"""

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.default_scee = self.default_scnb = 1.0

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)

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

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

<parmed.parameters.ParameterSet at 0x7f88757de090>

"""

# 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:

"""

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)

""" 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]):