def SaveITPFile(path, mol, pmol=None):
print("Saving molecule %s to ITP file at path %s." %
(mol.GetName(), str(os.path.join(os.getcwd(), path))))
path = Path(path)
h_mass = ix.GetPeriodicTable()["H"].GetAtomicMass()
path.parent.mkdir(parents=True, exist_ok=True)
file = path.open('w')
# header printing
header = """; File generated by the indigox package
; No guarantees are provided for the usefulness of this file
[ moleculetype ]
; Name nrexcl
TEST 3
[ atoms ]"""
print(header, file=file)
# atom printing
atm_fmt_str = "{index:>5} {type:>6} {residx:>5} {resname:>8} {name:>7} {chargegroup:>5} {charge:>11.5f} {mass:>9.4f} {extra}"
for atom in mol.GetAtoms():
atm_dat = {
"index": atom.GetIndex() + 1,
"type": atom.GetType().GetName() if atom.HasType() else "%%%",
"residx": atom.GetResidueID(),
"resname": atom.GetResidueName(),
"name": atom.GetName(),
"chargegroup": atom.GetChargeGroupID() + 1,
"charge": atom.GetPartialCharge(),
"mass": atom.GetElement().GetAtomicMass() +
atom.GetImplicitCount() * h_mass,
"extra": ""
}
if pmol is not None:
patom = pmol.GetAtom(atom)
extra_info = ";"
if not len(patom.GetMappedCharges()):
extra_info += " UNMAPPED"
else:
mu = patom.MeanCharge()
eta = patom.MedianCharge()
sigma = patom.StandardDeviationCharge()
delta = patom.RedistributedChargeAdded()
to_add = []
if round(mu, 5) != round(eta, 5) or round(sigma, 5) != 0.0:
to_add.append("mean: {:.5f}".format(mu))
to_add.append("median: {:.5f}".format(eta))
to_add.append("stdev: {:.5f}".format(sigma))
if round(delta, 5) != 0.0:
to_add.append("added: {:.5f}".format(delta))
extra_info += " " + ','.join(to_add)
if extra_info == ";":
atm_dat["extra"] = ""
else:
atm_dat["extra"] = extra_info
print(atm_fmt_str.format(**atm_dat), file=file)
# bond printing
print("\n[ bonds ]", file=file)
bnd_fmt_str = "{atoma:>5} {atomb:>5} {typecode:>5} gb_{typeid} {extra}"
for bond in sorted(mol.GetBonds(), key=lambda x: x.HasType()):
bnd_dat = {
"atoma": bond.GetAtoms()[0].GetIndex() + 1,
"atomb": bond.GetAtoms()[1].GetIndex() + 1,
"typecode": 2,
"typeid": bond.GetType().GetID() if bond.HasType() else "UNMAPPED"
}
if pmol is not None and bond.HasType():
pbond = pmol.GetBond(bond)
other = [
"gb_{}".format(tm.GetID())
for tm in pbond.GetMappedTypeCounts()
]
bnd_dat["extra"] = ", ".join(
x for x in other if x != "gb_{}".format(bnd_dat["typeid"]))
else:
bnd_dat["extra"] = ""
if bnd_dat["extra"]:
bnd_dat["extra"] = "; Other terms: " + bnd_dat["extra"]
print(bnd_fmt_str.format(**bnd_dat), file=file)
# pairs printing
print("\n[ pairs ]", file=file)
pair_fmt_str = "{atoma:>5} {atomb:>5} 1"
for dhd in mol.GetDihedrals():
atoms = dhd.GetAtoms()
if not mol.HasBond(atoms[0], atoms[1]):
continue
if not mol.HasBond(atoms[1], atoms[2]):
continue
if not mol.HasBond(atoms[2], atoms[3]):
continue
if ((mol.GetBond(atoms[0], atoms[1]).GetOrder()
== ix.BondOrder.Aromatic) and (mol.GetBond(
atoms[1], atoms[2]).GetOrder() == ix.BondOrder.Aromatic)
and (mol.GetBond(atoms[2], atoms[3]).GetOrder()
== ix.BondOrder.Aromatic)):
continue
if atoms[0].GetIndex() > atoms[3].GetIndex():
pair_dat = {
"atoma": atoms[3].GetIndex() + 1,
"atomb": atoms[0].GetIndex() + 1
}
else:
pair_dat = {
"atoma": atoms[0].GetIndex() + 1,
"atomb": atoms[3].GetIndex() + 1
}
print(pair_fmt_str.format(**pair_dat), file=file)
