def __init__(self, filename=None, name=None, rtf=None, prm=None, netcharge=None, method=FFTypeMethod.CGenFF_2b6,
qm=None, outdir="./", mol=None, acCharges=None):
if filename is not None and not filename.endswith('.mol2'):
raise ValueError('Input file must be mol2 format')
if mol is None:
super().__init__(filename=filename, name=name)
else:
for v in mol.__dict__:
self.__dict__[v] = deepcopy(mol.__dict__[v])
# Guess bonds
if len(self.bonds) == 0:
logger.warning('No bonds found! Guessing them...')
self.bonds = self._guessBonds()
# Guess angles and dihedrals
self.angles, self.dihedrals = guessAnglesAndDihedrals(self.bonds, cyclicdih=True)
# Detect equivalent atoms
equivalents = detectEquivalents(self)
self._equivalent_atom_groups = equivalents[0] # List of groups of equivalent atoms
self._equivalent_atoms = equivalents[1] # List of equivalent atoms, indexed by atom
self._equivalent_group_by_atom = equivalents[2] # Mapping from atom index to equivalent atom group
# Detect rotatable dihedrals
self._rotatable_dihedrals = detectSoftDihedrals(self, equivalents)
# Set total charge
if netcharge is None:
self.netcharge = int(round(np.sum(self.charge)))
else:
self.netcharge = int(round(netcharge))
# Canonicalise the names
self._rename()
# Assign atom types, charges, and initial parameters
self.method = method
if rtf and prm:
# If the user has specified explicit RTF and PRM files go ahead and load those
self._rtf = RTF(rtf)
self._prm = PRM(prm)
logger.info('Reading FF parameters from %s and %s' % (rtf, prm))
elif method == FFTypeMethod.NONE:
pass # Don't assign any atom types
else:
# Otherwise make atom types using the specified method
fftype = FFType(self, method=self.method, acCharges=acCharges)
logger.info('Assigned atom types with %s' % self.method.name)
self._rtf = fftype._rtf
self._prm = fftype._prm
if hasattr(self, '_rtf'):
self.atomtype[:] = [self._rtf.type_by_name[name] for name in self.name]
self.charge[:] = [self._rtf.charge_by_name[name] for name in self.name]
self.impropers = np.array(self._rtf.impropers)
# Set atom masses
# TODO: maybe move to molecule
if self.masses.size == 0:
if hasattr(self, '_rtf'):
self.masses[:] = [self._rtf.mass_by_type[self._rtf.type_by_index[i]] for i in range(self.numAtoms)]
else:
self.masses[:] = [vdw.massByElement(element) for element in self.element]
self.qm = qm if qm else Psi4()
self.outdir = outdir
def _guessMass(element):
from htmd.molecule import vdw
return vdw.massByElement(element)
def _guessMass(element):
from htmd.molecule import vdw
return vdw.massByElement(element)
def __init__(self,
filename=None,
name=None,
rtf=None,
prm=None,
netcharge=None,
method=FFTypeMethod.CGenFF_2b6,
qm=None,
outdir="./",
mol=None,
acCharges=None):
if filename is not None and not filename.endswith('.mol2'):
raise ValueError('Input file must be mol2 format')
if mol is None:
super().__init__(filename=filename, name=name)
else:
for v in mol.__dict__:
self.__dict__[v] = deepcopy(mol.__dict__[v])
# Guess bonds
if len(self.bonds) == 0:
logger.warning('No bonds found! Guessing them...')
self.bonds = self._guessBonds()
# Guess angles and dihedrals
self.angles, self.dihedrals = guessAnglesAndDihedrals(self.bonds,
cyclicdih=True)
# Detect equivalent atoms
equivalents = detectEquivalents(self)
self._equivalent_atom_groups = equivalents[
0] # List of groups of equivalent atoms
self._equivalent_atoms = equivalents[
1] # List of equivalent atoms, indexed by atom
self._equivalent_group_by_atom = equivalents[
2] # Mapping from atom index to equivalent atom group
# Detect rotatable dihedrals
self._rotatable_dihedrals = detectSoftDihedrals(self, equivalents)
# Set total charge
if netcharge is None:
self.netcharge = int(round(np.sum(self.charge)))
else:
self.netcharge = int(round(netcharge))
# Canonicalise the names
self._rename()
# Assign atom types, charges, and initial parameters
self.method = method
if rtf and prm:
# If the user has specified explicit RTF and PRM files go ahead and load those
self._rtf = RTF(rtf)
self._prm = PRM(prm)
logger.info('Reading FF parameters from %s and %s' % (rtf, prm))
elif method == FFTypeMethod.NONE:
pass # Don't assign any atom types
else:
# Otherwise make atom types using the specified method
fftype = FFType(self, method=self.method, acCharges=acCharges)
logger.info('Assigned atom types with %s' % self.method.name)
self._rtf = fftype._rtf
self._prm = fftype._prm
if hasattr(self, '_rtf'):
self.atomtype[:] = [
self._rtf.type_by_name[name] for name in self.name
]
self.charge[:] = [
self._rtf.charge_by_name[name] for name in self.name
]
self.impropers = np.array(self._rtf.impropers)
# Check if atom type names are compatible
for type_ in self._rtf.types:
if re.match(FFMolecule._ATOM_TYPE_REG_EX, type_):
raise ValueError(
'Atom type %s is incompatable. It cannot finish with "x" + number!'
% type_)
# Set atom masses
# TODO: maybe move to molecule
if self.masses.size == 0:
if hasattr(self, '_rtf'):
self.masses[:] = [
self._rtf.mass_by_type[self._rtf.type_by_index[i]]
for i in range(self.numAtoms)
]
else:
self.masses[:] = [
vdw.massByElement(element) for element in self.element
]
self.qm = qm if qm else Psi4()
self.outdir = outdir