Module hypothesis

Module for reading and writing Phase hypotheses.

Classes

[hide private]

_HypothesisFeature
Class representing a hypothesis feature.

Hypothesis

Functions

[hide private]

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)

Variables

[hide private]

maestro = schrodinger.get_maestro()

DEBUG = False
hash(x)

create_hypoFiles = '/nfs/builds/objects/NB/2016-2/Linux-x86_64...

create_hypoTabFile = '/nfs/builds/objects/NB/2016-2/Linux-x86_...

__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

Variables Details

[hide private]

create_hypoFiles

Value:

'/nfs/builds/objects/NB/2016-2/Linux-x86_64/build-131/utilities/create
_hypoFiles'

create_hypoTabFile

Value:

'/nfs/builds/objects/NB/2016-2/Linux-x86_64/build-131/utilities/create
_hypoTabFile'