# angle printing
print("\n[ angles ]", file=file)
ang_fmt_str = "{atoma:>5} {atomb:>5} {atomc:>5} {typecode:>5} ga_{typeid} {extra}"
for angle in sorted(mol.GetAngles(), key=lambda x: x.HasType()):
atoms = angle.GetAtoms()
ang_dat = {
"atoma": atoms[0].GetIndex() + 1,
"atomb": atoms[1].GetIndex() + 1,
"atomc": atoms[2].GetIndex() + 1,
"typecode": 2,
"typeid":
angle.GetType().GetID() if angle.HasType() else "UNMAPPED",
"extra": ""
}
if pmol is not None and angle.HasType():
pangle = pmol.GetAngle(angle)
other = [
"ga_{}".format(tm.GetID())
for tm in pangle.GetMappedTypeCounts()
]
ang_dat["extra"] = ", ".join(
x for x in other if x != "ga_{}".format(ang_dat["typeid"]))
if ang_dat["extra"]:
ang_dat["extra"] = "; Other terms: " + ang_dat["extra"]
print(ang_fmt_str.format(**ang_dat), file=file)
# dihedral printing
print("\n[ dihedrals ]", file=file)
dhd_fmt_str = "{atoma:>5} {atomb:>5} {atomc:>5} {atomd:>5} {typecode:>5} {typeid} {extra}"
done_dhds = []
for bnd in mol.GetBonds():
dhds = _GetBondDihedrals(bnd)
if not dhds:
continue
param_dhd = [x for x in dhds if x.HasType()]
if not param_dhd:
done_dhds.append(dhds[0])
else:
done_dhds.extend(param_dhd)
for dhd in mol.GetDihedrals():
if dhd.HasType() and dhd not in done_dhds:
done_dhds.append(dhd)
for dhd in sorted(done_dhds, key=lambda x: x.HasType()):
atoms = dhd.GetAtoms()
if not dhd.HasType():
dhd_dat = {
"atoma": atoms[0].GetIndex() + 1,
"atomb": atoms[1].GetIndex() + 1,
"atomc": atoms[2].GetIndex() + 1,
"atomd": atoms[3].GetIndex() + 1,
"extra": "",
"typecode": "",
"typeid": "UNMAPPED"
}
print(dhd_fmt_str.format(**dhd_dat), file=file)
else:
for t in dhd.GetTypes():
dhd_dat = {
"atoma": atoms[0].GetIndex() + 1,
"atomb": atoms[1].GetIndex() + 1,
"atomc": atoms[2].GetIndex() + 1,
"atomd": atoms[3].GetIndex() + 1,
"extra": ""
}
if t.GetType() == ix.DihedralType.Proper:
dhd_dat["typecode"] = 1
dhd_dat["typeid"] = "gd_{}".format(t.GetID())
else:
dhd_dat["typecode"] = 2
dhd_dat["typeid"] = "gi_{}".format(t.GetID())
print(dhd_fmt_str.format(**dhd_dat), file=file)
file.close()
def LoadIFPFile(path):
pt = ix.GetPeriodicTable()
data = list(ix.LoadFile(path.expanduser()))
blocks = [data[0]]
for i in range(len(data) - 1):
if data[i] == 'END':
blocks.append(data[i + 1])
ff = ix.Forcefield(ix.FFFamily.GROMOS, path.stem)
for b in blocks:
start = data.index(b) + 1
end = data[start:].index('END') + start
if b == 'BONDSTRETCHTYPECODE':
ff.ReserveBondTypes(ix.BondType.Harmonic,
int(data[start].split()[0]))
ff.ReserveBondTypes(ix.BondType.Quartic,
int(data[start].split()[0]))
for line in data[start + 1:end]:
idx, kq, kh, b0 = map(float, line.split())
ff.LinkBondTypes(
ff.NewBondType(ix.BondType.Harmonic, int(idx), kh, b0),
ff.NewBondType(ix.BondType.Quartic, int(idx), kq, b0))
elif b == 'BONDANGLEBENDTYPECODE':
ff.ReserveAngleTypes(ix.AngleType.Harmonic,
int(data[start].split()[0]))
ff.ReserveAngleTypes(ix.AngleType.CosineHarmonic,
int(data[start].split()[0]))
for line in data[start + 1:end]:
idx, kch, kh, t0 = map(float, line.split())
ff.LinkAngleTypes(
ff.NewAngleType(ix.AngleType.Harmonic, int(idx), kh, t0),
ff.NewAngleType(ix.AngleType.CosineHarmonic, int(idx), kch,
t0))
elif b == 'IMPDIHEDRALTYPECODE':
ff.ReserveDihedralTypes(ix.DihedralType.Improper,
