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, thephase.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 objectReturns: 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.
-
__class__
¶ alias of
builtins.SwigPyObjectType
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.phase.hypothesis', '__init__': <function PhaseHypothesis.__init__>, 'title': <property object>, 'property': <property object>, 'getSiteNumber': <function PhaseHypothesis.getSiteNumber>, 'addFeatureTypeEquivalencies': <function PhaseHypothesis.addFeatureTypeEquivalencies>, 'write': <function PhaseHypothesis.write>, 'visibleXvol': <function PhaseHypothesis.visibleXvol>, 'visibleRefCt': <function PhaseHypothesis.visibleRefCt>, 'visibleTol': <function PhaseHypothesis.visibleTol>, 'visiblePropLabels': <function PhaseHypothesis.visiblePropLabels>, 'manageXvolIsOpen': <function PhaseHypothesis.manageXvolIsOpen>, '__weakref__': <attribute '__weakref__' of 'PhaseHypothesis' objects>, '__doc__': None})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__int__
¶ int(self)
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.phase.hypothesis'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
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
-
__class__
¶ alias of
builtins.SwigPyObjectType
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.phase.hypothesis', '__doc__': '\n Phase hypothesis created from standard sites found in the given reference\n ligand. Phase default feature defintions are used if not supplied.\n ', '__init__': <function PhaseHypothesisStandard.__init__>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__int__
¶ int(self)
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.phase.hypothesis'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
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 objectReturns: 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, thephase.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
-
__class__
¶ alias of
builtins.SwigPyObjectType
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.phase.hypothesis', '__doc__': '\n Phase hypothesis created from sites which will all be converted into static\n fragment sites. Phase default feature defintions are used if not supplied.\n ', '__init__': <function PhaseHypothesisStatic.__init__>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__int__
¶ int(self)
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.phase.hypothesis'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
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 objectReturns: 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, thephase.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) – hypothesis reference ligand
- feature_defintions (list of
phase.PhpFeatureDefinition
) – feature definitions used in the hypothesis
-
__class__
¶ alias of
builtins.SwigPyObjectType
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.phase.hypothesis', '__doc__': '\n Phase hypothesis created from both sites which will all be converted into\n static fragment sites, as well as standard sites found in the given\n reference ligand. Phase default feature defintions are used if not supplied.\n ', '__init__': <function PhaseHypothesisHybrid.__init__>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__int__
¶ int(self)
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.phase.hypothesis'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
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 objectReturns: 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, thephase.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
-
__class__
¶ alias of
builtins.SwigPyObjectType
-
__delattr__
¶ Implement delattr(self, name).
-
__dict__
= mappingproxy({'__module__': 'schrodinger.application.phase.hypothesis', '__doc__': '\n Phase hypothesis created from all mappable features in the given ligand.\n Phase default feature defintions are used if not supplied.\n ', '__init__': <function PhaseHypothesisFromLigand.__init__>})¶
-
__dir__
() → list¶ default dir() implementation
-
__eq__
¶ Return self==value.
-
__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
-
__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
-
__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
-
__int__
¶ int(self)
-
__le__
¶ Return self<=value.
-
__lt__
¶ Return self<value.
-
__module__
= 'schrodinger.application.phase.hypothesis'¶
-
__ne__
¶ Return self!=value.
-
__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__repr__
¶ Return repr(self).
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__str__
¶ Return str(self).
-
__subclasshook__
()¶ Abstract classes can override this to customize issubclass().
This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).
-
__weakref__
¶ list of weak references to the object (if defined)
-
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 objectReturns: 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, thephase.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 structuresReturns: hypothesis, reference ligand, additional hypothesis ligands Return type: Structure
,Structure
, list ofStructure
-
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
- hypotheses (list of