""" This module contains classes for parsing and processing CHARMM parameter, topology, and stream files. It only extracts atom properties from the topology files and extracts all parameters from the parameter files Author: Jason M. Swails """ from __future__ import absolute_import, division, print_function import warnings from collections import OrderedDict from copy import copy from itertools import permutations from .exceptions import ParameterError, ParameterWarning from .topologyobjects import (AtomType, DihedralType, DihedralTypeList, NoUreyBradley, UnassignedAtomType) from .utils.six import iteritems, itervalues from .utils.six.moves import range #pylint: disable=W0622,E0401 class ParameterSet(object): """ Stores a parameter set defining a force field Attributes ---------- atom_types : dict(str:AtomType) Dictionary mapping the names of the atom types to the corresponding AtomType instances atom_types_int : dict(int:AtomType) Dictionary mapping the serial indexes of the atom types to the corresponding AtomType instances atom_types_tuple : dict((str,int):AtomType) Dictionary mapping the (name,number) tuple of the atom types to the corresponding AtomType instances bond_types : dict((str,str):AtomType) Dictionary mapping the 2-element tuple of the names of the two atom types involved in the bond to the BondType instances angle_types : dict((str,str,str):AngleType) Dictionary mapping the 3-element tuple of the names of the three atom types involved in the angle to the AngleType instances urey_bradley_types : dict((str,str,str):BondType) Dictionary mapping the 3-element tuple of the names of the three atom types involved in the angle to the BondType instances of the Urey-Bradley terms dihedral_types : dict((str,str,str,str):list(DihedralType)) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the dihedral to the DihedralType instances. Since each torsion term can be a multiterm expansion, each item corresponding to a key in this dict is a list of `DihedralType`s for each term in the expansion improper_types : dict((str,str,str,str):ImproperType) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the improper torsion to the ImproperType instances improper_periodic_types : dict((str,str,str,str):DihedralType) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the improper torsion (modeled as a Fourier series) to the DihedralType instances. Note, the central atom should always be put in the *third* position of the key rb_torsion_types : dict((str,str,str,str):RBTorsionType) Dictionary mapping the 4-element tuple of the names of the four atom types involved in the Ryckaert-Bellemans torsion to the RBTorsionType instances cmap_types : dict((str,str,str,str,str,str,str,str):CmapType) Dictionary mapping the 5-element tuple of the names of the five atom types involved in the correction map to the CmapType instances nbfix_types : dict((str,str):(float,float)) Dictionary mapping the 2-element tuple of the names of the two atom types whose LJ terms are modified to the tuple of the (epsilon,rmin) terms for that off-diagonal term pair_types : dict((str,str):NonbondedExceptionType) Dictionary mapping the 2-element tuple of atom type names for which explicit exclusion rules should be applied parametersets : list(str) List of parameter set names processed in the current ParameterSet residues : dict(str:ResidueTemplate|ResidueTemplateContainer) A library of ResidueTemplate objects mapped to the residue name defined in the force field library files """ def __init__(self): # Instantiate the list types self.atom_types = self.atom_types_str = OrderedDict() self.atom_types_int = OrderedDict() self.atom_types_tuple = OrderedDict() self.bond_types = OrderedDict() self.angle_types = OrderedDict() self.urey_bradley_types = OrderedDict() self.dihedral_types = OrderedDict() self.improper_types = OrderedDict() self.improper_periodic_types = OrderedDict() self.rb_torsion_types = OrderedDict() self.cmap_types = OrderedDict() self.nbfix_types = OrderedDict() self.pair_types = OrderedDict() self.parametersets = [] self._combining_rule = 'lorentz' self.residues = OrderedDict() self.patches = OrderedDict() self.default_scee = self.default_scnb = 1.0 self._improper_key_map = OrderedDict() def __copy__(self): other = type(self)() for key, item in iteritems(self.atom_types): other.atom_types[key] = copy(item) for key, item in iteritems(self.atom_types_int): other.atom_types_int[key] = copy(item) for key, item in iteritems(self.atom_types_tuple): other.atom_types_tuple[key] = copy(item) for key, item in iteritems(self.bond_types): if key in other.bond_types: continue typ = copy(item) other.bond_types[key] = typ other.bond_types[tuple(reversed(key))] = typ for key, item in iteritems(self.pair_types): if key in other.pair_types: continue