int(data[start].split()[0]))
for line in data[start + 1:end]:
idx, k, epsilon = map(float, line.split())
ff.NewDihedralType(ix.DihedralType.Improper, int(idx), k,
epsilon)
elif b == 'TORSDIHEDRALTYPECODE':
ff.ReserveDihedralTypes(ix.DihedralType.Proper,
int(data[start].split()[0]))
for line in data[start + 1:end]:
idx, k, phase, m = map(float, line.split())
ff.NewDihedralType(ix.DihedralType.Proper, int(idx), k, phase,
int(m))
elif b == 'SINGLEATOMLJPAIR':
num_lines = int((end - start - 1) / int(data[start]))
atm_count = int(data[start])
ff.ReserveAtomTypes(atm_count)
for i in range(atm_count):
lines = []
for j in range(num_lines):
lines.append(data[start + 1 + j + i * num_lines])
dat = " ".join(x for x in lines).split()
atm_dat = {
'int_code': int(dat[0]),
'name': dat[1],
'c6': float(dat[2])**2,
'c12': [
float(dat[3])**2,
float(dat[4])**2,
float(dat[5])**2,
],
'c6_1_4': float(dat[6])**2,
'c12_1_4': float(dat[7])**2,
'interactions': dict(),
}
ff.NewAtomType(int(dat[0]), dat[1], pt[dat[1][0]])
return ff
def SaveRTPFile(path, mol, pmol=None):
print("Saving molecule %s to RTP file at path %s." %
(mol.GetName(), str(os.path.join(os.getcwd(), path))))
path = Path(path)
h_mass = ix.GetPeriodicTable()["H"].GetAtomicMass()
path.parent.mkdir(parents=True, exist_ok=True)
file = path.open('w')
# header printing
header = """; File generated by the indigox package
; No guarantees are provided for the usefulness of this file
[ {} ]
[ atoms ]"""
print(header.format(mol.GetAtoms()[0].GetResidueName()), file=file)
# atom printing
atm_fmt_str = "{name:>5} {type:>6} {charge:>11.5f} {chargegroup:>5} {extra}"
for atom in mol.GetAtoms():
atm_dat = {
"type": atom.GetType().GetName() if atom.HasType() else "%%%",
"name": atom.GetName(),
"chargegroup": atom.GetChargeGroupID() + 1,
"charge": atom.GetPartialCharge(),
"extra": ""
}
if pmol is not None:
patom = pmol.GetAtom(atom)
extra_info = ";"
if not len(patom.GetMappedCharges()):
extra_info += " UNMAPPED"
else:
mu = patom.MeanCharge()
eta = patom.MedianCharge()
sigma = patom.StandardDeviationCharge()
delta = patom.RedistributedChargeAdded()
to_add = []
if round(mu, 5) != round(eta, 5) or round(sigma, 5) != 0.0:
to_add.append("mean: {:.5f}".format(mu))
to_add.append("median: {:.5f}".format(eta))
to_add.append("stdev: {:.5f}".format(sigma))
if round(delta, 5) != 0.0:
to_add.append("added: {:.5f}".format(delta))
extra_info += " " + ", ".join(to_add)
if extra_info == ";":
atm_dat["extra"] = ""
else:
atm_dat["extra"] = extra_info
print(atm_fmt_str.format(**atm_dat), file=file)
# bond printing
print(" [ bonds ]", file=file)
bnd_fmt_str = "{atoma:>5} {atomb:>5} {typeid} {extra}"
for bond in sorted(mol.GetBonds(), key=lambda x: x.HasType()):
bnd_dat = {
"atoma": bond.GetAtoms()[0].GetName(),
"atomb": bond.GetAtoms()[1].GetName(),
"extra": ""
}
if not bond.HasType(): bnd_dat["typeid"] = "UNMAPPED"
else:
t = bond.GetType()
if t.GetType() != ix.BondType.Quartic: t = t.GetLinkedType()
bnd_dat["typeid"] = "{:>.4f} {:>.4e}".format(
t.GetIdealLength(), t.GetForceConstant())
if pmol is not None and bond.HasType():
pbond = pmol.GetBond(bond)
other = [
"gb_{}".format(tm.GetID())
for tm in pbond.GetMappedTypeCounts()
]
bnd_dat["extra"] = ", ".join(
x for x in other
if x != "gb_{}".format(bond.GetType().GetID()))
