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

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Module hypothesis

Module for reading and writing Phase hypotheses.

Classes

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_HypothesisFeature
Class representing a hypothesis feature.

Hypothesis

PhaseHypothesis

Functions

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debug(*args)
Print the given arguments, if in debug mode.

_get_entry_hypo_data_file(entry)
Returns the PT entry's hypothesis file path (hypothesis.hyp).

phase.PhpHypoAdaptor

get_hypothesis_from_project(hypo_id)
Gets hypothesis with a given hypothesis id from the project.

get_entry_hypothesis(entry)
Extract the hypothesis from the given ProjectRow instance, and return a Hypothesis class for it.

generate_from_ligand(lig_file, hypo)
Given a structure file, generate a Hypothesis.

hypo_exists(hypo)
Returns True, if the hypothesis of the given path exists.

remove_hypo_if_present(hypo)
Remove the given hypothesis from disk (if present)

list of lists of ints

get_ligand_groups(ligand_sts)
Groups ligands in an analagous way to phase_database, iterating through the list of ligands and checking if the previous ligand has the same title and connectivity.

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

list of phase.PhpHypoAdaptor

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

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

Variables

[hide private]

maestro = schrodinger.get_maestro()

DEBUG = False
hash(x)

create_hypoFiles = '/scr/buildbot/savedbuilds/NB/2016-3/build-...

create_hypoTabFile = '/scr/buildbot/savedbuilds/NB/2016-3/buil...

__package__ = 'schrodinger.application.phase'

Function Details

[hide private]

_get_entry_hypo_data_file(entry)

Returns the PT entry's hypothesis file path (hypothesis.hyp). If not available (entry has no hypothesis), returns None.

get_hypothesis_from_project(hypo_id)

Gets hypothesis with a given hypothesis id from the project. It first searches for entries with the same hypothesis id and then creates a hypothesis object from found entries.

Parameters:

hypo_id (int) - hypothesis ID

Returns: phase.PhpHypoAdaptor

Phase hypothesis

get_entry_hypothesis(entry)

Extract the hypothesis from the given ProjectRow instance, and return a Hypothesis class for it.

Returns None if the entry has no hypothesis associated with it.

generate_from_ligand(lig_file, hypo)

Given a structure file, generate a Hypothesis. Only the first structure is read.

lig_file - path to the input ligand file hypo - path to the new hypothesis

get_ligand_groups(ligand_sts)

Groups ligands in an analagous way to phase_database, iterating through the list of ligands and checking if the previous ligand has the same title and connectivity.

Parameters:

ligand_sts (list of structure.Structure) - list of ligand structures

Returns: list of lists of ints

list of conformer index lists by ligand group

sorted_hypo_structures(hypothesis_sts)


Sorts a list of structures for PhpHypoAdaptor
- 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 phase.PhpHypoAdaptor

list of Phase hypotheses

write_hypotheses(hypotheses, filename, group=None)

Writes set of PhpHypoAdaptor objects to *_phypo.maegz file.

Parameters:

hypotheses (list of phase.PhpHypoAdaptor) - list of Phase hypotheses
filename (str) - *_phypo.mae.gz file containing Phase hypotheses
group - name to group all hypotheses under

Variables Details

[hide private]

create_hypoFiles

Value:

'/scr/buildbot/savedbuilds/NB/2016-3/build-133/utilities/create_hypoFi
les'

create_hypoTabFile

Value:

'/scr/buildbot/savedbuilds/NB/2016-3/build-133/utilities/create_hypoTa
bFile'