def __init__(self, name=None):
"""Initialize the MoleculeType container.
Args:
name (str): the name of the moleculetype to add
"""
if not name:
name = 'MOL'
self.name = name
self.molecules = OrderedSet()
self.bond_forces = set()
self.pair_forces = set()
self.angle_forces = set()
self.dihedral_forces = set()
self.virtual_forces = set()
self.torsiontorsion_forces = set()
self.constraints = set()
self.exclusions = set()
self.rigidwaters = set()
self.nrexcl = None
class MoleculeType(object):
"""An abstract container for molecules of one type. """
def __init__(self, name=None):
"""Initialize the MoleculeType container.
Args:
name (str): the name of the moleculetype to add
"""
if not name:
name = 'MOL'
self.name = name
self.molecules = OrderedSet()
self.bond_forces = set()
self.pair_forces = set()
self.angle_forces = set()
self.dihedral_forces = set()
self.virtual_forces = set()
self.torsiontorsion_forces = set()
self.constraints = set()
self.exclusions = set()
self.rigidwaters = set()
self.nrexcl = None
def add_molecule(self, molecule):
"""Add a molecule into the moleculetype. """
self.molecules.add(molecule)
# These three functions could probably be made faster through some sort of list comprehension
# rather than iterating explicitly over the lists
def _match_two_atoms(self, newforce, oldforces):
""" find and return any force with the same three atoms. For now, respect ordering in matches. """
newatoms = [newforce.atom1, newforce.atom2]
for force in oldforces:
oldatoms = [force.atom1, force.atom2]
if newatoms == oldatoms:
return force
return False
def _match_three_atoms(self, newforce, oldforces):
""" find and return any force with the same three atoms. For now, respect ordering in matches. """
newatoms = [newforce.atom1, newforce.atom2, newforce.atom3]
for force in oldforces:
oldatoms = [force.atom1, force.atom2, force.atom3]
if newatoms == oldatoms:
return force
return False
def _match_four_atoms(self, newforce, oldforces):
""" find and return any force with the same three atoms. For now, respect ordering in matches. """
newatoms = [newforce.atom1, newforce.atom2, newforce.atom3, newforce.atom4]
for force in oldforces:
oldatoms = [force.atom1, force.atom2, force.atom3, force.atom4]
if newatoms == oldatoms:
return force
return False
def match_bonds(self, bond):
return self._match_two_atoms(bond, self.bond_forces)
def match_pairs(self, pair):
return self._match_two_atoms(pair, self.pair_forces)
def match_angles(self, angle):
return self._match_three_atoms(angle, self.angle_forces)
def match_dihedrals(self, dihedral):
return self._match_four_atoms(dihedral, self.dihedral_forces)
def __repr__(self):
return "MoleculeType '{}' with {} molecules".format(
self.name, len(self.molecules))
def __str__(self):
return "MoleculeType{} '{}' with {} molecules".format(
id(self), self.name, len(self.molecules))
