def _process_mass_line(self, line):
words = line.split()
try:
mass = float(words[1])
except ValueError:
raise ParameterError('Could not convert mass to float [%s]' % words[1])
except IndexError:
raise ParameterError('Error parsing MASS line. Not enough tokens')
if words[0] in self.atom_types:
self.atom_types[words[0]].mass = mass
elif words[0] in ('EP', 'LP'):
atype = AtomType(words[0], len(self.atom_types)+1, mass, 0)
self.atom_types[words[0]] = atype
else:
atype = AtomType(words[0], len(self.atom_types)+1, mass,
AtomicNum[element_by_mass(mass)])
self.atom_types[words[0]] = atype
def create_random_structure(parametrized, novalence=False):
""" Create a random Structure with random attributes
Parameters
----------
parametrized : bool
If True, add at least two of all kinds of parameters to the
generated random structure. If False, just fill in the atoms and
residues and some random valence terms, but no "types"
novalence : bool, optional
If True, no valence terms will be added. Default is False. This is
set to False if parametrized is True
"""
from parmed.topologyobjects import (
Atom, Bond, AtomType, BondType, AngleType, DihedralType, ImproperType,
CmapType, OutOfPlaneBendType, StretchBendType, TorsionTorsionType,
AmoebaNonbondedExceptionType, Angle, UreyBradley, Dihedral, Improper,
Cmap, TrigonalAngle, OutOfPlaneBend, StretchBend, PiTorsion,
TorsionTorsion, AcceptorDonor, Group, ChiralFrame, MultipoleFrame,
NonbondedException, RBTorsionType)
from parmed import structure
from copy import copy
if parametrized: novalence = False
# Generate random atom and parameter types
atom_types = [
AtomType(''.join(random.sample(uppercase, 3)), i,
random.random() * 16 + 1, random.randint(1, 8))
for i in range(random.randint(8, 20))
]
bond_types = [
BondType(random.random() * 2,
random.random() * 100) for i in range(random.randint(10, 20))
]
angle_types = [
AngleType(random.random() * 50,
random.random() * 120) for i in range(random.randint(10, 20))
]
dihed_types = [
DihedralType(random.random() * 10, random.randint(1, 6),
random.choice([0, 180]))
for i in range(random.randint(10, 20))
]
rb_types = [RBTorsionType(*[random.random() * 10 for i in range(6)])]
imp_types = [
ImproperType(random.random() * 100, random.choice([0, 180]))
for i in range(random.randint(10, 20))
]
cmap_types = [
CmapType(24, [random.random() * 5 for i in range(24 * 24)])
for i in range(random.randint(5, 10))
]
oop_types = [
OutOfPlaneBendType(random.random() * 100)
for i in range(random.randint(10, 20))
]
strbnd_types = [
StretchBendType(random.random() * 10,
random.random() * 10,
random.random() * 2,
random.random() * 2,
random.random() * 120)
for i in range(random.randint(10, 20))
]
ang1, ang2 = list(range(-180, 180, 36)), list(range(-180, 180, 18))
tortor_types = [
TorsionTorsionType((10, 20), ang1[:], ang2[:],
[random.random() * 10 for j in range(200)])
for i in range(random.randint(5, 10))
]
for typ in atom_types:
typ.set_lj_params(random.random() * 2, random.random() * 2)
struct = structure.Structure()
# Add atoms in residues
for res in range(random.randint(20, 30)):
resname = ''.join(random.sample(uppercase, 3))
resid = res + 1
for i in range(random.randint(10, 25)):
name = ''.join(random.sample(uppercase, 4))
if parametrized:
typ = random.choice(atom_types)
type = str(typ)
mass = typ.mass
atomic_number = typ.atomic_number
else:
type = ''.join(random.sample(uppercase, 3))
mass = random.random() * 16 + 1
