def dock(self, engine, protein, *args, **kwargs):
"""Docking procedure.
Parameters
----------
engine: string
Which docking engine to use.
Note
----
Additional parameters are passed directly to the engine.
"""
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)
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)))
else:
docking_results = (engine.dock(lig, single=True) for lig in self._pipe)
self._pipe = chain.from_iterable(docking_results)
def dock(self, engine, protein, *args, **kwargs):
"""Docking procedure.
Parameters
----------
engine: string
Which docking engine to use.
Returns
-------
None
Note
----
Additional parameters are passed directly to the engine.
Following docking engines are supported:
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)
self._pipe.append(partial(method_caller, engine, 'dock'))
def dock(self, engine, protein, *args, **kwargs):
"""Docking procedure.
Parameters
----------
engine: string
Which docking engine to use.
Note
----
Additional parameters are passed directly to the engine.
"""
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)
def _iter_conf(results):
""" Generator to go through docking results, and put them to pipe """
for confs in results:
for conf in confs:
yield conf
if self.n_cpu != 1:
_parallel_helper_partial = partial(_parallel_helper, engine, 'dock')
docking_results = self._pool.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)
self._pipe = _iter_conf(docking_results)
def __init__(self, protein=None, vina_scores=None):
self.protein = protein
self.vina = autodock_vina(protein)
self.vina_scores = vina_scores or [
'vina_affinity', 'vina_gauss1', 'vina_gauss2', 'vina_repulsion',
'vina_hydrophobic', 'vina_hydrogen'
]
self.titles = self.vina_scores
def score(self, function, protein = None, *args, **kwargs):
"""Scoring procedure.
Parameters
----------
function: string
Which scoring function to use.
protein: oddt.toolkit.Molecule
Default protein to use as reference
Note
----
Additional parameters are passed directly to the scoring function.
"""
if type(protein) is str:
extension = protein.split('.')[-1]
protein = six.next(toolkit.readfile(extension, protein))
protein.protein = True
# trigger cache
protein.atom_dict
if type(function) is str:
if function.lower().startswith('rfscore'):
from oddt.scoring.functions.RFScore import rfscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
elif bit.startswith('v'):
new_kwargs['version'] = int(bit.replace('v', ''))
sf = rfscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower().startswith('nnscore'):
from oddt.scoring.functions.NNScore import nnscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
sf = nnscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower() == 'autodock_vina':
from oddt.docking import autodock_vina
sf = autodock_vina(protein, *args, **kwargs)
sf.set_protein(protein)
else:
raise ValueError('Scoring Function %s was not implemented in ODDT' % function)
else:
if hasattr(function, 'set_protein') and hasattr(function, 'predict_ligands') and hasattr(function, 'predict_ligand'):
sf = function
sf.set_protein(protein)
else:
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')
self._pipe = Pool(self.n_cpu if self.n_cpu > 0 else None).imap(_parallel_helper_partial, ({'ligand': lig} for lig in self._pipe), chunksize=100)
else:
self._pipe = sf.predict_ligands(self._pipe)
def score(self, function, protein = None, *args, **kwargs):
"""Scoring procedure.
Parameters
----------
function: string
Which scoring function to use.
protein: oddt.toolkit.Molecule
Default protein to use as reference
Note
----
Additional parameters are passed directly to the scoring function.
"""
if type(protein) is str:
extension = protein.split('.')[-1]
protein = toolkit.readfile(extension, protein).next()
protein.protein = True
# trigger cache
protein.atom_dict
if type(function) is str:
if function.lower().startswith('rfscore'):
from oddt.scoring.functions.RFScore import rfscore
tmp = function.lower().split('_')
v = int(tmp[-1][1:]) if len(tmp) > 1 else 1
sf = rfscore.load(version=v)
sf.set_protein(protein)
elif function.lower() == 'nnscore':
from oddt.scoring.functions.NNScore import nnscore
sf = nnscore.load()
sf.set_protein(protein)
elif function.lower() == 'autodock_vina':
from oddt.docking import autodock_vina
sf = autodock_vina(protein, *args, **kwargs)
sf.set_protein(protein)
else:
raise ValueError('Scoring Function %s was not implemented in ODDT' % function)
else:
if hasattr(function, 'set_protein') and hasattr(function, 'predict_ligands') and hasattr(function, 'predict_ligand'):
sf = function
sf.set_protein(protein)
else:
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')
self._pipe = self._pool.imap(_parallel_helper_partial, ({'ligand': lig} for lig in self._pipe), chunksize=100)
else:
self._pipe = sf.predict_ligands(self._pipe)
def __init__(
self,
protein=None,
vina_scores=[
"vina_affinity",
"vina_gauss1",
"vina_gauss2",
"vina_repulsion",
"vina_hydrophobic",
"vina_hydrogen",
],
):
self.protein = protein
self.vina = autodock_vina(protein)
self.vina_scores = vina_scores
def __init__(self, protein = None):
""" Descriptor build from binana script (as used in NNScore 2.0
Parameters
----------
protein: oddt.toolkit.Molecule object (default=None)
Protein object to be used while generating descriptors.
