def writeRTF(mol, parameters, netcharge, filename):
import periodictable
from htmd.version import version as htmdversion
f = open(filename, "w")
print("* Charmm RTF built by HTMD parameterize version {}".format(htmdversion()), file=f)
print("* ", file=f)
print(" 22 0", file=f)
types = getSortedAndUniqueTypes(mol.atomtype, 'atom_types')
for type in types:
val = parameters.atom_types[type]
print("MASS %5d %s %8.5f %s" % (val.number, type, val.mass, periodictable.elements[val.atomic_number]), file=f)
print("\nAUTO ANGLES DIHE\n", file=f)
assert np.unique(mol.resname).size == 1 # Check if all atoms have the same residue name
print("RESI %s %8.5f" % (mol.resname[0], netcharge), file=f)
print("GROUP", file=f)
maxnamelen = max(4, np.max([len(na) for na in mol.name])) # Minimum field size of 4
maxatomtypelen = max(6, np.max([len(at) for at in mol.atomtype])) # Minimum field size of 6
for n, a, c in zip(mol.name, mol.atomtype, mol.charge):
print("ATOM {0:>{1}s} {2:>{3}s} {4:8.6f}".format(n, maxnamelen, a, maxatomtypelen, c), file=f)
for a in mol.bonds:
print("BOND {:>4s} {:>4s}".format(*sorted([mol.name[a[0]], mol.name[a[1]]])), file=f)
for a in mol.impropers:
print("IMPR %4s %4s %4s %4s" % (mol.name[a[0]], mol.name[a[1]], mol.name[a[2]], mol.name[a[3]]),
file=f)
print("PATCH FIRST NONE LAST NONE", file=f)
print("\nEND", file=f)
f.close()
def writeRTF(mol, parameters, netcharge, filename):
import periodictable
from htmd.version import version as htmdversion
f = open(filename, "w")
print("* Charmm RTF built by HTMD parameterize version {}".format(
htmdversion()),
file=f)
print("* ", file=f)
print(" 22 0", file=f)
types = getSortedAndUniqueTypes(mol.atomtype, 'atom_types')
for type in types:
val = parameters.atom_types[type]
print("MASS %5d %s %8.5f %s" %
(val.number, type, val.mass,
periodictable.elements[val.atomic_number]),
file=f)
print("\nAUTO ANGLES DIHE\n", file=f)
print("RESI MOL %8.5f" % netcharge, file=f)
print("GROUP", file=f)
for n, a, c in zip(mol.name, mol.atomtype, mol.charge):
print("ATOM %4s %6s %8.6f" % (n, a, c), file=f)
for a in mol.bonds:
print("BOND {:>4s} {:>4s}".format(
*sorted([mol.name[a[0]], mol.name[a[1]]])),
file=f)
for a in mol.impropers:
print("IMPR %4s %4s %4s %4s" %
(mol.name[a[0]], mol.name[a[1]], mol.name[a[2]], mol.name[a[3]]),
file=f)
print("PATCH FIRST NONE LAST NONE", file=f)
print("\nEND", file=f)
f.close()
def write(self, filename):
f = open(filename, "w")
print("* Charmm RTF built by HTMD parameterize version {}".format(
htmdversion()),
file=f)
print("* ", file=f)
print(" 22 0", file=f)
for a in self.types:
print("MASS %5d %s %8.5f %s" %
(self.typeindex_by_type[a], a, self.mass_by_type[a],
self.element_by_type[a]),
file=f)
print("\nAUTO ANGLES DIHE\n", file=f)
print("RESI MOL %8.5f" % self.netcharge, file=f)
print("GROUP", file=f)
for a in self.names:
print("ATOM %4s %6s %8.6f" %
(a, self.type_by_name[a], self.charge_by_name[a]),
file=f)
for a in self.bonds:
print("BOND %4s %4s" % (self.names[a[0]], self.names[a[1]]),
file=f)
for a in self.impropers:
print("IMPR %4s %4s %4s %4s" %
(self.names[a[0]], self.names[a[1]], self.names[a[2]],
self.names[a[3]]),
file=f)
print("PATCH FIRST NONE LAST NONE", file=f)
print("\nEND", file=f)
f.close()
def writeRTF(mol, parameters, netcharge, filename):
import periodictable
from htmd.version import version as htmdversion
f = open(filename, "w")
print("* Charmm RTF built by HTMD parameterize version {}".format(htmdversion()), file=f)
print("* ", file=f)
print(" 22 0", file=f)