else:
bnd_dat["extra"] = ""
if bnd_dat["extra"]:
bnd_dat["extra"] = "; Other terms: " + bnd_dat["extra"]
print(bnd_fmt_str.format(**bnd_dat), file=file)
# exclusions printing
print(" [ exclusions ]", file=file)
pair_fmt_str = "{atoma:>5} {atomb:>5}"
for dhd in mol.GetDihedrals():
atoms = dhd.GetAtoms()
if not mol.HasBond(atoms[0], atoms[1]):
continue
if not mol.HasBond(atoms[1], atoms[2]):
continue
if not mol.HasBond(atoms[2], atoms[3]):
continue
rot_bond = mol.GetBond(atoms[1], atoms[2])
if rot_bond.GetOrder() == ix.BondOrder.Aromatic:
pair_dat = {
"atoma": atoms[3].GetName(),
"atomb": atoms[0].GetName()
}
print(pair_fmt_str.format(**pair_dat), file=file)
# angle printing
print(" [ angles ]", file=file)
ang_fmt_str = "{atoma:>5} {atomb:>5} {atomc:>5} {typeid} {extra}"
for angle in sorted(mol.GetAngles(), key=lambda x: x.HasType()):
atoms = angle.GetAtoms()
ang_dat = {
"atoma": atoms[0].GetName(),
"atomb": atoms[1].GetName(),
"atomc": atoms[2].GetName(),
"extra": ""
}
if not angle.HasType(): ang_dat["typeid"] = "UNMAPPED"
else:
t = angle.GetType()
if t.GetType() != ix.AngleType.CosineHarmonic:
t = t.GetLinkedType()
ang_dat["typeid"] = "{:>.2f} {:>.2f}".format(
t.GetIdealAngle(), t.GetForceConstant())
if pmol is not None and angle.HasType():
pangle = pmol.GetAngle(angle)
other = [
"ga_{}".format(tm.GetID())
for tm in pangle.GetMappedTypeCounts()
]
ang_dat["extra"] = ", ".join(
x for x in other
if x != "ga_{}".format(angle.GetType().GetID()))
if ang_dat["extra"]:
ang_dat["extra"] = "; Other terms: " + ang_dat["extra"]
print(ang_fmt_str.format(**ang_dat), file=file)
# improper printing
done_dhds = []
print(" [ impropers ]", file=file)
dhd_fmt_str = "{atoma:>5} {atomb:>5} {atomc:>5} {atomd:>5} {typeid} {extra}"
for imp in mol.GetDihedrals():
if not imp.HasType(): continue
for t in imp.GetTypes():
if t.GetType() != ix.DihedralType.Improper: continue
atoms = imp.GetAtoms()
imp_dat = {
"atoma":
atoms[0].GetName(),
"atomb":
atoms[1].GetName(),
"atomc":
atoms[2].GetName(),
"atomd":
atoms[3].GetName(),
"typeid":
"{:>.5f} {:>.5f}".format(
t.GetIdealAngle(),
t.GetForceConstant() * improper_correction),
"extra":
""
}
print(dhd_fmt_str.format(**imp_dat), file=file)
# dihedral printing
print(" [ dihedrals ]", file=file)
for bnd in mol.GetBonds():
dhds = _GetBondDihedrals(bnd)
if not dhds: continue
param_dhd = [x for x in dhds if x.HasType()]
if not param_dhd: done_dhds.append(dhds[0])
else: done_dhds.extend(param_dhd)
for dhd in mol.GetDihedrals():
if dhd.HasType() and dhd not in done_dhds: done_dhds.append(dhd)
for dhd in sorted(done_dhds, key=lambda x: x.HasType()):
atoms = dhd.GetAtoms()
if not dhd.HasType():
dhd_dat = {
"atoma": atoms[0].GetName(),
"atomb": atoms[1].GetName(),
"atomc": atoms[2].GetName(),
"atomd": atoms[3].GetName(),
"extra": "",
"typeid": "UNMAPPED"
}
print(dhd_fmt_str.format(**dhd_dat), file=file)
else:
for t in dhd.GetTypes():
dhd_dat = {
"atoma": atoms[0].GetName(),
"atomb": atoms[1].GetName(),
"atomc": atoms[2].GetName(),
"atomd": atoms[3].GetName(),
"extra": ""
}
if t.GetType() == ix.DihedralType.Proper:
dhd_dat["typeid"] = "{:.4f} {:.4f} {}".format(
t.GetPhaseShift(), t.GetForceConstant(),
t.GetMultiplicity())
print(dhd_fmt_str.format(**dhd_dat), file=file)
file.close()