNumber(site)

Determines site number for the given feature site by comparing its name with names of all the current ‘reference’ sites.

Parameters:site (phase.PhpSite) – feature site object
Returns:site number of the current feature in the hypothesis
Return type:int or None
getSiteTypes() → std::string
getSummary(bool extended=False, std::string header) → std::string

getSummary(bool extended=False) -> std::string getSummary() -> std::string

getTol() → PhpDeltaHypo
getXvol() → PhpExclVol
hasAddCts() → bool
hasCnst() → bool
hasIvol() → bool
hasMask() → bool
hasProp(std::string const & propName) → bool
hasQsar() → bool
hasRad() → bool
hasRefCt() → bool
hasRules() → bool
hasTol() → bool
hasXvol() → bool
isStatic() → bool
manageXvolIsOpen()

Returns True if manage excluded volumes panel for this hypothesis is open.

merge(PhpHypoAdaptor rhs, double tol)

merge(PhpHypoAdaptor rhs)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property

Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct. When adding a value into the property dictionary, the phase.PhpHypoAdaptor addProp interface is used.

save(std::string const & hypoID, bool overwrite)
setHypoID(std::string const & hypoID)
setRefCtTitle(std::string const & title)
this
thisown
title

Returns the hypothesis ID as the title

Returns:hypothesis ID title
Return type:str
transform(std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & rotation, std::vector< double, std::allocator< double > > const & translation)
updateSite(size_t siteIndex, PhpSite site)
visiblePropLabels()

Returns if the property labels should be shown.

visibleRefCt()

Returns if the reference ligand visibility property is enabled.

visibleTol()

Returns if the tolerances visibility property is enabled.

visibleXvol()

Returns if the excluded volume visibility property is enabled.

write(filename)

Writes the hypothesis to disk in the single file *.phypo format

Parameters:filename – hypothesis filename to write to
Type:str
writeSummary(std::ostream & os, bool extended=False, std::string header)

writeSummary(std::ostream & os, bool extended=False) writeSummary(std::ostream & os)

class schrodinger.application.phase.hypothesis.PhaseHypothesisFromLigand(ligand, feature_definitions=None)

Bases: schrodinger.application.phase.hypothesis.PhaseHypothesis

Phase hypothesis created from all mappable features in the given ligand. Phase default feature defintions are used if not supplied.

__init__(ligand, feature_definitions=None)
Parameters:
  • ligand (structure.Structure) – reference ligand, from which to extract all features
  • feature_definitions (list of phase.PhpFeatureDefinition) – feature definitions used in the hypothesis
acquire()

acquires ownership of the pointer

addAttr(std::string const & fileName, bool hydrogens=False)

addAttr(std::string const & fileName)

addCnst(PhpSiteConstrainer cnst)
addCt(MM_Index ctHandle, std::string const & role)
addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters:equiv_pairs (list) – list of equivalency feauture types
addIvol(PhpExclVol ivol)
addMask(PhpSiteMask mask)
addProp(std::string const & propName, std::string const & propValue)

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

addQsar(PhpQSAR qsar)
addRad(PhpFeatureData rad)
addRules(PhpFeatureRules rules)
addSite(PhpSite site)
addTol(PhpDeltaHypo tol)
addTolByType(PhpFeatureData tol)
addXvol(PhpExclVol xvol, bool hydrogens=False)

addXvol(PhpExclVol xvol)

append()

appends another ‘this’ object

buildAllAttr(bool alwaysBuild=False)

buildAllAttr()

