def add_missing(param_list, param, sample_n5=False):
"""
Update param set with missing multiplicities. The modifications are in place.
Parameters
----------
param_list : list of tuples
list of parameters to add missing. Format (A, B, C, D)
param : parmed.charmm.CharmmParameterSet
parameter set to add missing parameters.
sample_n5 : bool
Flag if multiplicity of 5 should be added. Default False.
"""
multiplicities = [1, 2, 3, 4, 6]
if sample_n5:
multiplicities = [1, 2, 3, 4, 5, 6]
if type(param_list) is not list:
param_list = [param_list]
for p in param_list:
reverse = tuple(reversed(p))
per = []
for i in range(len(param.dihedral_types[p])):
per.append(param.dihedral_types[p][i].per)
per.append(param.dihedral_types[reverse][i].per)
for j in multiplicities:
if j not in per:
param.dihedral_types[p].append(DihedralType(0, j, 0))
param.dihedral_types[reverse].append(DihedralType(0, j, 0))
def test_vectorToParams(self):
from parmed.parameters import ParameterSet
from parmed.topologyobjects import DihedralTypeList, DihedralType
params = ParameterSet()
dihlist = DihedralTypeList()
for i in range(6):
dihtype = DihedralType(float(i) + 10, i + 1, float(i) + 20)
dihlist.append(dihtype)
params.dihedral_types[('x', 'x', 'x', 'x')] = dihlist
self.df.dihedrals = [[0, 1, 2, 3]]
self.df.parameters = params
self.df._dihedral_atomtypes = [('x', 'x', 'x', 'x')]
vector = np.array([30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 50])
new_params = self.df._vectorToParams(vector)
self.assertFalse(params is new_params)
self.assertEqual(len(new_params.dihedral_types[('x', 'x', 'x', 'x')]),
6)
for i, param in enumerate(new_params.dihedral_types[('x', 'x', 'x',
'x')]):
self.assertEqual(param.phi_k, i + 30)
self.assertEqual(param.per, i + 1)
self.assertAlmostEqual(np.deg2rad(param.phase), i + 40)
def test_paramsToVector(self):
from parmed.parameters import ParameterSet
from parmed.topologyobjects import DihedralTypeList, DihedralType
params = ParameterSet()
dihlist = DihedralTypeList()
for i in range(6):
dihtype = DihedralType(float(i) + 10, i + 1, float(i) + 20)
dihlist.append(dihtype)
params.dihedral_types[('x', 'x', 'x', 'x')] = dihlist
self.df.dihedrals = [
(0, 0, 0, 0),
]
self.df._dihedral_atomtypes = [('x', 'x', 'x', 'x')]
vector = self.df._paramsToVector(params)
self.assertListEqual(list(vector), [
10, 11, 12, 13, 14, 15,
np.deg2rad(20),
np.deg2rad(21),
np.deg2rad(22),
np.deg2rad(23),
np.deg2rad(24),
np.deg2rad(25), 0.
])
def from_dih_params(filename=None, dih_params=None, rj=False, continuous=False, n_increments=13, sample_phase=False):
"""
Parameters
----------
filename : str
name of file with serialized dihedral parameters
rj : bool
Flag if using reversible jump. Default it True
continuous : bool
Flag if sampling continuous phase. Default is False
n_increments : int
incermentation of torsion drive
sample_phase : bool
Flag if sampling phase. Default is False (K is allowed to go negative when sample_phase is False)
Returns
-------
ToyModel with true and initial value from saved file.
"""
if filename is None and dih_params is None:
msg = 'You must provide either an npy file or a numpy array with true and initial values for the toy model'
raise Exception(msg)
if filename is not None:
dih_params = np.load(filename)
dih_tlist_true = DihedralTypeList()
dih_tlist_init = DihedralTypeList()
true = dih_params[0]
init = dih_params[1]
for dih in true:
if not np.isnan(dih[0]):
dih_tlist_true.append(DihedralType(per=dih[0], phi_k=dih[1], phase=dih[2]))
for dih in init:
if not np.isnan(dih[0]):
dih_tlist_init.append(DihedralType(per=dih[0], phi_k=dih[1], phase=dih[2]))
return ToyModel(true_value=dih_tlist_true, initial_value=dih_tlist_init, rj=rj, continuous=continuous,
n_increments=n_increments, sample_phase=sample_phase)
def _process_improper_line(self, line):
rematch = _impropre.match(line)
if not rematch:
raise ParameterError('Could not understand IMPROPER line '
'[%s]' % line)
a1, a2, a3, a4, k, phi, per = rematch.groups()
a1 = a1.strip(); a2 = a2.strip();
a3 = a3.strip(); a4 = a4.strip()