atomic_number = random.randint(1, 8)
charge = random.random() * 2 - 1
solvent_radius = random.random() * 2
screen = random.random() * 2
atom = Atom(atomic_number=atomic_number,
type=type,
charge=charge,
mass=mass,
solvent_radius=solvent_radius,
screen=screen,
name=name)
if parametrized:
atom.atom_type = typ
struct.add_atom(atom, resname, resid)
if novalence:
return struct
# Possibly add parameter type lists
if parametrized:
struct.bond_types.extend([copy(x) for x in bond_types])
struct.bond_types.claim()
struct.angle_types.extend([copy(x) for x in angle_types])
struct.angle_types.claim()
struct.dihedral_types.extend([copy(x) for x in dihed_types])
struct.dihedral_types.claim()
struct.rb_torsion_types.extend([copy(x) for x in rb_types])
struct.rb_torsion_types.claim()
struct.urey_bradley_types.extend([copy(x) for x in bond_types])
struct.urey_bradley_types.claim()
struct.improper_types.extend([copy(x) for x in imp_types])
struct.improper_types.claim()
struct.cmap_types.extend([copy(x) for x in cmap_types])
struct.cmap_types.claim()
struct.trigonal_angle_types.extend([copy(x) for x in angle_types])
struct.trigonal_angle_types.claim()
struct.out_of_plane_bend_types.extend([copy(x) for x in oop_types])
struct.out_of_plane_bend_types.claim()
struct.pi_torsion_types.extend([copy(x) for x in dihed_types])
struct.pi_torsion_types.claim()
struct.stretch_bend_types.extend([copy(x) for x in strbnd_types])
struct.stretch_bend_types.claim()
struct.torsion_torsion_types.extend([copy(x) for x in tortor_types])
struct.torsion_torsion_types.claim()
struct.adjust_types.extend([
AmoebaNonbondedExceptionType(0.5, 0.5, 0.6, 0.6, 0.7)
for i in range(random.randint(10, 20))
])
struct.adjust_types.claim()
# Add valence terms with optional
for i in range(random.randint(40, 50)):
struct.bonds.append(Bond(*random.sample(struct.atoms, 2)))
if parametrized:
struct.bonds[-1].type = random.choice(struct.bond_types)
for i in range(random.randint(35, 45)):
struct.angles.append(Angle(*random.sample(struct.atoms, 3)))
if parametrized:
struct.angles[-1].type = random.choice(struct.angle_types)
for i in range(random.randint(35, 45)):
struct.urey_bradleys.append(
UreyBradley(*random.sample(struct.atoms, 2)))
if parametrized:
struct.urey_bradleys[-1].type = random.choice(
struct.urey_bradley_types)
for i in range(random.randint(30, 40)):
struct.dihedrals.append(
Dihedral(*random.sample(struct.atoms, 4),
improper=random.choice([True, False])))
if parametrized:
struct.dihedrals[-1].type = random.choice(struct.dihedral_types)
for i in range(random.randint(30, 40)):
struct.rb_torsions.append(Dihedral(*random.sample(struct.atoms, 4)))
if parametrized:
struct.rb_torsions[-1].type = random.choice(
struct.rb_torsion_types)
for i in range(random.randint(10, 20)):
struct.impropers.append(Improper(*random.sample(struct.atoms, 4)))
if parametrized:
struct.impropers[-1].type = random.choice(struct.improper_types)
for i in range(random.randint(25, 35)):
struct.cmaps.append(Cmap(*random.sample(struct.atoms, 5)))
if parametrized:
struct.cmaps[-1].type = random.choice(struct.cmap_types)
for i in range(random.randint(30, 40)):
struct.trigonal_angles.append(
TrigonalAngle(*random.sample(struct.atoms, 4)))
if parametrized:
struct.trigonal_angles[-1].type = random.choice(
struct.trigonal_angle_types)
for i in range(random.randint(30, 40)):
struct.out_of_plane_bends.append(
OutOfPlaneBend(*random.sample(struct.atoms, 4)))
if parametrized:
