Package schrodinger :: Package application :: Package phase :: Module hypothesis

Module hypothesis

Module for reading and writing Phase hypotheses.

Classes

PhaseHypothesisStandard
Phase hypothesis created from standard sites found in the given reference ligand.

PhaseHypothesisStatic
Phase hypothesis created from sites which will all be converted into static fragment sites.

PhaseHypothesisHybrid
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.

Functions

[hide private]

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

list of PhaseHypothesis

extract_hypotheses(filename)
Extracts all hypotheses from Phase hypothesis file containing multiple hypotheses

write_hypotheses(hypotheses, filename, group=None)
Writes set of PhaseHypothesis objects to *_phypo.maegz file.

Variables

[hide private]

__package__ = 'schrodinger.application.phase'

Function Details

[hide private]

sorted_hypo_structures(hypothesis_sts)


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

@param hypothesis_sts: list of structures
@type hypothesis_sts: list of L{Structure}

@return: hypothesis, reference ligand, additional hypothesis ligands
@rtype: L{Structure}, L{Structure}, list of L{Structure}

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 PhaseHypothesis

list of Phase hypotheses

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