def _load_improper_info(self):
""" Loads the CHARMM Improper types and array """
del self.impropers[:]
del self.improper_types[:]
for k, eq in zip(self.parm_data['CHARMM_IMPROPER_FORCE_CONSTANT'],
self.parm_data['CHARMM_IMPROPER_PHASE']):
# Previous versions of ParmEd stored improper phases as degrees,
# whereas it should really be stored in radians. So do a simple
# heuristic check to see if a conversion is necessary so we support
# all versions.
eq = eq * RAD_TO_DEG if abs(eq) <= 2 * pi else eq
self.improper_types.append(ImproperType(k, eq,
self.improper_types))
it = iter(self.parm_data['CHARMM_IMPROPERS'])
for i, j, k, l, m in zip(it, it, it, it, it):
self.impropers.append(
Improper(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1],
self.improper_types[m - 1]))
# Make sure that if we have a comment in the CHARMM impropers, we fix it
# to say the units are in radians
for i in range(len(self.parm_comments.get('CHARMM_IMPROPER_PHASE',
[]))):
comment = self.parm_comments['CHARMM_IMPROPER_PHASE'][i]
if 'degrees' in comment:
self.parm_comments['CHARMM_IMPROPER_PHASE'][i] = \
comment.replace('degrees', 'radians')
def _load_improper_info(self):
""" Loads the CHARMM Improper types and array """
del self.impropers[:]
del self.improper_types[:]
for k, eq in zip(self.parm_data['CHARMM_IMPROPER_FORCE_CONSTANT'],
self.parm_data['CHARMM_IMPROPER_PHASE']):
self.improper_types.append(ImproperType(k, eq,
self.improper_types))
it = iter(self.parm_data['CHARMM_IMPROPERS'])
for i, j, k, l, m in zip(it, it, it, it, it):
self.impropers.append(
Improper(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1],
self.improper_types[m - 1]))
def _process_improper(struct, force):
""" Processes a CustomTorsionForce and looks at the energy expression to see
if it's a quadratic improper torsion. Then adds the parameters if applicable
Returns
-------
is_improper : bool
Returns True if the energy expression is recognized as a quadratic
improper, and False otherwise
"""
eqn = force.getEnergyFunction().replace(' ', '')
# Don't try to be fancy with regexes for fear of making a possible mistake.
# ParmEd and OpenMM use only these two eqns for the improper torsions:
# k*(theta-theta0)^2 vs. 0.5*k*(theta-theta0)^2
# So only recognize the above 2 forms
if eqn not in ('0.5*k*(theta-theta0)^2', 'k*(theta-theta0)^2'):
return False
if eqn == '0.5*k*(theta-theta0)^2':
fac = 0.5
else:
fac = 1
typemap = dict()
for ii in range(force.getNumTorsions()):
# All formulations put k first and equilibrium angle second, in radians
i, j, k, l, (psi_k, psi_eq) = force.getTorsionParameters(ii)
ai, aj = struct.atoms[i], struct.atoms[j]
ak, al = struct.atoms[k], struct.atoms[l]
key = (psi_k, psi_eq)
if key in typemap:
imp_type = typemap[key]
else:
imp_type = ImproperType(
psi_k * fac * u.kilojoule_per_mole / u.radian**2,
psi_eq * u.radian)
typemap[key] = imp_type
struct.improper_types.append(imp_type)
struct.impropers.append(Improper(ai, aj, ak, al, type=imp_type))
struct.improper_types.claim()
return True
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 __init__(self, psf_name=None):
"""
Opens and parses a PSF file, then instantiates a CharmmPsfFile
instance from the data.
"""
global _resre
Structure.__init__(self)
# Bail out if we don't have a filename
if psf_name is None:
return
conv = CharmmPsfFile._convert
# Open the PSF and read the first line. It must start with "PSF"
with closing(genopen(psf_name, 'r')) as psf:
self.name = psf_name
line = psf.readline()
if not line.startswith('PSF'):
raise CharmmError('Unrecognized PSF file. First line is %s' %
line.strip())
# Store the flags
psf_flags = line.split()[1:]
# Now get all of the sections and store them in a dict
psf.readline()
# Now get all of the sections
psfsections = _ZeroDict()
while True:
try:
sec, ptr, data = CharmmPsfFile._parse_psf_section(psf)
except _FileEOF:
break
psfsections[sec] = (ptr, data)
# store the title
self.title = psfsections['NTITLE'][1]
# Next is the number of atoms
natom = conv(psfsections['NATOM'][0], int, 'natom')
# Parse all of the atoms
for i in range(natom):
words = psfsections['NATOM'][1][i].split()
atid = int(words[0])
if atid != i + 1:
raise CharmmError('Nonsequential atoms detected!')
