Module hypothesis

Module for reading and writing Phase hypotheses.

Classes

_HypothesisFeature
Class representing a hypothesis feature.

Hypothesis

Functions

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).

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

DEBUG = False

create_hypoFiles = '/nfs/builds/objects/OB/alpaca/Linux-x86_64...

create_hypoTabFile = '/nfs/builds/objects/OB/alpaca/Linux-x86_...

feature_types = {'A': 'Acceptor', 'D': 'Donor', 'H': 'Hydropho...

__package__ = 'schrodinger.application.phase'

Function Details

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

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.

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

Value:

'/nfs/builds/objects/OB/alpaca/Linux-x86_64/build23/utilities/create_h
ypoFiles'

Value:

'/nfs/builds/objects/OB/alpaca/Linux-x86_64/build23/utilities/create_h
ypoTabFile'

Value:

{'A': 'Acceptor',
 'D': 'Donor',
 'H': 'Hydrophobic',
 'N': 'Negative',
 'P': 'Positive',
 'R': 'Aromatic Ring'}