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

property title

Returns the hypothesis ID as the title

Returns

hypothesis ID title

Return type

str

property 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.

visibleFeatureLabels()

Returns if the feature labels should be shown.

visiblePropLabels()

Returns if the property labels should be shown. If feature labels are not shown property labels will be always be hidden.

manageXvolIsOpen()

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

acquire()

acquires ownership of the pointer

addAttr(self, fileName, hydrogens=False)

addCnst(self, cnst)

addCt(self, ctHandle, role)

addIvol(self, ivol)

addMask(self, mask)

addProp(self, propName, propValue)

addProp(self, propName, propValue) → None

addProp(self, propName, propValue) → None

addQsar(self, qsar)

addRad(self, rad)

addRules(self, rules)

addSite(self, site)

addTol(self, tol)

addTolByType(self, tol)

addXvol(self, xvol, hydrogens=False)

append()

appends another ‘this’ object

buildAllAttr(self, alwaysBuild=False)

convert(self, fd)

convertToStatic(self, fd)

convertToStatic(self) → None

deleteAttr(self, attr_name)

deleteProp(self, propName)

deleteSite(self, siteIndex)

deleteSiteFast(self, siteIndex)

disown()

releases ownership of the pointer

getAddCtCount(self) → int

getAddCts(self) → std::vector< MM_Index,std::allocator< MM_Index > >

getCnst(self) → PhpSiteConstrainer

getFd(self) → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getHypoCt(self) → MM_Index

getHypoID(self) → std::string

getHypoSites(self, wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getIvol(self) → PhpExclVol

getMask(self) → PhpSiteMask

getProp(self, propName) → std::string

getQsar(self) → PhpQSAR

getRad(self) → PhpFeatureData

getRefCt(self) → MM_Index

getRefSites(self, wantProj=False, append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRules(self) → PhpFeatureRules

getSite(self, siteIndex) → PhpSite

getSiteByDisplayName(self, displayName) → PhpSite

getSiteCount(self) → int

getSiteIndexFromDisplayName(self, displayName) → size_t

getSiteTypes(self) → std::string

getSummary(self, extended=False, header='Hypothesis Summary') → std::string

getTol(self) → PhpDeltaHypo

getXvol(self) → PhpExclVol

hasAddCts(self) → bool

hasCnst(self) → bool

hasIvol(self) → bool

hasMask(self) → bool

hasProp(self, propName) → bool

hasQsar(self) → bool

hasRad(self) → bool

hasRefCt(self) → bool

hasRules(self) → bool

hasTol(self) → bool

hasXvol(self) → bool

isStatic(self) → bool

merge(self, rhs, tol=PHASE_REDUN_TOL)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

save(self, hypoID, overwrite)

setHypoID(self, hypoID)

setRefCtTitle(self, title)

this

thisown

transform(self, rotation, translation)

updateSite(self, siteIndex, site)

writeSummary(self, os, extended=False, header='Hypothesis Summary')

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 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(self, fileName, hydrogens=False)

addCnst(self, cnst)

addCt(self, ctHandle, role)

addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters

equiv_pairs (list) – list of equivalency feauture types

addIvol(self, ivol)

addMask(self, mask)

addProp(self, propName, propValue)

addProp(self, propName, propValue) → None

addProp(self, propName, propValue) → None

addQsar(self, qsar)

addRad(self, rad)

addRules(self, rules)

addSite(self, site)

addTol(self, tol)

addTolByType(self, tol)

addXvol(self, xvol, hydrogens=False)

append()

appends another ‘this’ object

buildAllAttr(self, alwaysBuild=False)

convert(self, fd)

convertToStatic(self, fd)

convertToStatic(self) → None

deleteAttr(self, attr_name)

deleteProp(self, propName)

deleteSite(self, siteIndex)

deleteSiteFast(self, siteIndex)

disown()

releases ownership of the pointer

getAddCtCount(self) → int

getAddCts(self) → std::vector< MM_Index,std::allocator< MM_Index > >

getCnst(self) → PhpSiteConstrainer

getFd(self) → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getHypoCt(self) → MM_Index

getHypoID(self) → std::string

getHypoSites(self, wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getIvol(self) → PhpExclVol

getMask(self) → PhpSiteMask

getProp(self, propName) → std::string

getQsar(self) → PhpQSAR

getRad(self) → PhpFeatureData

getRefCt(self) → MM_Index

getRefSites(self, wantProj=False, append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRules(self) → PhpFeatureRules

getSite(self, siteIndex) → PhpSite

getSiteByDisplayName(self, displayName) → PhpSite

getSiteCount(self) → int

getSiteIndexFromDisplayName(self, 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(self) → std::string

getSummary(self, extended=False, header='Hypothesis Summary') → std::string

getTol(self) → PhpDeltaHypo

getXvol(self) → PhpExclVol

hasAddCts(self) → bool

hasCnst(self) → bool

hasIvol(self) → bool

hasMask(self) → bool

hasProp(self, propName) → bool

hasQsar(self) → bool

hasRad(self) → bool

hasRefCt(self) → bool

hasRules(self) → bool

hasTol(self) → bool

hasXvol(self) → bool

isStatic(self) → bool

manageXvolIsOpen()

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

merge(self, rhs, tol=PHASE_REDUN_TOL)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property 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(self, hypoID, overwrite)

setHypoID(self, hypoID)

setRefCtTitle(self, title)

this

thisown

property title

Returns the hypothesis ID as the title

Returns

hypothesis ID title

Return type

str

transform(self, rotation, translation)

updateSite(self, siteIndex, site)

visibleFeatureLabels()

Returns if the feature labels should be shown.

visiblePropLabels()

Returns if the property labels should be shown. If feature labels are not shown property labels will be always be hidden.