segid = words[1]
rematch = _resre.match(words[2])
if not rematch:
raise CharmmError('Could not interpret residue number %s'
% # pragma: no cover
words[2])
resid, inscode = rematch.groups()
resid = conv(resid, int, 'residue number')
resname = words[3]
name = words[4]
attype = words[5]
# Try to convert the atom type to an integer a la CHARMM
try:
attype = int(attype)
except ValueError:
pass
charge = conv(words[6], float, 'partial charge')
mass = conv(words[7], float, 'atomic mass')
props = words[8:]
atom = Atom(name=name, type=attype, charge=charge, mass=mass)
atom.props = props
self.add_atom(atom,
resname,
resid,
chain=segid,
inscode=inscode,
segid=segid)
# Now get the number of bonds
nbond = conv(psfsections['NBOND'][0], int, 'number of bonds')
if len(psfsections['NBOND'][1]) != nbond * 2:
raise CharmmError(
'Got %d indexes for %d bonds' % # pragma: no cover
(len(psfsections['NBOND'][1]), nbond))
it = iter(psfsections['NBOND'][1])
for i, j in zip(it, it):
self.bonds.append(Bond(self.atoms[i - 1], self.atoms[j - 1]))
# Now get the number of angles and the angle list
ntheta = conv(psfsections['NTHETA'][0], int, 'number of angles')
if len(psfsections['NTHETA'][1]) != ntheta * 3:
raise CharmmError(
'Got %d indexes for %d angles' % # pragma: no cover
(len(psfsections['NTHETA'][1]), ntheta))
it = iter(psfsections['NTHETA'][1])
for i, j, k in zip(it, it, it):
self.angles.append(
Angle(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1]))
self.angles[-1].funct = 5 # urey-bradley
# Now get the number of torsions and the torsion list
nphi = conv(psfsections['NPHI'][0], int, 'number of torsions')
if len(psfsections['NPHI'][1]) != nphi * 4:
raise CharmmError(
'Got %d indexes for %d torsions' % # pragma: no cover
(len(psfsections['NPHI']), nphi))
it = iter(psfsections['NPHI'][1])
for i, j, k, l in zip(it, it, it, it):
self.dihedrals.append(
Dihedral(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1]))
self.dihedrals.split = False
# Now get the number of improper torsions
nimphi = conv(psfsections['NIMPHI'][0], int, 'number of impropers')
if len(psfsections['NIMPHI'][1]) != nimphi * 4:
raise CharmmError(
'Got %d indexes for %d impropers' % # pragma: no cover
(len(psfsections['NIMPHI'][1]), nimphi))
it = iter(psfsections['NIMPHI'][1])
for i, j, k, l in zip(it, it, it, it):
self.impropers.append(
Improper(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1]))
# Now handle the donors (what is this used for??)
ndon = conv(psfsections['NDON'][0], int, 'number of donors')
if len(psfsections['NDON'][1]) != ndon * 2:
raise CharmmError(
'Got %d indexes for %d donors' % # pragma: no cover
(len(psfsections['NDON'][1]), ndon))
it = iter(psfsections['NDON'][1])
for i, j in zip(it, it):
self.donors.append(
AcceptorDonor(self.atoms[i - 1], self.atoms[j - 1]))
# Now handle the acceptors (what is this used for??)
nacc = conv(psfsections['NACC'][0], int, 'number of acceptors')
if len(psfsections['NACC'][1]) != nacc * 2:
raise CharmmError(
'Got %d indexes for %d acceptors' % # pragma: no cover
(len(psfsections['NACC'][1]), nacc))
it = iter(psfsections['NACC'][1])
for i, j in zip(it, it):
self.acceptors.append(
AcceptorDonor(self.atoms[i - 1], self.atoms[j - 1]))
# Now get the group sections
try:
ngrp, nst2 = psfsections['NGRP NST2'][0]
except ValueError: # pragma: no cover
raise CharmmError(
'Could not unpack GROUP pointers') # pragma: no cover
tmp = psfsections['NGRP NST2'][1]
self.groups.nst2 = nst2
# Now handle the groups
if len(psfsections['NGRP NST2'][1]) != ngrp * 3:
raise CharmmError(
'Got %d indexes for %d groups' % # pragma: no cover
(len(tmp), ngrp))
it = iter(psfsections['NGRP NST2'][1])
for i, j, k in zip(it, it, it):
self.groups.append(Group(self.atoms[i], j, k))
# Assign all of the atoms to molecules recursively
tmp = psfsections['MOLNT'][1]
set_molecules(self.atoms)
molecule_list = [a.marked for a in self.atoms]
if len(tmp) == len(self.atoms):
if molecule_list != tmp:
warnings.warn(
'Detected PSF molecule section that is WRONG. '
'Resetting molecularity.', CharmmWarning)
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
if numlp != 0 or numlph != 0:
raise NotImplementedError(
'Cannot currently handle PSFs with '
'lone pairs defined in the NUMLP/'
'NUMLPH section.')
# Now do the CMAPs
ncrterm = conv(psfsections['NCRTERM'][0], int,
'Number of cross-terms')
if len(psfsections['NCRTERM'][1]) != ncrterm * 8:
raise CharmmError('Got %d CMAP indexes for %d cmap terms'
% # pragma: no cover
(len(psfsections['NCRTERM']), ncrterm))
it = iter(psfsections['NCRTERM'][1])
for i, j, k, l, m, n, o, p in zip(it, it, it, it, it, it, it, it):
self.cmaps.append(
Cmap.extended(self.atoms[i - 1], self.atoms[j - 1],
self.atoms[k - 1], self.atoms[l - 1],
self.atoms[m - 1], self.atoms[n - 1],
self.atoms[o - 1], self.atoms[p - 1]))
self.unchange()
self.flags = psf_flags