struct.out_of_plane_bends[-1].type = random.choice(
struct.out_of_plane_bend_types)
for i in range(random.randint(30, 40)):
struct.stretch_bends.append(
StretchBend(*random.sample(struct.atoms, 3)))
if parametrized:
struct.stretch_bends[-1].type = random.choice(
struct.stretch_bend_types)
for i in range(random.randint(20, 30)):
struct.pi_torsions.append(PiTorsion(*random.sample(struct.atoms, 6)))
if parametrized:
struct.pi_torsions[-1].type = random.choice(
struct.pi_torsion_types)
for i in range(random.randint(10, 20)):
struct.torsion_torsions.append(
TorsionTorsion(*random.sample(struct.atoms, 5)))
if parametrized:
struct.torsion_torsions[-1].type = random.choice(
struct.torsion_torsion_types)
# Now use some lesser-used features
for i in range(random.randint(5, 10)):
struct.acceptors.append(AcceptorDonor(*random.sample(struct.atoms, 2)))
struct.donors.append(AcceptorDonor(*random.sample(struct.atoms, 2)))
struct.groups.append(Group(random.choice(struct.atoms), 2, 0))
struct.chiral_frames.append(
ChiralFrame(*random.sample(struct.atoms, 2),
chirality=random.choice([-1, 1])))
struct.multipole_frames.append(
MultipoleFrame(random.choice(struct.atoms), 0, 1, 2, 3))
for i in range(random.randint(20, 30)):
struct.adjusts.append(
NonbondedException(*random.sample(struct.atoms, 2)))
if parametrized:
struct.adjusts[-1].type = random.choice(struct.adjust_types)
struct.prune_empty_terms()
struct.unchange()
struct.update_dihedral_exclusions()
return struct
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.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
key = (dihedral.atom1.type, dihedral.atom2.type,
dihedral.atom3.type, dihedral.atom4.type)
if dihedral.improper:
key = cls._periodic_improper_key(
dihedral.atom1, dihedral.atom2,
dihedral.atom3, dihedral.atom4,
)
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:
# 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
for urey in struct.urey_bradleys:
if urey.type is None or urey.type is NoUreyBradley: continue
key = (urey.atom1.type, urey.atom2.type)
if key not in params.urey_bradley_types:
warnings.warn('Angle corresponding to Urey-Bradley type not '
'found')
typ = copy(urey.type)
params.urey_bradley_types[key] = typ
params.urey_bradley_types[tuple(reversed(key))] = typ
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 _process_nonbonded(struct, force):
""" Adds nonbonded parameters to the structure """
typemap = dict()
element_typemap = defaultdict(int)
assert force.getNumParticles() == len(struct.atoms), "Atom # mismatch"
for i in range(force.getNumParticles()):
atom = struct.atoms[i]
chg, sig, eps = force.getParticleParameters(i)
atype_name = Element[atom.atomic_number]
key = (atype_name, sig._value, eps._value)
if key in typemap:
atom_type = typemap[key]
else:
element_typemap[atype_name] += 1
atype_name = '%s%d' % (atype_name, element_typemap[atype_name])
atom_type = AtomType(atype_name, None, atom.mass,
atom.atomic_number)
atom.charge = chg.value_in_unit(u.elementary_charge)
rmin = sig.value_in_unit(u.angstroms) * 2**(1/6) / 2 # to rmin/2
eps = eps.value_in_unit(u.kilocalories_per_mole)
atom_type.set_lj_params(eps, rmin)
atom.atom_type = atom_type
atom.type = atom_type.name
explicit_exceptions = defaultdict(set)
bond_graph_exceptions = defaultdict(set)
for atom in struct.atoms:
for a2 in atom.bond_partners:
bond_graph_exceptions[atom].add(a2)
for a3 in a2.bond_partners:
bond_graph_exceptions[atom].add(a3)
