def __init__(self, threshold=0.0, target=None, cavities=False,
*args, **kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.threshold = threshold
self._target = target
self.cavities = cavities
self.evaluate = self.evaluate_convexhull if self.cavities else self.evaluate_volume
def __init__(self,
probes=None,
radius=5.0,
which='hydrophobic',
clash_threshold=0.6,
hydrophobic_threshold=-0.4,
cutoff=0.0,
hydrophobic_elements=('C', 'S'),
bond_separation=4,
same_residue=True,
only_internal=False,
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.which = which
self.radius = radius
self.clash_threshold = clash_threshold
self.hydrophobic_threshold = hydrophobic_threshold
self.cutoff = cutoff
self.hydrophobic_elements = set(hydrophobic_elements)
self.bond_separation = bond_separation
self.same_residue = same_residue
self._probes = probes
self.only_internal = only_internal
if which == 'hydrophobic':
self.evaluate = self.evaluate_hydrophobic
self.threshold = hydrophobic_threshold
else:
self.evaluate = self.evaluate_clashes
self.threshold = clash_threshold
def __init__(self,
binary=None,
potentials=None,
proteins=('Protein', ),
ligands=('Ligand', ),
terms=None,
sorting=1,
cofactor_mode=0,
with_covalent=False,
with_metals=True,
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.binary = find_executable(
'drugscorex') if binary is None else binary
if not self.binary:
raise ValueError(
'Could not find `drugscorex` executable. Please install it '
'with `conda install -c insilichem drugscorex` or manually '
'specify the location with `binary` and `potentials` keys.')
self.potentials = potentials
self.protein_names = proteins
self.ligand_names = ligands
self.terms = terms
self.sorting = sorting
self.cofactor_mode = cofactor_mode
self.with_covalent = with_covalent
self.with_metals = with_metals
self._oldworkingdir = os.getcwd()
self._paths = {}
if os.name == 'posix' and os.path.exists('/dev/shm'):
self.tmpdir = '/dev/shm'
else:
self.tmpdir = default_tempdir()
def __init__(self,
targets=None,
forcefields=('amber99sbildn.xml', ),
auto_parametrize=None,
parameters=None,
platform=None,
*args,
**kwargs):
if kwargs.get('precision', 6) < 6:
kwargs['precision'] = 6
ObjectiveProvider.__init__(self, **kwargs)
self.auto_parametrize = auto_parametrize
self._targets = targets
self._parameters = parameters
self.platform = platform
self.topology = None
self._simulation = None
additional_ffxml = []
if parameters:
additional_ffxml.append(create_ffxml_file(*zip(*parameters)))
if auto_parametrize:
filenames = [
g.path for m in auto_parametrize
for g in self.environment.cfg.genes if g.name == m
]
additional_ffxml.append(self._gaff2xml(*filenames))
self._forcefields = tuple(forcefields) + tuple(additional_ffxml)
self.forcefield = openmm_app.ForceField(*self._forcefields)
def __init__(self,
protein='Protein',
ligand='Ligand',
scoring='chemscore',
score_component='Score',
radius=10,
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.protein_names = [protein]
self.ligand_names = [ligand]
self.scoring = scoring
self.score_component = score_component
self.radius = radius
self.executable = find_executable('gold_auto')
if self.executable is None:
sys.exit(
'GOLD could not be found in $PATH. Is it (correctly) installed?'