# Pre-sort the improper types, assuming atom3 is the central atom (which
# it must be in Amber parameter files!!!!)
a1, a2, a4 = sorted([a1, a2, a4])
key = (a1, a2, a3, a4)
self.improper_periodic_types[key] = \
DihedralType(float(k), float(per), float(phi))
def test_paramsToVector(self):
from parmed.parameters import ParameterSet
from parmed.topologyobjects import DihedralTypeList, DihedralType
params = ParameterSet()
dihlist = DihedralTypeList()
for i in range(6):
dihtype = DihedralType(float(i)+10, i+1, float(i)+20)
dihlist.append(dihtype)
params.dihedral_types[('x', 'x', 'x', 'x')] = dihlist
self.df.dihedrals = [(0, 0, 0, 0),]
vector = self.df._paramsToVector(params, [('x', 'x', 'x', 'x'),])
self.assertListEqual(list(vector), [10., 11., 12., 13., 14., 15., 20., 21., 22., 23., 24., 25., 0.])
def _process_dihedral(struct, force):
""" Adds periodic torsions to the structure """
typemap = dict()
for ii in range(force.getNumTorsions()):
i, j, k, l, per, phase, phi_k = force.getTorsionParameters(ii)
ai, aj = struct.atoms[i], struct.atoms[j]
ak, al = struct.atoms[k], struct.atoms[l]
key = (per, phase._value, phi_k._value)
if key in typemap:
dihed_type = typemap[key]
else:
dihed_type = DihedralType(phi_k, per, phase)
typemap[key] = dihed_type
struct.dihedral_types.append(dihed_type)
improper = (ai in ak.bond_partners and aj in ak.bond_partners
and al in ak.bond_partners)
struct.dihedrals.append(
Dihedral(ai, aj, ak, al, improper=improper, type=dihed_type))
struct.dihedral_types.claim()
def test_vectorToParams(self):
from parmed.parameters import ParameterSet
from parmed.topologyobjects import DihedralTypeList, DihedralType
params = ParameterSet()
dihlist = DihedralTypeList()
for i in range(6):
dihtype = DihedralType(float(i)+10, i+1, float(i)+20)
dihlist.append(dihtype)
params.dihedral_types[('x', 'x', 'x', 'x')] = dihlist
self.df.dihedrals = [[0, 1, 2, 3]]
vector = np.array([30., 31., 32., 33., 34., 35., 40., 41., 42., 43., 44., 45., 50.])
self.df._vectorToParams(params, [('x', 'x', 'x', 'x'),], vector)
self.assertEqual(len(params.dihedral_types[('x', 'x', 'x', 'x')]), 6)
for i, param in enumerate(params.dihedral_types[('x', 'x', 'x', 'x')]):
self.assertEqual(param.phi_k, i+30)
self.assertEqual(param.per, i+1)
self.assertEqual(param.phase, i+40)
def _randomize_dih_param(self, return_dih=False):
"""
generates random dihedral parameters
"""
dih_tlist = DihedralTypeList()
multiplicities = [1, 2, 3, 4, 6]
terms = np.random.randint(1, 5+1)
np.random.shuffle(multiplicities)
for i in range(terms):
k = np.random.uniform(0.0, 20.0)
n = multiplicities[i]
phase = np.random.randint(0, 1+1)
if phase == 1:
phase = 180
dih_tlist.append(DihedralType(k, n, phase, 1.00, 1.00))
self._param.dihedral_types[self._dih_type] = dih_tlist
if return_dih:
_dih_tlist = copy.deepcopy(dih_tlist)
return _dih_tlist
def createMultitermDihedralTypes(parameters, nterms=6, scee=1.2, scnb=2):
from parmed.topologyobjects import DihedralTypeList, DihedralType
from copy import deepcopy
parameters = deepcopy(parameters)
for key, val in parameters.dihedral_types.items():
dihlist = DihedralTypeList()
for i in range(1, nterms + 1):
found = False
for d in val: # Check if this term already exists in the parameters.