"""
self.protein = protein
self.vina = autodock_vina(protein)
# Close contacts descriptor generators
cc_4_types = (('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'), ('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'), ('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'), ('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'), ('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'), ('C', 'MG'), ('C', 'MN'), ('C', 'N'), ('C', 'NA'), ('C', 'OA'), ('C', 'SA'), ('C', 'ZN'), ('CL', 'FE'), ('CL', 'HD'), ('CL', 'MG'), ('CL', 'N'), ('CL', 'OA'), ('CL', 'ZN'), ('F', 'HD'), ('F', 'N'), ('F', 'OA'), ('F', 'SA'), ('FE', 'HD'), ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'), ('HD', 'I'), ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'), ('HD', 'NA'), ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'), ('HD', 'SA'), ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'), ('MN', 'N'), ('MN', 'OA'), ('N', 'N'), ('N', 'NA'), ('N', 'OA'), ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'), ('NA', 'SA'), ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'), ('OA', 'ZN'), ('S', 'ZN'), ('SA', 'ZN'), ('A', 'BR'), ('A', 'I'), ('A', 'P'), ('A', 'S'), ('BR', 'N'), ('BR', 'SA'), ('C', 'FE'), ('C', 'I'), ('C', 'P'), ('C', 'S'), ('CL', 'MN'), ('CL', 'NA'), ('CL', 'P'), ('CL', 'S'), ('CL', 'SA'), ('CU', 'HD'), ('CU', 'N'), ('FE', 'NA'), ('FE', 'SA'), ('I', 'N'), ('I', 'OA'), ('MG', 'N'), ('MG', 'P'), ('MG', 'S'), ('MG', 'SA'), ('MN', 'NA'), ('MN', 'P'), ('MN', 'S'), ('MN', 'SA'), ('N', 'P'), ('N', 'S'), ('NA', 'P'), ('NA', 'S'), ('OA', 'P'), ('OA', 'S'), ('P', 'S'), ('P', 'SA'), ('P', 'ZN'), ('S', 'SA'), ('SA', 'SA'), ('A', 'CU'), ('C', 'CD') )
cc_4_rec_types, cc_4_lig_types = zip(*cc_4_types)
self.cc_4 = cc_4_nn = close_contacts(protein, cutoff=4, protein_types=cc_4_rec_types, ligand_types=cc_4_lig_types, mode='atom_types_ad4', aligned_pairs=True)
cc_25_types = [('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'), ('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'), ('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'), ('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'), ('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'), ('C', 'MG'), ('C', 'MN'), ('C', 'N'), ('C', 'NA'), ('C', 'OA'), ('C', 'SA'), ('C', 'ZN'), ('CD', 'OA'), ('CL', 'FE'), ('CL', 'HD'), ('CL', 'MG'), ('CL', 'N'), ('CL', 'OA'), ('CL', 'ZN'), ('F', 'HD'), ('F', 'N'), ('F', 'OA'), ('F', 'SA'), ('F', 'ZN'), ('FE', 'HD'), ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'), ('HD', 'I'), ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'), ('HD', 'NA'), ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'), ('HD', 'SA'), ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'), ('MN', 'N'), ('MN', 'OA'), ('N', 'N'), ('N', 'NA'), ('N', 'OA'), ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'), ('NA', 'SA'), ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'), ('OA', 'ZN'), ('S', 'ZN'), ('SA', 'ZN')]
cc_25_rec_types, cc_25_lig_types = zip(*cc_25_types)
self.cc_25 = close_contacts(protein, cutoff=2.5, protein_types=cc_25_rec_types, ligand_types=cc_25_lig_types, mode='atom_types_ad4', aligned_pairs=True)
def dock(self, engine, protein, *args, **kwargs):
"""Docking procedure.
Parameters
----------
engine: string
Which docking engine to use.
Notes
-----
Additional parameters are passed directly to the engine.
Following docking engines are supported:
1. Audodock Vina (```engine="autodock_vina"```), see
:class:`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)
self._pipe.append(partial(method_caller, engine, 'dock'))
def dock(self, engine, protein, *args, **kwargs):
"""Docking procedure.