# TODO should we compress exception types?
for ii in range(force.getNumExceptions()):
i, j, q, sig, eps = force.getExceptionParameters(ii)
q = q.value_in_unit(u.elementary_charge**2)
sig = sig.value_in_unit(u.angstrom)
eps = eps.value_in_unit(u.kilocalorie_per_mole)
ai, aj = struct.atoms[i], struct.atoms[j]
if q == 0 and (sig == 0 or eps == 0):
explicit_exceptions[ai].add(aj)
explicit_exceptions[aj].add(ai)
continue
try:
chgscale = q / (ai.charge * aj.charge)
except ZeroDivisionError:
if q != 0:
raise TypeError('Cannot scale charge product of 0 to match '
'%s' % q)
chgscale = 1
nbtype = NonbondedExceptionType(sig*2**(1/6), eps, chgscale)
struct.adjusts.append(NonbondedException(ai, aj, type=nbtype))
struct.adjust_types.append(nbtype)
struct.adjust_types.claim()
# Check that all of our exceptions are accounted for
for ai, exceptions in iteritems(bond_graph_exceptions):
if exceptions - explicit_exceptions[ai]:
warnings.warn('Detected incomplete exceptions. Not supported.',
OpenMMWarning)
struct.unknown_functional = True
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.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
key = (dihedral.atom1.type, dihedral.atom2.type,
dihedral.atom3.type, dihedral.atom4.type)
if dihedral.improper:
key = cls._periodic_improper_key(
dihedral.atom1,
dihedral.atom2,
dihedral.atom3,
dihedral.atom4,
)
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:
# 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
for urey in struct.urey_bradleys:
if urey.type is None or urey.type is NoUreyBradley: continue
key = (urey.atom1.type, urey.atom2.type)
if key not in params.urey_bradley_types:
warnings.warn('Angle corresponding to Urey-Bradley type not '
'found')
typ = copy(urey.type)
params.urey_bradley_types[key] = typ
params.urey_bradley_types[tuple(reversed(key))] = typ
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 _process_nonbonded(struct, force):
""" Adds nonbonded parameters to the structure """
typemap = dict()
element_typemap = defaultdict(int)
assert force.getNumParticles() == len(struct.atoms), "Atom # mismatch"
for i in range(force.getNumParticles()):
atom = struct.atoms[i]
chg, sig, eps = force.getParticleParameters(i)
atype_name = Element[atom.atomic_number]
key = (atype_name, sig._value, eps._value)
if key in typemap:
atom_type = typemap[key]
else:
element_typemap[atype_name] += 1
atype_name = '%s%d' % (atype_name, element_typemap[atype_name])
typemap[key] = atom_type = AtomType(atype_name, None, atom.mass,
atom.atomic_number)
atom.charge = chg.value_in_unit(u.elementary_charge)
rmin = sig.value_in_unit(u.angstroms) * 2**(1.0 / 6) / 2 # to rmin/2
eps = eps.value_in_unit(u.kilocalories_per_mole)
atom_type.set_lj_params(eps, rmin)
atom.atom_type = atom_type
atom.type = atom_type.name
explicit_exceptions = defaultdict(set)
bond_graph_exceptions = defaultdict(set)
for atom in struct.atoms:
for a2 in atom.bond_partners:
if atom is not a2:
bond_graph_exceptions[atom].add(a2)
for a3 in a2.bond_partners:
if a3 is atom: continue
if atom is not a3:
bond_graph_exceptions[atom].add(a3)
# TODO should we compress exception types?
for ii in range(force.getNumExceptions()):
i, j, q, sig, eps = force.getExceptionParameters(ii)
q = q.value_in_unit(u.elementary_charge**2)
sig = sig.value_in_unit(u.angstrom)
eps = eps.value_in_unit(u.kilocalorie_per_mole)
ai, aj = struct.atoms[i], struct.atoms[j]
if q == 0 and (sig == 0 or eps == 0):
explicit_exceptions[ai].add(aj)
explicit_exceptions[aj].add(ai)
continue
try:
chgscale = q / (ai.charge * aj.charge)
except ZeroDivisionError:
if q != 0:
raise TypeError('Cannot scale charge product of 0 to match '
'%s' % q)
chgscale = 1
nbtype = NonbondedExceptionType(sig * 2**(1.0 / 6), eps, chgscale)
struct.adjusts.append(NonbondedException(ai, aj, type=nbtype))
struct.adjust_types.append(nbtype)
struct.adjust_types.claim()
# Check that all of our exceptions are accounted for
for ai, exceptions in iteritems(bond_graph_exceptions):
if exceptions - explicit_exceptions[ai]:
struct.unknown_functional = True
warnings.warn('Detected incomplete exceptions. Not supported.',
OpenMMWarning)
break