types = getSortedAndUniqueTypes(mol.atomtype, 'atom_types')
for type in types:
val = parameters.atom_types[type]
print("MASS %5d %s %8.5f %s" % (val.number, type, val.mass, periodictable.elements[val.atomic_number]), file=f)
print("\nAUTO ANGLES DIHE\n", file=f)
print("RESI MOL %8.5f" % netcharge, file=f)
print("GROUP", file=f)
maxnamelen = max(4, np.max([len(na) for na in mol.name])) # Minimum field size of 4
maxatomtypelen = max(6, np.max([len(at) for at in mol.atomtype])) # Minimum field size of 6
for n, a, c in zip(mol.name, mol.atomtype, mol.charge):
print("ATOM {0:>{1}s} {2:>{3}s} {4:8.6f}".format(n, maxnamelen, a, maxatomtypelen, c), file=f)
for a in mol.bonds:
print("BOND {:>4s} {:>4s}".format(*sorted([mol.name[a[0]], mol.name[a[1]]])), file=f)
for a in mol.impropers:
print("IMPR %4s %4s %4s %4s" % (mol.name[a[0]], mol.name[a[1]], mol.name[a[2]], mol.name[a[3]]),
file=f)
print("PATCH FIRST NONE LAST NONE", file=f)
print("\nEND", file=f)
f.close()
def write(self, filename):
for i in self.dihedrals:
if i.e14 != 1.0:
raise ValueError(
"Can't express 1-4 electrostatic scaling in Charmm file format"
)
f = open(filename, "w")
print("* prm file built by HTMD parameterize version {}".format(
htmdversion()),
file=f)
print("*\n", file=f)
print("BONDS", file=f)
for a in self.bonds:
print("%-6s %-6s %8.2f %8.4f" %
(a.types[0], a.types[1], a.k0, a.r0),
file=f)
print("\nANGLES", file=f)
for a in self.angles:
if a.kUB > 0.:
print("%-6s %-6s %-6s %8.2f %8.2f %8.2f %8.2f" %
(a.types[0], a.types[1], a.types[2], a.k0, a.theta0,
a.kUB, a.rUB),
file=f)
else:
print("%-6s %-6s %-6s %8.2f %8.2f" %
(a.types[0], a.types[1], a.types[2], a.k0, a.theta0),
file=f)
print("\nDIHEDRALS", file=f)
for a in self.dihedrals:
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" %
(a.types[0], a.types[1], a.types[2], a.types[3], a.k0, a.n,
a.phi0),
file=f)
print("\nIMPROPER", file=f)
for a in self.impropers:
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" %
(a.types[0], a.types[1], a.types[2], a.types[3], a.k0, a.n,
a.phi0),
file=f)
print(
"\nNONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -",
file=f)
print("cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5",
file=f)
for a in self.nonbonded:
if a.emin_14 is not None:
# Charmm prm stores rmin/2
print("%-6s 0.0000 %8.4f %8.4f 0.0000 %8.4f %8.4f" %
(a.types[0], a.emin, a.rmin / 2., a.emin_14,
a.rmin_14 / 2.),
file=f)
else:
print("%-6s 0.0000 %8.4f %8.4f" %
(a.types[0], a.emin, a.rmin / 2.),
file=f)
f.close()
def writePRM(mol, parameters, filename):
from htmd.version import version as htmdversion
from htmd.util import ensurelist
# for type, val in parameters.atom_types.items():
# if val.epsilon_14 != 1.0:
# raise ValueError("Can't express 1-4 electrostatic scaling in Charmm file format")
f = open(filename, "w")
print("* prm file built by HTMD parameterize version {}".format(htmdversion()), file=f)
print("*\n", file=f)
print("BONDS", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.bonds], 'bond_types')
for type in types:
val = getParameter(type, parameters.bond_types)
print("%-6s %-6s %8.2f %8.4f" % (type[0], type[1], val.k, val.req), file=f)
print("\nANGLES", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.angles], 'angle_types')
for type in types:
val = getParameter(type, parameters.angle_types)
print("%-6s %-6s %-6s %8.2f %8.2f" % (type[0], type[1], type[2], val.k, val.theteq), file=f)
print("\nDIHEDRALS", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.dihedrals], 'dihedral_types')
for type in types:
