schrodinger.application.phase.hypothesis module

Module for reading and writing Phase hypotheses.

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

Bases: 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.

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.

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.

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.

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.

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