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

convertToStatic()

deleteAttr(std::string const & attr_name)
deleteProp(std::string const & propName)
deleteSite(size_t siteIndex)
deleteSiteFast(size_t siteIndex)
disown()

releases ownership of the pointer

getAddCtCount() → int
getAddCts() → std::vector< MM_Index,std::allocator< MM_Index > >
getCnst() → PhpSiteConstrainer
getFd() → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >
getHypoCt() → MM_Index
getHypoID() → std::string
getHypoSites(bool wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getHypoSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getIvol() → PhpExclVol
getMask() → PhpSiteMask
getProp(std::string const & propName) → std::string
getQsar() → PhpQSAR
getRad() → PhpFeatureData
getRefCt() → MM_Index
getRefSites(bool wantProj=False, bool append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRefSites(bool wantProj=False) -> std::vector< PhpSite,std::allocator< PhpSite > > getRefSites() -> std::vector< PhpSite,std::allocator< PhpSite > >

getRules() → PhpFeatureRules
getSite(size_t siteIndex) → PhpSite
getSiteByDisplayName(std::string const & displayName) → PhpSite
getSiteCount() → int
getSiteIndexFromDisplayName(std::string const & displayName) → size_t
getSiteNumber(site)

Determines site number for the given feature site by comparing its name with names of all the current ‘reference’ sites.

Parameters:site (phase.PhpSite) – feature site object
Returns:site number of the current feature in the hypothesis
Return type:int or None
getSiteTypes() → std::string
getSummary(bool extended=False, std::string header) → std::string

getSummary(bool extended=False) -> std::string getSummary() -> std::string

getTol() → PhpDeltaHypo
getXvol() → PhpExclVol
hasAddCts() → bool
hasCnst() → bool
hasIvol() → bool
hasMask() → bool
hasProp(std::string const & propName) → bool
hasQsar() → bool
hasRad() → bool
hasRefCt() → bool
hasRules() → bool
hasTol() → bool
hasXvol() → bool
isStatic() → bool
manageXvolIsOpen()

Returns True if manage excluded volumes panel for this hypothesis is open.

merge(PhpHypoAdaptor rhs, double tol)

merge(PhpHypoAdaptor rhs)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property

Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct. When adding a value into the property dictionary, the phase.PhpHypoAdaptor addProp interface is used.

save(std::string const & hypoID, bool overwrite)
setHypoID(std::string const & hypoID)
setRefCtTitle(std::string const & title)
this
thisown
title

Returns the hypothesis ID as the title

Returns:hypothesis ID title
Return type:str
transform(std::vector< std::vector< double, std::allocator< double > >, std::allocator< std::vector< double, std::allocator< double > > > > const & rotation, std::vector< double, std::allocator< double > > const & translation)
updateSite(size_t siteIndex, PhpSite site)
visiblePropLabels()

Returns if the property labels should be shown.

visibleRefCt()

Returns if the reference ligand visibility property is enabled.

visibleTol()

Returns if the tolerances visibility property is enabled.

visibleXvol()

Returns if the excluded volume visibility property is enabled.

write(filename)

Writes the hypothesis to disk in the single file *.phypo format

Parameters:filename – hypothesis filename to write to
Type:str
writeSummary(std::ostream & os, bool extended=False, std::string header)

writeSummary(std::ostream & os, bool extended=False) writeSummary(std::ostream & os)

schrodinger.application.phase.hypothesis.sorted_hypo_structures(hypothesis_sts)

Sorts a list of structures for PhaseHypothesis - Phase hypothesis CT - Phase hypothesis reference ligand - Any additional Phase hypothesis ligands

Parameters:hypothesis_sts (list of Structure) – list of structures
Returns:hypothesis, reference ligand, additional hypothesis ligands
Return type:Structure, Structure, list of Structure
schrodinger.application.phase.hypothesis.extract_hypotheses(filename)

Extracts all hypotheses from Phase hypothesis file containing multiple hypotheses

Parameters:filename (str) – *_phypo.mae.gz file containing Phase hypotheses
Returns:list of Phase hypotheses
Return type:list of PhaseHypothesis
schrodinger.application.phase.hypothesis.write_hypotheses(hypotheses, filename, group=None)

Writes set of PhaseHypothesis objects to *_phypo.maegz file.

Parameters:
  • hypotheses (list of PhaseHypothesis) – list of Phase hypotheses
  • filename (str) – *_phypo.mae.gz file containing Phase hypotheses
  • group (str) – name to group all hypotheses under