val = getParameter(type, parameters.dihedral_types)
for term in val:
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (type[0], type[1], type[2], type[3], term.phi_k, term.per, term.phase), file=f)
print("\nIMPROPER", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.impropers], 'improper_types')
for type in types:
type, field = findImproperType(type, parameters)
val = parameters.__dict__[field][type]
if field == 'improper_periodic_types':
for term in ensurelist(val):
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (type[0], type[1], type[2], type[3], term.phi_k, term.per, term.phase), file=f)
elif field == 'improper_types':
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (type[0], type[1], type[2], type[3], val.psi_k, 0, val.psi_eq), file=f)
print("\nNONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -", file=f)
print("cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5", file=f)
types = getSortedAndUniqueTypes(mol.atomtype, 'atom_types')
for type in types:
val = parameters.atom_types[type]
if val.epsilon_14 != val.epsilon:
print("%-6s 0.0000 %8.4f %8.4f 0.0000 %8.4f %8.4f" % (type, val.epsilon, val.rmin, val.epsilon_14, val.rmin_14), file=f)
else:
print("%-6s 0.0000 %8.4f %8.4f" % (type, val.epsilon, val.rmin), file=f)
f.close()
def writePRM(mol, parameters, filename):
from htmd.version import version as htmdversion
from htmd.util import ensurelist
# for type, val in parameters.atom_types.items():
# if val.epsilon_14 != 1.0:
# raise ValueError("Can't express 1-4 electrostatic scaling in Charmm file format")
f = open(filename, "w")
print("* prm file built by HTMD parameterize version {}".format(htmdversion()), file=f)
print("*\n", file=f)
print("BONDS", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.bonds], 'bond_types')
for type in types:
val = parameters.bond_types[type]
print("%-6s %-6s %8.2f %8.4f" % (type[0], type[1], val.k, val.req), file=f)
print("\nANGLES", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.angles], 'angle_types')
for type in types:
val = parameters.angle_types[type]
print("%-6s %-6s %-6s %8.2f %8.2f" % (type[0], type[1], type[2], val.k, val.theteq), file=f)
print("\nDIHEDRALS", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.dihedrals], 'dihedral_types')
for type in types:
val = parameters.dihedral_types[type]
for term in val:
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (type[0], type[1], type[2], type[3], term.phi_k, term.per, term.phase), file=f)
print("\nIMPROPER", file=f)
types = getSortedAndUniqueTypes(mol.atomtype[mol.impropers], 'improper_types')
for type in types:
val, field = getImproperParameter(type, parameters)
if field == 'improper_periodic_types':
for term in ensurelist(val):
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (type[0], type[1], type[2], type[3], term.phi_k, term.per, term.phase), file=f)
elif field == 'improper_types':
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (type[0], type[1], type[2], type[3], val.psi_k, 0, val.psi_eq), file=f)
print("\nNONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -", file=f)
print("cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5", file=f)
types = getSortedAndUniqueTypes(mol.atomtype, 'atom_types')
for type in types:
val = parameters.atom_types[type]
if val.epsilon_14 != val.epsilon:
print("%-6s 0.0000 %8.4f %8.4f 0.0000 %8.4f %8.4f" % (type, val.epsilon, val.rmin, val.epsilon_14, val.rmin_14), file=f)
else:
print("%-6s 0.0000 %8.4f %8.4f" % (type, val.epsilon, val.rmin), file=f)
f.close()
def write(self, filename):