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(self, os, extended=False, header='Hypothesis Summary')

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(self, fileName, hydrogens=False)

addCnst(self, cnst)

addCt(self, ctHandle, role)

addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters

equiv_pairs (list) – list of equivalency feauture types

addIvol(self, ivol)

addMask(self, mask)

addProp(self, propName, propValue)

addProp(self, propName, propValue) → None

addProp(self, propName, propValue) → None

addQsar(self, qsar)

addRad(self, rad)

addRules(self, rules)

addSite(self, site)

addTol(self, tol)

addTolByType(self, tol)

addXvol(self, xvol, hydrogens=False)

append()

appends another ‘this’ object

buildAllAttr(self, alwaysBuild=False)

convert(self, fd)

convertToStatic(self, fd)

convertToStatic(self) → None

deleteAttr(self, attr_name)

deleteProp(self, propName)

deleteSite(self, siteIndex)

deleteSiteFast(self, siteIndex)

disown()

releases ownership of the pointer

getAddCtCount(self) → int

getAddCts(self) → std::vector< MM_Index,std::allocator< MM_Index > >

getCnst(self) → PhpSiteConstrainer

getFd(self) → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getHypoCt(self) → MM_Index

getHypoID(self) → std::string

getHypoSites(self, wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getIvol(self) → PhpExclVol

getMask(self) → PhpSiteMask

getProp(self, propName) → std::string

getQsar(self) → PhpQSAR

getRad(self) → PhpFeatureData

getRefCt(self) → MM_Index

getRefSites(self, wantProj=False, append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRules(self) → PhpFeatureRules

getSite(self, siteIndex) → PhpSite

getSiteByDisplayName(self, displayName) → PhpSite

getSiteCount(self) → int

getSiteIndexFromDisplayName(self, 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(self) → std::string

getSummary(self, extended=False, header='Hypothesis Summary') → std::string

getTol(self) → PhpDeltaHypo

getXvol(self) → PhpExclVol

hasAddCts(self) → bool

hasCnst(self) → bool

hasIvol(self) → bool

hasMask(self) → bool

hasProp(self, propName) → bool

hasQsar(self) → bool

hasRad(self) → bool

hasRefCt(self) → bool

hasRules(self) → bool

hasTol(self) → bool

hasXvol(self) → bool

isStatic(self) → bool

manageXvolIsOpen()

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

merge(self, rhs, tol=PHASE_REDUN_TOL)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property 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(self, hypoID, overwrite)

setHypoID(self, hypoID)

setRefCtTitle(self, title)

this

thisown

property title

Returns the hypothesis ID as the title

Returns

hypothesis ID title

Return type

str

transform(self, rotation, translation)

updateSite(self, siteIndex, site)

visibleFeatureLabels()

Returns if the feature labels should be shown.

visiblePropLabels()

Returns if the property labels should be shown. If feature labels are not shown property labels will be always be hidden.

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(self, os, extended=False, header='Hypothesis Summary')

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(self, fileName, hydrogens=False)

addCnst(self, cnst)

addCt(self, ctHandle, role)

addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters

equiv_pairs (list) – list of equivalency feauture types

addIvol(self, ivol)

addMask(self, mask)

addProp(self, propName, propValue)

addProp(self, propName, propValue) → None

addProp(self, propName, propValue) → None

addQsar(self, qsar)

addRad(self, rad)

addRules(self, rules)

addSite(self, site)

addTol(self, tol)

addTolByType(self, tol)

addXvol(self, xvol, hydrogens=False)

append()

appends another ‘this’ object

buildAllAttr(self, alwaysBuild=False)

convert(self, fd)

convertToStatic(self, fd)

convertToStatic(self) → None

deleteAttr(self, attr_name)

deleteProp(self, propName)

deleteSite(self, siteIndex)

deleteSiteFast(self, siteIndex)

disown()

releases ownership of the pointer

getAddCtCount(self) → int

getAddCts(self) → std::vector< MM_Index,std::allocator< MM_Index > >

getCnst(self) → PhpSiteConstrainer

getFd(self) → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getHypoCt(self) → MM_Index

getHypoID(self) → std::string

getHypoSites(self, wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getIvol(self) → PhpExclVol

getMask(self) → PhpSiteMask

getProp(self, propName) → std::string

getQsar(self) → PhpQSAR

getRad(self) → PhpFeatureData

getRefCt(self) → MM_Index

getRefSites(self, wantProj=False, append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRules(self) → PhpFeatureRules

getSite(self, siteIndex) → PhpSite

getSiteByDisplayName(self, displayName) → PhpSite

getSiteCount(self) → int

getSiteIndexFromDisplayName(self, 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(self) → std::string

getSummary(self, extended=False, header='Hypothesis Summary') → std::string

getTol(self) → PhpDeltaHypo

getXvol(self) → PhpExclVol

hasAddCts(self) → bool

hasCnst(self) → bool

hasIvol(self) → bool

hasMask(self) → bool

hasProp(self, propName) → bool

hasQsar(self) → bool

hasRad(self) → bool

hasRefCt(self) → bool

hasRules(self) → bool

hasTol(self) → bool

hasXvol(self) → bool

isStatic(self) → bool

manageXvolIsOpen()