)
self._oldworkingdir = os.getcwd()
self._paths = {}
if os.name == 'posix' and os.path.exists('/dev/shm'):
self.tmpdir = '/dev/shm'
else:
self.tmpdir = default_tempdir()
def __init__(self, probes=None, radius=5.0, distance_tolerance=0.4, angle_tolerance=20.0,
only_intermolecular=True, *args, **kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self._probes = probes
self.distance_tolerance = distance_tolerance
self.angle_tolerance = angle_tolerance
self.radius = radius
self.intramodel = False if only_intermolecular else True
def __init__(self, receptor='Protein', ligand='Ligand', *args, **kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.receptor = receptor
self.ligand = ligand
self._paths = []
if os.name == 'posix' and os.path.exists('/dev/shm'):
self.tmpdir = '/dev/shm'
else:
self.tmpdir = _get_default_tempdir()
def __init__(self, threshold=None, tolerance=None, target=None, probes=None,
center_of_mass=False, *args, **kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.threshold = threshold
self.tolerance = tolerance
self.center_of_mass = center_of_mass
self._probes = probes
self._target = target
if self.center_of_mass:
self.evaluate = self.evaluate_center_of_mass
else:
self.evaluate = self.evaluate_distances
def __init__(self,
probes=None,
radius=5.0,
distance_tolerance=0.4,
angle_tolerance=20.0,
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self._probes = probes
self.distance_tolerance = distance_tolerance
self.angle_tolerance = angle_tolerance
self.radius = radius
def __init__(self,
targets=None,
threshold=0.0,
radius=5.0,
method='area',
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self._targets = targets
self.threshold = threshold
self.radius = radius
self.method = method
if method == 'area':
self.evaluate = self.evaluate_area
else:
self.evaluate = self.evaluate_volume
def __init__(self,
template=None,
targets=('Ligand', ),
parser=None,
title=None,
executable=None,
basis_library=None,
processors=None,
*args,
**kwargs):
if kwargs.get('precision', 6) < 6:
kwargs['precision'] = 6
ObjectiveProvider.__init__(self, **kwargs)
self.targets = targets
self.executable = find_executable(
'nwchem') if executable is None else executable
if self.executable is None:
sys.exit(
'NWChem could not be found in $PATH. Is it (correctly) installed?'
)
self._nprocessors = processors
self._mpirun = find_executable('mpirun') if processors else None
self._title = title if title is not None else self.environment.cfg.output.name
if template is None:
self.template = TEMPLATE
elif os.path.isfile(template):
with open(template) as f:
self.template = f.read()
else:
self.template = template
self.template = self.template.replace('$TITLE', self._title)
if parser is not None:
self.parse_output = imp.load_source('_nwchem_parser',
parser).parse_output
if basis_library is not None and os.path.isdir(basis_library):
if basis_library[-1] != '/':
basis_library += '/'
os.environ['NWCHEM_BASIS_LIBRARY'] = basis_library
self._oldworkingdir = os.getcwd()
self._paths = {}
if os.name == 'posix' and os.path.exists('/dev/shm'):
self.tmpdir = '/dev/shm'
else:
self.tmpdir = default_tempdir()
def __init__(self,
receptor='Protein',
ligand='Ligand',
scoring=None,
custom_scoring=None,
custom_atoms=None,
prepare_each=False,
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.receptor = receptor
self.ligand = ligand
self.scoring = scoring
self.custom_scoring = custom_scoring
self.custom_atoms = custom_atoms
self.prepare_each = prepare_each
self._paths = []
self._tmpfile = None
if os.name == 'posix' and os.path.exists('/dev/shm'):
self.tmpdir = '/dev/shm'
else:
self.tmpdir = _get_default_tempdir()
def __init__(self,
proteins=('Protein', ),
ligands=('Ligand', ),
method='pose',
binary=None,
library=None,
*args,
**kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.protein_names = proteins
self.ligand_names = ligands
self.binary = find_executable(
'ligand_score') if binary is None else binary
self.library = library
self.method = method
self._oldworkingdir = os.getcwd()
self._paths = {}
if os.name == 'posix' and os.path.exists('/dev/shm'):
self.tmpdir = '/dev/shm'
else:
self.tmpdir = default_tempdir()
def __init__(self, reference=None, targets=None, only_primaries=False,
threshold=0.84, *args, **kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.threshold = threshold
self._reference = reference
self._targets = targets
def __init__(self, threshold=None, probes=None, *args, **kwargs):
ObjectiveProvider.__init__(self, **kwargs)
self.threshold = threshold
self._probes = probes