f = open(filename, "w")
print("* Charmm RTF built by HTMD parameterize version {}".format(htmdversion()), file=f)
print("* ", file=f)
print(" 22 0", file=f)
for a in self.types:
print(
"MASS %5d %s %8.5f %s" % (self.typeindex_by_type[a], a, self.mass_by_type[a], self.element_by_type[a]),
file=f)
print("\nAUTO ANGLES DIHE\n", file=f)
print("RESI MOL %8.5f" % self.netcharge, file=f)
print("GROUP", file=f)
for a in self.names:
print("ATOM %4s %6s %8.6f" % (a, self.type_by_name[a], self.charge_by_name[a]), file=f)
for a in self.bonds:
print("BOND %4s %4s" % (self.names[a[0]], self.names[a[1]]), file=f)
for a in self.impropers:
print("IMPR %4s %4s %4s %4s" % (self.names[a[0]], self.names[a[1]], self.names[a[2]], self.names[a[3]]),
file=f)
print("PATCH FIRST NONE LAST NONE", file=f)
print("\nEND", file=f)
f.close()
def write(self, filename):
for i in self.dihedrals:
if i.e14 != 1.0:
raise ValueError("Can't express 1-4 electrostatic scaling in Charmm file format")
f = open(filename, "w")
print("* prm file built by HTMD parameterize version {}".format(htmdversion()), file=f)
print("*\n", file=f)
print("BONDS", file=f)
for a in self.bonds:
print("%-6s %-6s %8.2f %8.4f" % (a.types[0], a.types[1], a.k0, a.r0), file=f)
print("\nANGLES", file=f)
for a in self.angles:
if a.kUB > 0.:
print("%-6s %-6s %-6s %8.2f %8.2f %8.2f %8.2f" % (
a.types[0], a.types[1], a.types[2], a.k0, a.theta0, a.kUB, a.rUB), file=f)
else:
print("%-6s %-6s %-6s %8.2f %8.2f" % (a.types[0], a.types[1], a.types[2], a.k0, a.theta0), file=f)
print("\nDIHEDRALS", file=f)
for a in self.dihedrals:
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (
a.types[0], a.types[1], a.types[2], a.types[3], a.k0, a.n, a.phi0), file=f)
print("\nIMPROPER", file=f)
for a in self.impropers:
print("%-6s %-6s %-6s %-6s %12.8f %d %12.8f" % (
a.types[0], a.types[1], a.types[2], a.types[3], a.k0, a.n, a.phi0), file=f)
print("\nNONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -", file=f)
print("cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5", file=f)
for a in self.nonbonded:
if a.emin_14 is not None:
# Charmm prm stores rmin/2
print("%-6s 0.0000 %8.4f %8.4f 0.0000 %8.4f %8.4f" % (
a.types[0], a.emin, a.rmin / 2., a.emin_14, a.rmin_14 / 2.), file=f)
else:
print("%-6s 0.0000 %8.4f %8.4f" % (a.types[0], a.emin, a.rmin / 2.), file=f)
f.close()
def writeFRCMOD(mol, parameters, filename, typemap=None):
from htmd.version import version as htmdversion
if typemap is not None:
parameters = mapAtomTypesParameterSet(parameters, typemap)
atomtypes = np.vectorize(typemap.get)(mol.atomtype)
else:
atomtypes = mol.atomtype
f = open(filename, "w")
print("Frcmod generated by HTMD parameterize version {}".format(
htmdversion()),
file=f)
print("MASS", file=f)
for at in np.unique(atomtypes):
print("%s %f %f" % (at, parameters.atom_types[at].mass, 0.), file=f)
print("\nBOND", file=f)
types = getSortedAndUniqueTypes(atomtypes[mol.bonds], 'bond_types')
for type in types:
val = getParameter(type, parameters.bond_types)
print("%s %f %f" % ('-'.join(type), val.k, val.req), file=f)
print("\nANGL", file=f)
types = getSortedAndUniqueTypes(atomtypes[mol.angles], 'angle_types')
for type in types:
val = getParameter(type, parameters.angle_types)
print("%s %f %f" % ('-'.join(type), val.k, val.theteq), file=f)
print("\nDIHE", file=f)
types = getSortedAndUniqueTypes(atomtypes[mol.dihedrals], 'dihedral_types')
for type in types:
val = getParameter(type, parameters.dihedral_types)
toprint = []
for term in val:
if term.phi_k == 0:
continue
toprint.append(term)
