Package schrodinger :: Package application :: Package phase :: Module hypothesis
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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).
 
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]
  DEBUG = log.get_environ_log_level() <= log.DEBUG
  create_hypoFiles = os.path.join(os.environ ["SCHRODINGER"], "u...
  create_hypoTabFile = os.path.join(os.environ ["SCHRODINGER"], ...
  feature_types = {"A": "Acceptor", "D": "Donor", "H": "Hydropho...
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_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:
os.path.join(os.environ ["SCHRODINGER"], "utilities", "create_hypoFile\
s")

create_hypoTabFile

Value:
os.path.join(os.environ ["SCHRODINGER"], "utilities", "create_hypoTabF\
ile")

feature_types

Value:
{"A": "Acceptor", "D": "Donor", "H": "Hydrophobic", "R": "Aromatic Rin\
g", "P": "Positive", "N": "Negative",}