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 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'))