# HACK: print at least one dihedral, even if the force constant is 0, otherwise "tleap" is not happy!
if len(toprint) == 0:
toprint.append(val[0])
for i, term in enumerate(toprint):
# All terms of the same dihedral except the last one should be negative. http://ambermd.org/formats.html#frcmod
if i == len(toprint) - 1:
print("%s 1 %12.6f %12.6f %12.6f %12.6f %12.6f" %
('-'.join(type), term.phi_k, term.phase, term.per,
term.scee, term.scnb),
file=f)
else:
print("%s 1 %12.6f %12.6f %12.6f %12.6f %12.6f" %
('-'.join(type), term.phi_k, term.phase, -term.per,
term.scee, term.scnb),
file=f)
print("\nIMPR", file=f)
types = getSortedAndUniqueTypes(atomtypes[mol.impropers], 'improper_types')
for type in types:
val, field = getImproperParameter(type, parameters)
if field == 'improper_periodic_types':
if val.phi_k == 0:
continue
print("%s %f %f %f" %
('-'.join(type), val.phi_k, val.phase, val.per),
file=f)
elif field == 'improper_types':
if val.psi_k == 0:
continue
print("%s %f %f %f" %
('-'.join(type), val.psi_k, val.psi_eq, 1),
file=f)
print("\nNONB", file=f)
# Have to iterate over the types in use, which include cloned types, and map them back
# to original type (which has the same vdw params), because a copy of a copy won't be in self.nonbonded.
types = getSortedAndUniqueTypes(atomtypes, 'atom_types')
for type in types:
val = parameters.atom_types[type]
print("%s %f %f" % (type, val.rmin, val.epsilon), file=f)
print("", file=f)
f.close()
def writeFrcmod(self, rtf, filename):
t = dict()
# Make a type mapping for any name != 2 chars in length
# Because Amber file formats are horrid
idx = 97
for tt in rtf.types:
n = tt
if len(tt) != 2:
n = "z%c" % idx
idx += 1
t[tt] = n
# check to see whether the parameters can be expressed in Amber FRCMOD format
if len(self.impropers) != 0:
raise ValueError("Can't express CHARMM-style impropers in Amber file format")
for i in self.angles:
if i.rUB != 0. or i.kUB != 0.:
raise ValueError("Can't express Urey-Bradley terms in Amber file format")
for i in self.nonbonded:
if i.rmin_14 is None or i.emin_14 is None:
raise ValueError("Can't express unset 1-4 VdW terms in Amber file format")
eps = math.fabs(i.emin - i.emin_14 * 2.)
if i.rmin != i.rmin_14 or eps > 1.e-6:
raise ValueError("Can't express 1-4 VdW terms that aren't 0.5x scaled in Amber file format")
f = open(filename, "w")
print("Frcmod generated by HTMD parameterize version {}".format(htmdversion()), file=f)
print("MASS", file=f)
for i in rtf.types:
print("%s %f %f" % (t[i], rtf.mass_by_type[i], 0.), file=f)
print("\nBOND", file=f)
for i in self.bonds:
print("%s-%s %f %f" % (t[i.types[0]], t[i.types[1]], i.k0, i.r0), file=f)
print("\nANGL", file=f)
for i in self.angles:
print("%s-%s-%s %f %f" % (t[i.types[0]], t[i.types[1]], t[i.types[2]], i.k0, i.theta0), file=f)
print("\nDIHE", file=f)
output = dict()
for i in self.dihedrals:
if(i.improper == False):
name = "%s-%s-%s-%s" % (t[i.types[0]], t[i.types[1]], t[i.types[2]], t[i.types[3]])
if not (name in output):
output[name] = 1
prm = self.dihedralParam(i.types[0], i.types[1], i.types[2], i.types[3])
for pi in range(len(prm)):
p = prm[pi]
sign = 1
scee = p.e14
scnb = 2.