if d.per == i:
dihlist.append(d)
found = True
break
if not found: # Else create an unparametrized term
dihtype = DihedralType(0, i, 0, scee=scee, scnb=scnb)
dihlist.append(dihtype)
parameters.dihedral_types[key] = dihlist
return parameters
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 _process_dihedral_line(self, line, finished_diheds, last_key):
""" Processes a dihedral line, possibly part of a multi-term dihedral
Parameters
----------
line : str
Line of the file that contains a dihedral term
finished_diheds : dict
Dictionary of dihedral parameters whose final term has been read in
already (which means additional terms will overwrite, not add)
last_key : str or None
If not None, this is the key for the last dihedral type that should
be implied if the atom types are missing. Atom types seem to only be
required for the first term in a multi-term torsion definition
Returns
-------
key or None
If a negative periodicity indicates another term is coming, the
current key is returned so it can be passed as key to the next
_process_dihedral_call
"""
rematch = _dihedre.match(line)
if not rematch and last_key is None:
raise ParameterError('Could not understand DIHEDRAL line '
'[%s]' % line)
elif not rematch:
rematch = _dihed2re.match(line)
if not rematch:
raise ParameterError('Could not understand DIHEDRAL line '
'[%s]' % line)
div, k, phi, per = rematch.groups()
key = last_key
rkey = tuple(reversed(key))
assert key in finished_diheds
if finished_diheds[key]:
raise AssertionError('Cannot have an implied torsion that '
'has already finished!')
else:
a1, a2, a3, a4, div, k, phi, per = rematch.groups()
a1, a2, a3, a4 = a1.strip(), a2.strip(), a3.strip(), a4.strip()
key = (a1, a2, a3, a4)
rkey = (a4, a3, a2, a1)
if last_key is not None and (last_key != key and last_key != rkey):
warnings.warn('Expecting next term in dihedral %r, got '
'definition for dihedral %r' % (last_key, key),
ParameterWarning)
scee = [float(x) for x in _sceere.findall(line)] or [1.2]
scnb = [float(x) for x in _scnbre.findall(line)] or [2.0]
per = float(per)
typ = DihedralType(float(k)/float(div), abs(per), float(phi),
scee[0], scnb[0])
if finished_diheds[key]:
# This dihedral is already finished its definition, which means
# we go ahead and add a new one to override it
typs = DihedralTypeList()
typs.append(typ)
self.dihedral_types[key] = self.dihedral_types[rkey] = typs
else:
self.dihedral_types[key].append(typ)
finished_diheds[key] = finished_diheds[rkey] = per >= 0
if per < 0:
return key
min_n = max(equil_t[:, 0])
# draw indices randomly to
idx_1 = np.random.randint(min_n, len(db.trace(torsion_k)[:]), 200)
idx_2 = np.random.randint(min_n, len(db.trace(torsion_k)[:]), 200)
#samples_with_replacement = [[data[i] for i in index] for index in idx]
# Add missing parameters
multiplicities = [1, 2, 3, 4, 5, 6]
p = ('CG331', 'CG321', 'CG321', 'CG331')
per = []
for i in range(len(param_1.dihedral_types[p])):
per.append(param_1.dihedral_types[p][i].per)
for j in multiplicities:
if j not in per:
param_1.dihedral_types[p].append(DihedralType(0, j, 0))
param_2.dihedral_types[p].append(DihedralType(0, j, 0))
# Set phase to 0
param_1.dihedral_types[p][1].phase = 0.0
param_2.dihedral_types[p][1].phase = 0.0
# Create 2 systems tied to the 2 different parameter sets for solvated and vacuum
# parameterize without deep copy parameters
pdb_solvate = app.PDBFile('../structure/butane_solvated.pdb')
coords = pdb_solvate.positions
min_crds = [coords[0][0], coords[0][1], coords[0][2]]
max_crds = [coords[0][0], coords[0][1], coords[0][2]]
equil_t = 8443
# draw indices randomly to
idx = np.random.randint(equil_t,
len(db.trace('{}_1_K'.format(param_to_opt[0]))[:]),
200)
# Add missing parameters
multiplicities = [1, 2, 3, 4, 5, 6]
for t in param_to_opt:
p = tuple(t.split('_'))
per = []
for i in range(len(param.dihedral_types[p])):
per.append(param.dihedral_types[p][i].per)
for j in multiplicities:
if j not in per:
param.dihedral_types[p].append(DihedralType(0, j, 0))
# parameterize without deep copy parameters
psf_solvate = database['solvated']['structure']
psf_solvate.load_parameters(param, copy_parameters=False)
system_solvate = psf_solvate.createSystem(nonbondedMethod=app.PME,
constraints=app.HBonds,
nonbondedCutoff=12.0 * u.angstroms,
switchDistance=10.0 * u.angstroms)
database['solvated']['system'] = system_solvate
# create openmm system in vacuum
psf_vacuum = database['vacuum']['structure']
psf_vacuum.load_parameters(param, copy_parameters=False)
system_vacuum = psf_vacuum.createSystem(nonbondedMethod=app.NoCutoff,
constraints=app.HBonds,