typ = copy(item) other.pair_types[key] = typ other.pair_types[tuple(reversed(key))] = typ for key, item in iteritems(self.angle_types): if key in other.angle_types: continue typ = copy(item) other.angle_types[key] = typ other.angle_types[tuple(reversed(key))] = typ for key, item in iteritems(self.dihedral_types): if key in other.dihedral_types: continue typ = copy(item) other.dihedral_types[key] = typ other.dihedral_types[tuple(reversed(key))] = typ for key, item in iteritems(self.rb_torsion_types): if key in other.rb_torsion_types: continue typ = copy(item) other.rb_torsion_types[key] = typ other.rb_torsion_types[tuple(reversed(key))] = typ for key, item in iteritems(self.improper_types): if key in other.improper_types: continue other.improper_types[key] = copy(item) for key, item in iteritems(self.improper_periodic_types): if key in other.improper_periodic_types: continue typ = copy(item) other.improper_periodic_types[key] = typ other.improper_periodic_types[tuple(reversed(key))] = typ for key, item in iteritems(self.urey_bradley_types): if key in other.urey_bradley_types: continue typ = copy(item) other.urey_bradley_types[key] = typ other.urey_bradley_types[tuple(reversed(key))] = typ for key, item in iteritems(self.cmap_types): if key in other.cmap_types: continue typ = copy(item) other.cmap_types[key] = typ other.cmap_types[tuple(reversed(key))] = typ for key, item in iteritems(self.residues): other.residues[key] = copy(item) for key, item in iteritems(self.patches): other.patches[key] = copy(item) other._improper_key_map = copy(self._improper_key_map) other.combining_rule = self.combining_rule return other @classmethod def from_structure(cls, struct, allow_unequal_duplicates=True): """ Extracts known parameters from a Structure instance Parameters ---------- struct : :class:`parmed.structure.Structure` The parametrized ``Structure`` instance from which to extract parameters into a ParameterSet allow_unequal_duplicates : bool, optional If True, if two or more unequal parameter types are defined by the same atom types, the last one encountered will be assigned. If False, an exception will be raised. Default is True Returns ------- params : :class:`ParameterSet` The parameter set with all parameters defined in the Structure Notes ----- The parameters here are copies of the ones in the Structure, so modifying the generated ParameterSet will have no effect on ``struct``. Furthermore, the *first* occurrence of each parameter will be used. If future ones differ, they will be silently ignored, since this is expected behavior in some instances (like with Gromacs topologies in the ff99sb-ildn force field) unless ``allow_unequal_duplicates`` is set to ``False`` Dihedrals are a little trickier. They can be multi-term, which can be represented either as a *single* entry in dihedrals with a type of DihedralTypeList or multiple entries in dihedrals with a DihedralType parameter type. In this case, the parameter is constructed from either the first DihedralTypeList found or the first DihedralType of each periodicity found if no matching DihedralTypeList is found. Raises ------ :class:`parmed.exceptions.ParameterError` if allow_unequal_duplicates is False and 2+ unequal parameters are defined between the same atom types. `NotImplementedError` if any AMOEBA potential terms are defined in the input structure """ params = cls() found_dihed_type_list = dict() for atom in struct.atoms: if atom.atom_type in (UnassignedAtomType, None): atom_type = AtomType(atom.type, None, atom.mass, atom.atomic_number) atom_type.set_lj_params(atom.epsilon, atom.rmin, atom.epsilon_14, atom.rmin_14) params.atom_types[atom.type] = atom_type else: atom_type = copy(atom.atom_type) params.atom_types[str(atom_type)] = atom_type if atom_type.number is not None: params.atom_types_int[int(atom_type)] = atom_type params.atom_types_tuple[(int(atom_type), str(atom_type))] = atom_type if struct.has_NBFIX(): for atom in struct.atoms: if atom.atom_type.nbfix: other_atoms = list(atom.atom_type.nbfix.keys()) for other_atom in other_atoms: (rmin, epsilon, rmin14, epsilon14) = atom.atom_type.nbfix[other_atom] if (other_atom, atom.type) in params.nbfix_types: continue params.nbfix_types[(atom.type, other_atom)] = (rmin, epsilon) for bond in struct.bonds: if bond.type is None: continue key = (bond.atom1.type, bond.atom2.type) if key in params.bond_types: if not allow_unequal_duplicates and params.bond_types[key] != bond.type: raise ParameterError('Unequal bond types defined between %s and %s' % key) continue # pragma: no cover typ = copy(bond.type) key = (bond.atom1.type, bond.atom2.type) params.bond_types[key] = typ params.bond_types[tuple(reversed(key))] = typ for angle in struct.angles: if angle.type is None: continue key = (angle.atom1.type, angle.atom2.type, angle.atom3.type) if key in params.angle_types: if not allow_unequal_duplicates and params.angle_types[key] != angle.type: raise ParameterError('Unequal angle types defined between %s, %s, and %s' % key) continue # pragma: no cover typ = copy(angle.type) key = (angle.atom1.type, angle.atom2.type, angle.atom3.type) params.angle_types[key] = typ params.angle_types[tuple(reversed(key))] = typ if angle.funct == 5: key = (angle.atom1.type, angle.atom2.type, angle.atom3.type) params.urey_bradley_types[key] = NoUreyBradley params.urey_bradley_types[tuple(reversed(key))] = NoUreyBradley for dihedral in struct.dihedrals: if dihedral.type is None: continue if dihedral.improper: # Make sure the central atom comes third, but add all permutations since it's not # clear which particular ordering the various programs require for key in _find_improper_keys(dihedral): if key in params.improper_periodic_types: if (not allow_unequal_duplicates and params.improper_periodic_types[key] != dihedral.type): raise ParameterError('Unequal dihedral types defined between %s, %s, ' '%s, and %s' % key) continue # pragma: no cover typ = copy(dihedral.type) params.improper_periodic_types[key] = typ else: key = (dihedral.atom1.type, dihedral.atom2.type, dihedral.atom3.type, dihedral.atom4.type) # Proper dihedral. Look out for multi-term forms if key in params.dihedral_types and found_dihed_type_list[key]: # Already found a multi-term dihedral type list if not allow_unequal_duplicates: if isinstance(dihedral.type, DihedralTypeList): if params.dihedral_types[key] != dihedral.type: raise ParameterError('Unequal dihedral types defined between %s, ' '%s, %s, and %s' % key) elif isinstance(dihedral.type, DihedralType): for dt in params.dihedral_types[key]: if dt == dihedral.type: break else: raise ParameterError('Unequal dihedral types defined between %s, ' '%s, %s, and %s' % key) continue # pragma: no cover elif key in params.dihedral_types: # We have one term of a potentially multi-term dihedral. if isinstance(dihedral.type, DihedralTypeList): # This is a full Fourier series list found_dihed_type_list[key] = True found_dihed_type_list[tuple(reversed(key))] = True typ = copy(dihedral.type) params.dihedral_types[key] = typ params.dihedral_types[tuple(reversed(key))] = typ else: # This *might* be another term. Make sure another term # with its periodicity does not already exist for t in params.dihedral_types[key]: if t.per == dihedral.type.per: if not allow_unequal_duplicates and t != dihedral.type: raise ParameterError('Unequal dihedral types defined bewteen ' '%s, %s, %s, and %s' % key) break else: # If we got here, we did NOT find this periodicity. # And since this is mutating a list in-place, it # automatically propagates to the reversed key typ = copy(dihedral.type) params.dihedral_types[key].append(typ) else: # New parameter. If it's a DihedralTypeList, assign it and # be done with it. If it's a DihedralType, start a # DihedralTypeList to be added to later. if isinstance(dihedral.type, DihedralTypeList): found_dihed_type_list[key] = True found_dihed_type_list[tuple(reversed(key))] = True typ = copy(dihedral.type) params.dihedral_types[key] = typ params.dihedral_types[tuple(reversed(key))] = typ else: found_dihed_type_list[key] = False found_dihed_type_list[tuple(reversed(key))] = False typ = DihedralTypeList() typ.append(copy(dihedral.type)) params.dihedral_types[key] = typ params.dihedral_types[tuple(reversed(key))] = typ for improper in struct.impropers: if improper.type is None: continue key = (improper.atom1.type, improper.atom2.type, improper.atom3.type, improper.atom4.type) if key in params.improper_types: if not allow_unequal_duplicates and params.improper_types[key] != improper.type: raise ParameterError('Unequal improper types defined between ' '%s, %s, %s, and %s' % key) continue # pragma: no cover params.improper_types[key] = copy(improper.type) for cmap in struct.cmaps: if cmap.type is None: continue key = (cmap.atom1.type, cmap.atom2.type, cmap.atom3.type, cmap.atom4.type, cmap.atom2.type, cmap.atom3.type, cmap.atom4.type, cmap.atom5.type) if key in params.cmap_types: if not allow_unequal_duplicates and cmap.type != params.cmap_types[key]: raise ParameterError('Unequal CMAP types defined between %s, %s, %s, %s, and ' '%s' % (key[0], key[1], key[2], key[3], key[7])) continue # pragma: no cover typ = copy(cmap.type) params.cmap_types[key] = typ params.cmap_types[tuple(reversed(key))] = typ urey_brads_preassigned = len(params.urey_bradley_types) > 0 for urey in struct.urey_bradleys: if urey.type is None or urey.type is NoUreyBradley: continue key = _find_ureybrad_key(urey) if key is None: continue if urey_brads_preassigned and key not in params.urey_bradley_types: warnings.warn('Angle corresponding to Urey-Bradley