if pi < (len(prm) - 1):
sign = -1
print("%2s-%2s-%2s-%2s 1 %f %f %f %f %f" %
(t[i.types[0]], t[i.types[1]], t[i.types[2]], t[i.types[3]], p.k0, p.phi0, sign * p.n, scee,
scnb),
file=f)
print("\nIMPR", file=f)
output = dict()
for i in self.dihedrals:
if(i.improper == True):
name = "%s-%s-%s-%s" % (t[i.types[0]], t[i.types[1]], t[i.types[2]], t[i.types[3]])
if not (name in output):
output[name] = 1
prm = self.dihedralParam(i.types[0], i.types[1], i.types[2], i.types[3])
for pi in range(len(prm)):
p = prm[pi]
sign = 1
if p.k0 != 0.:
print("%2s-%2s-%2s-%2s %f %f %f" %
(t[i.types[0]], t[i.types[1]], t[i.types[2]], t[i.types[3]], p.k0, p.phi0, sign * p.n ), file=f)
print("\nNONB", file=f)
# Have to iterate over the types in use
# which include cloned types, an map them back
# to original type (which has the same vdw params)
# because a copy of a copy won't be in self.nonbonded.
for i in set(rtf.types):
p = None
j = re.sub("x[0123456789]$", "", i)
for b in self.nonbonded:
if b.types[0] == j:
p = b
print("%s %f %f" % (t[i], 0.5 * p.rmin, -p.emin), file=f)
print("", file=f)
f.close()
return t
def writeFrcmod(self, rtf, filename):
t = dict()
# Make a type mapping for any name != 2 chars in length
# Because Amber file formats are horrid
idx = 97
for tt in rtf.types:
n = tt
if len(tt) != 2:
n = "z%c" % idx
idx += 1
t[tt] = n
# check to see whether the parameters can be expressed in Amber FRCMOD format
# if len(self.impropers) != 0:
# raise ValueError("Can't express CHARMM-style impropers in Amber file format")
for i in self.angles:
if i.rUB != 0. or i.kUB != 0.:
raise ValueError(
"Can't express Urey-Bradley terms in Amber file format")
for i in self.nonbonded:
if i.rmin_14 is None or i.emin_14 is None:
raise ValueError(
"Can't express unset 1-4 VdW terms in Amber file format")
eps = math.fabs(i.emin - i.emin_14 * 2.)
if i.rmin != i.rmin_14 or eps > 1.e-6:
raise ValueError(
"Can't express 1-4 VdW terms that aren't 0.5x scaled in Amber file format"
)
f = open(filename, "w")
print("Frcmod generated by HTMD parameterize version {}".format(
htmdversion()),
file=f)
print("MASS", file=f)
for i in rtf.types:
print("%s %f %f" % (t[i], rtf.mass_by_type[i], 0.), file=f)
print("\nBOND", file=f)
for i in self.bonds:
print("%s-%s %f %f" % (t[i.types[0]], t[i.types[1]], i.k0, i.r0),
file=f)
print("\nANGL", file=f)
for i in self.angles:
print(
"%s-%s-%s %f %f" %
(t[i.types[0]], t[i.types[1]], t[i.types[2]], i.k0, i.theta0),
file=f)
print("\nDIHE", file=f)
output = dict()
for i in self.dihedrals:
assert i.improper == False
name = "%s-%s-%s-%s" % (t[i.types[0]], t[i.types[1]],
t[i.types[2]], t[i.types[3]])
if not (name in output):
output[name] = 1
prmx = self.dihedralParam(i.types[0], i.types[1], i.types[2],
i.types[3])
# Prune prms that are zero
prm = list()
for pi in range(len(prmx)):
p = prmx[pi]
if p.k0 != 0.: prm.append(p)
# HACK: leave at least one dihedral, even if the force constant is 0,
# otherwise "tleap" is not happy!
if len(prm) == 0:
prm.append(prmx[0])
for p in prm:
scee = 1. / p.e14
scnb = 2.