Parameters
----------
engine: string
Which docking engine to use.
Note
----
Additional parameters are passed directly to the engine.
"""
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)
def _iter_conf(results):
""" Generator to go through docking results, and put them to pipe """
for confs in results:
for conf in confs:
yield conf
if self.n_cpu != 1:
_parallel_helper_partial = partial(_parallel_helper, engine,
'dock')
docking_results = self._pool.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)
self._pipe = _iter_conf(docking_results)
def score(self, function, protein=None, *args, **kwargs):
"""Scoring procedure compatible with any scoring function implemented
in ODDT and other pickled SFs which are subclasses of
`oddt.scoring.scorer`.
Parameters
----------
function: string
Which scoring function to use.
protein: oddt.toolkit.Molecule
Default protein to use as reference
Note
----
Additional parameters are passed directly to the scoring function.
"""
if isinstance(protein, six.string_types):
extension = protein.split('.')[-1]
protein = next(oddt.toolkit.readfile(extension, protein))
protein.protein = True
elif protein is None:
raise ValueError('Protein needs to be set for structure based '
'scoring')
# trigger cache
protein.atom_dict
if isinstance(function, six.string_types):
if isfile(function):
sf = scorer.load(function)
sf.set_protein(protein)
elif function.lower().startswith('rfscore'):
from oddt.scoring.functions.RFScore import rfscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
elif bit.startswith('v'):
new_kwargs['version'] = int(bit.replace('v', ''))
sf = rfscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower().startswith('nnscore'):
from oddt.scoring.functions.NNScore import nnscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
sf = nnscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower() == 'autodock_vina':
from oddt.docking import autodock_vina
sf = autodock_vina(protein, *args, **kwargs)
sf.set_protein(protein)
else:
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__)
self._pipe.append(partial(method_caller, sf, 'predict_ligands'))
def score(self, function, protein=None, *args, **kwargs):
"""Scoring procedure compatible with any scoring function implemented
in ODDT and other pickled SFs which are subclasses of
`oddt.scoring.scorer`.
Parameters
----------
function: string
Which scoring function to use.
protein: oddt.toolkit.Molecule
Default protein to use as reference
Notes
-----
Additional parameters are passed directly to the scoring function.
"""
if isinstance(protein, six.string_types):
extension = protein.split('.')[-1]
protein = next(oddt.toolkit.readfile(extension, protein))
protein.protein = True
elif protein is None:
raise ValueError('Protein needs to be set for structure based '
'scoring')
# trigger cache
protein.atom_dict
if isinstance(function, six.string_types):
if isfile(function):
sf = scorer.load(function)
sf.set_protein(protein)
elif function.lower().startswith('rfscore'):
from oddt.scoring.functions.RFScore import rfscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
elif bit.startswith('v'):
new_kwargs['version'] = int(bit.replace('v', ''))
sf = rfscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower().startswith('nnscore'):
from oddt.scoring.functions.NNScore import nnscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
sf = nnscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower().startswith('plec'):
from oddt.scoring.functions.PLECscore import PLECscore
new_kwargs = {}
for bit in function.lower().split('_'):
if bit.startswith('pdbbind'):
new_kwargs['pdbbind_version'] = int(bit.replace('pdbbind', ''))
elif bit.startswith('plec'):
new_kwargs['version'] = bit.replace('plec', '')
elif bit.startswith('p'):
new_kwargs['depth_protein'] = int(bit.replace('p', ''))
elif bit.startswith('l'):
new_kwargs['depth_ligand'] = int(bit.replace('l', ''))
elif bit.startswith('s'):
new_kwargs['size'] = int(bit.replace('s', ''))
sf = PLECscore.load(**new_kwargs)
sf.set_protein(protein)
elif function.lower() == 'autodock_vina':
from oddt.docking import autodock_vina
sf = autodock_vina(protein, *args, **kwargs)
sf.set_protein(protein)
else:
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__)
self._pipe.append(partial(method_caller, sf, 'predict_ligands'))
def __init__(self, protein = None, vina_scores = ['vina_affinity', 'vina_gauss1', 'vina_gauss2', 'vina_repulsion', 'vina_hydrophobic', 'vina_hydrogen']):
self.protein = protein
self.vina = autodock_vina(protein)
self.vina_scores = vina_scores
def __init__(self, protein=None):
""" Descriptor build from binana script (as used in NNScore 2.0
Parameters
----------
protein: oddt.toolkit.Molecule object (default=None)
Protein object to be used while generating descriptors.