type not found', ParameterWarning) typ = copy(urey.type) params.urey_bradley_types[key] = typ params.urey_bradley_types[tuple(reversed(key))] = typ if not urey_brads_preassigned and len(params.urey_bradley_types) > 0: # Go through all of our angle parameters and make sure there is a # matching Urey-Bradley list. If there's not, that means there is no # Urey-Bradley term for that angle for key in params.angle_types: if key in params.urey_bradley_types: continue params.urey_bradley_types[key] = NoUreyBradley for adjust in struct.adjusts: if adjust.type is None: continue key = (adjust.atom1.type, adjust.atom2.type) if key in params.pair_types: if not allow_unequal_duplicates and params.pair_types[key] != adjust.type: raise ParameterError('Unequal pair types defined between %s and %s' % key) continue # pragma: no cover typ = copy(adjust.type) params.pair_types[key] = typ params.pair_types[tuple(reversed(key))] = typ # Trap for Amoeba potentials if (struct.trigonal_angles or struct.out_of_plane_bends or struct.torsion_torsions or struct.stretch_bends or struct.trigonal_angles or struct.pi_torsions): raise NotImplementedError('Cannot extract parameters from an Amoeba-parametrized ' 'system yet') return params def condense(self, do_dihedrals=True): """ This function goes through each of the parameter type dicts and eliminates duplicate types. After calling this function, every unique bond, angle, dihedral, improper, or cmap type will pair with EVERY key in the type mapping dictionaries that points to the equivalent type Parameters ---------- do_dihedrals : bool=True Dihedrals can take the longest time to compress since testing their equality takes the longest (this is complicated by the existence of multi-term torsions). This flag will allow you to *skip* condensing the dihedral parameter types (for large parameter sets, this can cut the compression time in half) Returns ------- self The instance that is being condensed Notes ----- The return value allows you to condense the types at construction time. Example ------- >>> params = ParameterSet().condense() >>> params """ # First scan through all of the bond types self._condense_types(self.bond_types) self._condense_types(self.angle_types) self._condense_types(self.urey_bradley_types) if do_dihedrals: self._condense_types(self.dihedral_types) self._condense_types(self.rb_torsion_types) self._condense_types(self.improper_periodic_types) self._condense_types(self.improper_types) self._condense_types(self.cmap_types) return self @staticmethod def _condense_types(typedict): """ Loops through the given dict and condenses all types. Parameter --------- typedict : dict Type dictionary to condense """ keylist = list(typedict.keys()) for i in range(len(keylist) - 1): key1 = keylist[i] for j in range(i+1, len(keylist)): key2 = keylist[j] if typedict[key1] == typedict[key2]: typedict[key2] = typedict[key1] @property def combining_rule(self): return self._combining_rule @combining_rule.setter def combining_rule(self, value): if value not in ('lorentz', 'geometric'): raise ValueError('combining_rule must be "lorentz" or "geometric"') self._combining_rule = value def typeify_templates(self): """ Assign atom types to atom names in templates """ from parmed.modeller import ResidueTemplateContainer, ResidueTemplate for residue in itervalues(self.residues): if isinstance(residue, ResidueTemplateContainer): for res in residue: for atom in res: atom.atom_type = self.atom_types[atom.type] else: assert isinstance(residue, ResidueTemplate), 'Wrong type!' for atom in residue: atom.atom_type = self.atom_types[atom.type] def _find_ureybrad_key(urey): """ Finds a key for a given Urey-Bradley by finding the middle atom in an angle. Raises a ParameterWarning if no middle atom found """ a1, a2 = urey.atom1, urey.atom2 shared_bond_partners = set(a1.bond_partners) & set(a2.bond_partners) if len({a.type for a in shared_bond_partners}) != 1: warnings.warn('Urey-Bradley %r shares multiple central atoms', ParameterWarning) return (a1.type, list(shared_bond_partners)[0].type, a2.type) def _find_improper_keys(dih): """ Finds the central atom (i.e., that bonded to everything else) """ assert dih.improper, 'Should not be called on non-improper!' all_atoms = {dih.atom1, dih.atom2, dih.atom3, dih.atom4} for atom in all_atoms: for oatom in all_atoms: if oatom is atom: continue if oatom not in atom.bond_partners: break else: # This *is* the central atom for key in permutations([a.type for a in all_atoms if a is not atom]): yield (key[0], key[1], atom.type, key[2]) return # break out of the generator # If we got here, we found no central atom. *assume* it's the third spot already... for key in permutations([dih.atom1.type, dih.atom2.type, dih.atom4.type]): yield (key[0], key[1], dih.atom3.type, key[2])