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VS module cleanup and minor docstrings fix
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@mwojcikowski
mwojcikowski committed Nov 27, 2017
1 parent c28392d commit 8c36263
Showing 1 changed file with 42 additions and 22 deletions.
64 changes: 42 additions & 22 deletions oddt/virtualscreening.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@


def _parallel_helper(obj, methodname, kwargs):
"""Private helper to workaround Python 2 pickle limitations to paralelize methods"""
"""Private helper to workaround Python 2 methods picklinh limitations"""
return getattr(obj, methodname)(**kwargs)


Expand Down Expand Up @@ -58,7 +58,8 @@ def load_ligands(self, fmt, ligands_file, *args, **kwargs):
kwargs['opt']['c'] = None
else:
kwargs['opt'] = {'c': None}
new_pipe = self._ligand_pipe(toolkit.readfile(fmt, ligands_file, *args, **kwargs))
new_pipe = self._ligand_pipe(toolkit.readfile(fmt, ligands_file, *args,
**kwargs))
self._pipe = chain(self._pipe, new_pipe) if self._pipe else new_pipe

def _ligand_pipe(self, ligands):
Expand All @@ -69,7 +70,8 @@ def _ligand_pipe(self, ligands):

def apply_filter(self, expression, soft_fail=0):
"""Filtering method, can use raw expressions (strings to be evaled
in if statement, can use oddt.toolkit.Molecule methods, eg. 'mol.molwt < 500')
in if statement, can use oddt.toolkit.Molecule methods, eg.
`mol.molwt < 500`)
Currently supported presets:
* Lipinski Rule of 5 ('ro5' or 'l5')
* Fragment Rule of 3 ('ro3')
Expand All @@ -81,7 +83,8 @@ def apply_filter(self, expression, soft_fail=0):
Expresion(s) to be used while filtering.
soft_fail: int (default=0)
The number of faulures molecule can have to pass filter, aka. soft-fails.
The number of faulures molecule can have to pass filter, aka.
soft-fails.
"""
if expression in ['l5', 'ro5', 'ro3', 'pains']:
# define presets
Expand Down Expand Up @@ -158,8 +161,14 @@ def similarity(self, method, query, cutoff=0.9, protein=None):
Parameters
----------
method: string, one of ['ift', 'sift', 'usr', 'usr_cat', 'electroshape']
Similarity method used to compare molecules
method: string
Similarity method used to compare molecules. Avaiale methods:
* `ifp` - interaction fingerprint (requires a receptor)
* `sifp` - simple interaction fingerprint (requires a receptor)
* `usr` - Ultrafast Shape Reckognition
* `usr_cat` - USR, with CREDO atom types
* `electroshape` - Electroshape, USR with moments representing
partial charge
query: oddt.toolkit.Molecule or list of oddt.toolkit.Molecule
Query molecules to compare the pipeline to.
Expand All @@ -169,8 +178,8 @@ def similarity(self, method, query, cutoff=0.9, protein=None):
than it will be filtered out.
protein: oddt.toolkit.Molecule (default = None)
Protein for underling method. By default it's empty, but sturctural
fingerprints need one.
Protein for underling method. By default it's empty, but
sturctural fingerprints need one.
"""
if isinstance(query, toolkit.Molecule):
Expand All @@ -194,8 +203,10 @@ def similarity(self, method, query, cutoff=0.9, protein=None):
dist = usr_similarity
else:
raise Exception('Similarity filter "%s" is not supported.' % method)
query_fps = [(gen(q) if protein is None else gen(q, protein)) for q in query]
self._pipe = filter(lambda q: any(dist(gen(q) if protein is None else gen(q, protein),
query_fps = [(gen(q) if protein is None else gen(q, protein))
for q in query]
self._pipe = filter(lambda q: any(dist(gen(q) if protein is None
else gen(q, protein),
q_fp) >= float(cutoff)
for q_fp in query_fps),
self._pipe)
Expand All @@ -217,21 +228,25 @@ def dock(self, engine, protein, *args, **kwargs):
Additional parameters are passed directly to the engine.
Following docking engines are supported:
1. Audodock Vina (``engine="autodock_vina"``), see `oddt.docking.autodock_vina`.
1. Audodock Vina (``engine="autodock_vina"``), see
`oddt.docking.autodock_vina`.
"""
if engine.lower() == 'autodock_vina':
from oddt.docking import autodock_vina
engine = autodock_vina(protein, *args, **kwargs)
else:
raise ValueError('Docking engine %s was not implemented in ODDT' % engine)
raise ValueError('Docking engine %s was not implemented in ODDT'
% engine)
if self.n_cpu != 1:
_parallel_helper_partial = partial(_parallel_helper, engine, 'dock')
docking_results = (Pool(self.n_cpu if self.n_cpu > 0 else None)
.imap(_parallel_helper_partial, ({'ligands': lig,
'single': True}
for lig in self._pipe)))
docking_results = (
Pool(self.n_cpu if self.n_cpu > 0 else None)
.imap(_parallel_helper_partial, ({'ligands': lig,
'single': True}
for lig in self._pipe)))
else:
docking_results = (engine.dock(lig, single=True) for lig in self._pipe)
docking_results = (engine.dock(lig, single=True)
for lig in self._pipe)
self._pipe = chain.from_iterable(docking_results)

def score(self, function, protein=None, *args, **kwargs):
Expand Down Expand Up @@ -283,15 +298,18 @@ def score(self, function, protein=None, *args, **kwargs):
sf = scorer.load(function)
sf.set_protein(protein)
else:
raise ValueError('Scoring Function %s was not implemented in ODDT' % function)
raise ValueError('Scoring Function %s was not implemented in '
'ODDT' % function)
else:
if isinstance(function, scorer):
sf = function
sf.set_protein(protein)
else:
raise ValueError('Supplied object "%s" is not an ODDT scoring funtion' % function.__name__)
raise ValueError('Supplied object "%s" is not an ODDT scoring '
'funtion' % function.__name__)
if self.n_cpu != 1:
_parallel_helper_partial = partial(_parallel_helper, sf, 'predict_ligand')
_parallel_helper_partial = partial(_parallel_helper, sf,
'predict_ligand')
self._pipe = (Pool(self.n_cpu if self.n_cpu > 0 else None)
.imap(_parallel_helper_partial, ({'ligand': lig}
for lig in self._pipe),
Expand Down Expand Up @@ -351,7 +369,8 @@ def write(self, fmt, filename, csv_filename=None, **kwargs):
if len(data) > 0:
data['name'] = mol.title
else:
print("There is no data to write in CSV file", file=sys.stderr)
print("There is no data to write in CSV file",
file=sys.stderr)
return False
if csv_file is None:
csv_file = csv.DictWriter(f, data.keys(), **kwargs)
Expand Down Expand Up @@ -403,7 +422,8 @@ def write_csv(self, csv_filename, fields=None, keep_pipe=False, **kwargs):
print("There is no data to write in CSV file", file=sys.stderr)
return False
if csv_file is None:
csv_file = csv.DictWriter(f, fields or data.keys(), extrasaction='ignore', **kwargs)
csv_file = csv.DictWriter(f, fields or data.keys(),
extrasaction='ignore', **kwargs)
csv_file.writeheader()
csv_file.writerow(data)
if keep_pipe:
Expand Down

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