"""
self.protein = protein
self.vina = autodock_vina(protein)
# Close contacts descriptor generators
cc_4_types = (('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'),
('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'),
('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'),
('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'),
('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'), ('C',
'MG'),
('C', 'MN'), ('C', 'N'), ('C', 'NA'), ('C', 'OA'),
('C', 'SA'), ('C', 'ZN'), ('CL', 'FE'), ('CL', 'HD'),
('CL', 'MG'), ('CL', 'N'), ('CL', 'OA'), ('CL', 'ZN'),
('F', 'HD'), ('F', 'N'), ('F', 'OA'), ('F', 'SA'),
('FE', 'HD'), ('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'),
('HD', 'I'), ('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'),
('HD', 'NA'), ('HD', 'OA'), ('HD', 'P'), ('HD', 'S'),
('HD', 'SA'), ('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'),
('MN', 'N'), ('MN', 'OA'), ('N', 'N'), ('N', 'NA'),
('N', 'OA'), ('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'),
('NA', 'SA'), ('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'),
('OA', 'ZN'), ('S', 'ZN'), ('SA', 'ZN'), ('A', 'BR'),
('A', 'I'), ('A', 'P'), ('A', 'S'), ('BR', 'N'), ('BR',
'SA'),
('C', 'FE'), ('C', 'I'), ('C', 'P'), ('C', 'S'), ('CL',
'MN'),
('CL', 'NA'), ('CL', 'P'), ('CL', 'S'), ('CL', 'SA'),
('CU', 'HD'), ('CU', 'N'), ('FE', 'NA'), ('FE', 'SA'),
('I', 'N'), ('I', 'OA'), ('MG', 'N'), ('MG', 'P'), ('MG',
'S'),
('MG', 'SA'), ('MN', 'NA'), ('MN', 'P'), ('MN', 'S'),
('MN', 'SA'), ('N', 'P'), ('N', 'S'), ('NA', 'P'), ('NA',
'S'),
('OA', 'P'), ('OA',
'S'), ('P', 'S'), ('P', 'SA'), ('P', 'ZN'),
('S', 'SA'), ('SA', 'SA'), ('A', 'CU'), ('C', 'CD'))
cc_4_rec_types, cc_4_lig_types = zip(*cc_4_types)
self.cc_4 = cc_4_nn = close_contacts(protein,
cutoff=4,
protein_types=cc_4_rec_types,
ligand_types=cc_4_lig_types,
mode='atom_types_ad4',
aligned_pairs=True)
cc_25_types = [('A', 'A'), ('A', 'C'), ('A', 'CL'), ('A', 'F'),
('A', 'FE'), ('A', 'HD'), ('A', 'MG'), ('A', 'MN'),
('A', 'N'), ('A', 'NA'), ('A', 'OA'), ('A', 'SA'),
('A', 'ZN'), ('BR', 'C'), ('BR', 'HD'), ('BR', 'OA'),
('C', 'C'), ('C', 'CL'), ('C', 'F'), ('C', 'HD'),
('C', 'MG'), ('C', 'MN'), ('C', 'N'), ('C', 'NA'),
('C', 'OA'), ('C', 'SA'), ('C', 'ZN'), ('CD', 'OA'),
('CL', 'FE'), ('CL', 'HD'), ('CL', 'MG'), ('CL', 'N'),
('CL', 'OA'), ('CL', 'ZN'), ('F', 'HD'), ('F', 'N'),
('F', 'OA'), ('F', 'SA'), ('F', 'ZN'), ('FE', 'HD'),
('FE', 'N'), ('FE', 'OA'), ('HD', 'HD'), ('HD', 'I'),
('HD', 'MG'), ('HD', 'MN'), ('HD', 'N'), ('HD', 'NA'),
('HD', 'OA'), ('HD', 'P'), ('HD', 'S'), ('HD', 'SA'),
('HD', 'ZN'), ('MG', 'NA'), ('MG', 'OA'), ('MN', 'N'),
('MN', 'OA'), ('N', 'N'), ('N', 'NA'), ('N', 'OA'),
('N', 'SA'), ('N', 'ZN'), ('NA', 'OA'), ('NA', 'SA'),
('NA', 'ZN'), ('OA', 'OA'), ('OA', 'SA'), ('OA', 'ZN'),
('S', 'ZN'), ('SA', 'ZN')]
cc_25_rec_types, cc_25_lig_types = zip(*cc_25_types)
self.cc_25 = close_contacts(protein,
cutoff=2.5,
protein_types=cc_25_rec_types,
ligand_types=cc_25_lig_types,
mode='atom_types_ad4',
aligned_pairs=True)