print(
"%2s-%2s-%2s-%2s 1 %12.6f %12.6f %12.6f %12.6f %12.6f"
% (t[i.types[0]], t[i.types[1]], t[i.types[2]],
t[i.types[3]], p.k0, p.phi0, p.n, scee, scnb),
file=f)
print("\nIMPR", file=f)
output = dict()
for i in self.impropers:
if (i.improper == True):
name = "%s-%s-%s-%s" % (t[i.types[0]], t[i.types[1]],
t[i.types[2]], t[i.types[3]])
if not (name in output):
output[name] = 1
prm = self.improperParam(i.types[0], i.types[1],
i.types[2], i.types[3])
for pi in range(len(prm)):
p = prm[pi]
sign = 1
if p.k0 != 0.:
print("%2s-%2s-%2s-%2s %f %f %f" %
(t[i.types[0]], t[i.types[1]], t[i.types[2]],
t[i.types[3]], p.k0, p.phi0, sign * p.n),
file=f)
print("\nNONB", file=f)
# Have to iterate over the types in use
# which include cloned types, an map them back
# to original type (which has the same vdw params)
# because a copy of a copy won't be in self.nonbonded.
for i in set(rtf.types):
p = None
j = re.sub("x[0123456789]$", "", i)
for b in self.nonbonded:
if b.types[0] == j:
p = b
print("%s %f %f" % (t[i], 0.5 * p.rmin, -p.emin), file=f)
print("", file=f)
f.close()
return t
def writeFRCMOD(mol, parameters, filename, typemap=None):
from htmd.version import version as htmdversion
if typemap is not None:
parameters = mapAtomTypesParameterSet(parameters, typemap)
atomtypes = np.vectorize(typemap.get)(mol.atomtype)
else:
atomtypes = mol.atomtype
f = open(filename, "w")
f.write("Frcmod generated by HTMD parameterize version {}\n".format(htmdversion()))
f.write("MASS\n")
for at in np.unique(atomtypes):
f.write('{:<2s} {:>8.3f} {:>10.2f}\n'.format(at, parameters.atom_types[at].mass, 0.))
f.write('\nBOND\n')
types = getSortedAndUniqueTypes(atomtypes[mol.bonds], 'bond_types')
for type in types:
val = getParameter(type, parameters.bond_types)
f.write('{:<2s}-{:<2s} {:>10.3f}{:>8.3f}\n'.format(type[0], type[1], val.k, val.req))
f.write('\nANGL\n')
types = getSortedAndUniqueTypes(atomtypes[mol.angles], 'angle_types')
for type in types:
val = getParameter(type, parameters.angle_types)
f.write('{:<2s}-{:<2s}-{:<2s} {:>10.3f}{:>9.3f}\n'.format(type[0], type[1], type[2], val.k, val.theteq))
f.write('\nDIHE\n')
types = getSortedAndUniqueTypes(atomtypes[mol.dihedrals], 'dihedral_types')
for type in types:
val = getParameter(type, parameters.dihedral_types)
toprint = []
for term in val:
if term.phi_k < 1e-6:
continue
toprint.append(term)
# HACK: print at least one dihedral, even if the force constant is 0, otherwise "tleap" is not happy!
if len(toprint) == 0:
toprint.append(val[0])
for i, term in enumerate(toprint):
# All terms of the same dihedral except the last one should be negative. http://ambermd.org/formats.html#frcmod
per = term.per
if i != len(toprint)-1:
per = -per
fmt = '{:<2s}-{:<2s}-{:<2s}-{:<2s} {:>4d}{:>15.8f}{:>9.3f}{:>6.1f} SCEE={:1.1f} SCNB={:1.1f}\n'
f.write(fmt.format(type[0], type[1], type[2], type[3], 1, term.phi_k, term.phase, per, term.scee, term.scnb))
f.write('\nIMPR\n')
types = getSortedAndUniqueTypes(atomtypes[mol.impropers], 'improper_types')
for type in types:
type, field = findImproperType(type, parameters)
val = parameters.__dict__[field][type]
fmt = '{:<2s}-{:<2s}-{:<2s}-{:<2s} {:>10.8f}{:>9.3f}{:>6.1f}\n'
if field == 'improper_periodic_types':
if val.phi_k < 1e-6:
continue
f.write(fmt.format(type[0], type[1], type[2], type[3], val.phi_k, val.phase, val.per))
elif field == 'improper_types':
if val.psi_k < 1e-6:
continue
f.write(fmt.format(type[0], type[1], type[2], type[3], val.psi_k, val.psi_eq, 1))
f.write('\nNONB\n')
