Package schrodinger :: Package application :: Package phase :: Module hypothesis :: Class PhaseHypothesis

Class PhaseHypothesis

                object --+    
                         |    
infra.phase.PhpHypoAdaptor --+
                             |
                            PhaseHypothesis

Known Subclasses:

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
Initializes a Phase hypothesis from phase.PhpHypoAdaptor

str

title(self)
Returns the hypothesis ID as the title

int or None

getSiteNumber(self, site)
Determines site number for the given feature site by comparing its name with names of all the current 'reference' sites.

addFeatureTypeEquivalencies(self, equivalencies)
Applies feature presets to a given hypothesis.

setProjectTableEntry(self, entry_id)
Updates the structure in the project table for the given entry ID with the current PhaseHypothesis.

write(self, filename)
Writes the hypothesis to disk in the single file *.phypo format

visibleXvol(self)
Returns if the excluded volume visibility property is enabled.

visibleRefCt(self)
Returns if the reference ligand visibility property is enabled.

visibleTol(self)
Returns if the tolerances visibility property is enabled.

visiblePropLabels(self)
Returns if the property labels should be shown.

manageXvolIsOpen(self)
Returns True if manage excluded volumes panel for this hypothesis is open.

Inherited from infra.phase.PhpHypoAdaptor: __repr__, __swig_destroy__, addAttr, addCnst, addCt, addIvol, addMask, addProp, addQsar, addRad, addRules, addSite, addTol, addTolByType, addXvol, buildAllAttr, convert, convertToStatic, deleteAttr, deleteSite, deleteSiteFast, getAddCtCount, getAddCts, getCnst, getFd, getHypoCt, getHypoID, getHypoSites, getIvol, getMask, getProp, getQsar, getRad, getRefCt, getRefSites, getRules, getSite, getSiteByDisplayName, getSiteCount, getSiteIndexFromDisplayName, getSiteTypes, getSummary, getTol, getXvol, hasAddCts, hasCnst, hasIvol, hasMask, hasQsar, hasRad, hasRefCt, hasRules, hasTol, hasXvol, merge, save, setHypoID, setRefCtTitle, updateSite, writeSummary

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

Properties

[hide private]

property
Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct.

Inherited from infra.phase.PhpHypoAdaptor: thisown

Inherited from object: __class__

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)

Initializes a Phase hypothesis from phase.PhpHypoAdaptor

Overrides: object.__init__

title(self)

Returns the hypothesis ID as the title

Returns: str: hypothesis ID title

getSiteNumber(self, 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: int or None

site number of the current feature in the hypothesis

addFeatureTypeEquivalencies(self, equivalencies)

Applies feature presets to a given hypothesis.

Parameters:

equiv_pairs (list) - list of equivalency feauture types

setProjectTableEntry(self, entry_id)

Updates the structure in the project table for the given entry ID with the current PhaseHypothesis.

Parameters:

entry_id (int or str) - entry id to set hypothesis to

write(self, filename)

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

Parameters:

filename - hypothesis filename to write to

Property Details

[hide private]

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.

Get Method:: unreachable.property(self) - Make hypothesis property available as in structure.Structure, drawn from the hypothesis ct.

Class PhaseHypothesis

__init__(self, *args, **kwargs) (Constructor)

title(self)

getSiteNumber(self, site)

addFeatureTypeEquivalencies(self, equivalencies)

setProjectTableEntry(self, entry_id)

write(self, filename)

property

init(self, *args, **kwargs)
(Constructor)