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

merge(self, rhs, tol=PHASE_REDUN_TOL)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property 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(self, hypoID, overwrite)

setHypoID(self, hypoID)

setRefCtTitle(self, title)

this

thisown

property title

Returns the hypothesis ID as the title

Returns

hypothesis ID title

Return type

str

transform(self, rotation, translation)

updateSite(self, siteIndex, site)

visibleFeatureLabels()

Returns if the feature labels should be shown.

visiblePropLabels()

Returns if the property labels should be shown. If feature labels are not shown property labels will be always be hidden.

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(self, os, extended=False, header='Hypothesis Summary')

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 or int) – reference ligand, from which to extract all features which can be either structure (preferred) or structure handle

• feature_definitions (list of phase.PhpFeatureDefinition) – feature definitions used in the hypothesis

acquire()

acquires ownership of the pointer

addAttr(self, fileName, hydrogens=False)

addCnst(self, cnst)

addCt(self, ctHandle, role)

addFeatureTypeEquivalencies(equivalencies)

Applies feature presets to a given hypothesis.

Parameters

equiv_pairs (list) – list of equivalency feauture types

addIvol(self, ivol)

addMask(self, mask)

addProp(self, propName, propValue)

addProp(self, propName, propValue) → None

addProp(self, propName, propValue) → None

addQsar(self, qsar)

addRad(self, rad)

addRules(self, rules)

addSite(self, site)

addTol(self, tol)

addTolByType(self, tol)

addXvol(self, xvol, hydrogens=False)

append()

appends another ‘this’ object

buildAllAttr(self, alwaysBuild=False)

convert(self, fd)

convertToStatic(self, fd)

convertToStatic(self) → None

deleteAttr(self, attr_name)

deleteProp(self, propName)

deleteSite(self, siteIndex)

deleteSiteFast(self, siteIndex)

disown()

releases ownership of the pointer

getAddCtCount(self) → int

getAddCts(self) → std::vector< MM_Index,std::allocator< MM_Index > >

getCnst(self) → PhpSiteConstrainer

getFd(self) → std::vector< PhpFeatureDefinition,std::allocator< PhpFeatureDefinition > >

getHypoCt(self) → MM_Index

getHypoID(self) → std::string

getHypoSites(self, wantProj=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getIvol(self) → PhpExclVol

getMask(self) → PhpSiteMask

getProp(self, propName) → std::string

getQsar(self) → PhpQSAR

getRad(self) → PhpFeatureData

getRefCt(self) → MM_Index

getRefSites(self, wantProj=False, append=False) → std::vector< PhpSite,std::allocator< PhpSite > >

getRules(self) → PhpFeatureRules

getSite(self, siteIndex) → PhpSite

getSiteByDisplayName(self, displayName) → PhpSite

getSiteCount(self) → int

getSiteIndexFromDisplayName(self, 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(self) → std::string

getSummary(self, extended=False, header='Hypothesis Summary') → std::string

getTol(self) → PhpDeltaHypo

getXvol(self) → PhpExclVol

hasAddCts(self) → bool

hasCnst(self) → bool

hasIvol(self) → bool

hasMask(self) → bool

hasProp(self, propName) → bool

hasQsar(self) → bool

hasRad(self) → bool

hasRefCt(self) → bool

hasRules(self) → bool

hasTol(self) → bool

hasXvol(self) → bool

isStatic(self) → bool

manageXvolIsOpen()

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

merge(self, rhs, tol=PHASE_REDUN_TOL)

next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

property 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(self, hypoID, overwrite)

setHypoID(self, hypoID)

setRefCtTitle(self, title)

this

thisown

property title

Returns the hypothesis ID as the title

Returns

hypothesis ID title

Return type

str

transform(self, rotation, translation)

updateSite(self, siteIndex, site)

visibleFeatureLabels()

Returns if the feature labels should be shown.

visiblePropLabels()

Returns if the property labels should be shown. If feature labels are not shown property labels will be always be hidden.

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(self, os, extended=False, header='Hypothesis Summary')

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.extract_structures(hypothesis, group=None)

Generator extracting all structures from a PhaseHypothesis objects. If a group name is specified, hypothesis group properties will be added.

Parameters

• hypothesis (PhaseHypothesis) – Phase hypothesis

• group (str) – name to group all hypothesis structures under

Returns

next structure extracted from input hypothesis

Return type

structure.Structure