# Have to iterate over the types in use, which include cloned types, and map them back
# to original type (which has the same vdw params), because a copy of a copy won't be in self.nonbonded.
types = getSortedAndUniqueTypes(atomtypes, 'atom_types')
for type in types:
val = parameters.atom_types[type]
f.write('{:<2s} {:>10.8f} {:>10.8f}\n'.format(type, val.rmin, val.epsilon))
f.write('\n')
f.close()
def writeFRCMOD(mol, parameters, filename, typemap=None):
from htmd.version import version as htmdversion
if typemap is not None:
parameters = mapAtomTypesParameterSet(parameters, typemap)
atomtypes = np.vectorize(typemap.get)(mol.atomtype)
else:
atomtypes = mol.atomtype
f = open(filename, "w")
f.write("Frcmod generated by HTMD parameterize version {}\n".format(htmdversion()))
f.write("MASS\n")
for at in np.unique(atomtypes):
f.write('{:<2s} {:>8.3f} {:>10.2f}\n'.format(at, parameters.atom_types[at].mass, 0.))
f.write('\nBOND\n')
types = getSortedAndUniqueTypes(atomtypes[mol.bonds], 'bond_types')
for type in types:
val = getParameter(type, parameters.bond_types)
f.write('{:<2s}-{:<2s} {:>10.3f}{:>8.3f}\n'.format(type[0], type[1], val.k, val.req))
f.write('\nANGL\n')
types = getSortedAndUniqueTypes(atomtypes[mol.angles], 'angle_types')
for type in types:
val = getParameter(type, parameters.angle_types)
f.write('{:<2s}-{:<2s}-{:<2s} {:>10.3f}{:>9.3f}\n'.format(type[0], type[1], type[2], val.k, val.theteq))
f.write('\nDIHE\n')
types = getSortedAndUniqueTypes(atomtypes[mol.dihedrals], 'dihedral_types')
for type in types:
val = getParameter(type, parameters.dihedral_types)
toprint = []
for term in val:
if term.phi_k == 0:
continue
toprint.append(term)
# HACK: print at least one dihedral, even if the force constant is 0, otherwise "tleap" is not happy!
if len(toprint) == 0:
toprint.append(val[0])
for i, term in enumerate(toprint):
# All terms of the same dihedral except the last one should be negative. http://ambermd.org/formats.html#frcmod
per = term.per
if i != len(toprint)-1:
per = -per
fmt = '{:<2s}-{:<2s}-{:<2s}-{:<2s} {:>4d}{:>15.8f}{:>9.3f}{:>6.1f} SCEE={:1.1f} SCNB={:1.1f}\n'
f.write(fmt.format(type[0], type[1], type[2], type[3], 1, term.phi_k, term.phase, per, term.scee, term.scnb))
f.write('\nIMPR\n')
types = getSortedAndUniqueTypes(atomtypes[mol.impropers], 'improper_types')
for type in types:
val, field = getImproperParameter(type, parameters)
fmt = '{:<2s}-{:<2s}-{:<2s}-{:<2s} {:>10.8f}{:>9.3f}{:>6.1f}\n'
if field == 'improper_periodic_types':
if val.phi_k == 0:
continue
f.write(fmt.format(type[0], type[1], type[2], type[3], val.phi_k, val.phase, val.per))
elif field == 'improper_types':
if val.psi_k == 0:
continue
f.write(fmt.format(type[0], type[1], type[2], type[3], val.psi_k, val.psi_eq, 1))
f.write('\nNONB\n')
# Have to iterate over the types in use, which include cloned types, and map them back
# to original type (which has the same vdw params), because a copy of a copy won't be in self.nonbonded.
types = getSortedAndUniqueTypes(atomtypes, 'atom_types')
for type in types:
val = parameters.atom_types[type]
f.write('{:<2s} {:>10.8f} {:>10.8f}\n'.format(type, val.rmin, val.epsilon))
f.write('\n')
f.close()
