def testReadingMassDifferenceInMolfiles(self):
"""Previously we were rounding incorrectly when reading the mass diff"""
template = """
OpenBabel02181811152D
1 0 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 %2s %2d 0 0 0 0 0 0 0 0 0 0 0
M END
"""
# Positive test cases:
# These are the BIOVIA Draw answers for the first 50 elements for
# a mass diff of 1
answers = [2,5,8,10,12,13,15,17,20,21,24,25,28,29,32,33,36,41,40,41,46,49,52,53,56,57,60,60,65,66,71,74,76,80,81,85,86,89,90,92,94,97,99,102,104,107,109,113,116,120,123]
for idx, answer in enumerate(answers):
elem = idx + 1
molfile = template % (ob.GetSymbol(elem), 1)
mol = pybel.readstring("mol", molfile).OBMol
iso = mol.GetAtom(1).GetIsotope()
self.assertEqual(answer, iso)
# Also test D and T - BIOVIA Draw ignores the mass diff
for elem, answer in zip("DT", [2, 3]):
molfile = template % (elem, 1)
mol = pybel.readstring("mol", molfile).OBMol
iso = mol.GetAtom(1).GetIsotope()
self.assertEqual(answer, iso)
# Negative test cases:
# Test error message for out-of-range values
for value in [5, -4]:
molfile = template % ("C", value)
mol = pybel.readstring("mol", molfile).OBMol
iso = mol.GetAtom(1).GetIsotope()
self.assertEqual(0, iso)
def testWhetherAllElementsAreSupported(self):
"""Check whether a new element has been correctly added"""
N = 0
while ob.GetSymbol(N+1):
N += 1
# Is the symbol parsed?
symbol = ob.GetSymbol(N)
self.assertEqual(N, ob.GetAtomicNum(symbol))
# Has an exact mass been set?
self.assertNotEqual(0.0, ob.GetExactMass(N))
# Has the symbol been added to the SMILES parser?
numatoms = pybel.readstring("smi", "[%s]" % symbol).OBMol.NumAtoms()
self.assertEqual(numatoms, 1)
# Check whether the element is available as a constant
self.assertEqual(N, getattr(ob, ob.GetName(N)))
self.assertTrue(N > 100)
def read_txt_to_mol(txtfile):
# lists to store the charges and LJ parameters
q = []
eps = []
sig = []
# convert the .txt to a .xyz to read in pybel mol to perceive all the bonds, angles, dihedrals..
fd, temp_path = tempfile.mkstemp(suffix=".xyz")
fxyz = os.fdopen(fd, 'w')
# table to convert atomic number to symbols
if not ob3:
etab = openbabel.OBElementTable()
with open(txtfile, 'r') as f:
line = f.readline()
combrule = line.strip()
line = f.readline()
if int(line.strip()) != 1:
print(
"Your .txt should have only one molecule, the one present in the .dfr"
)
sys.exit(0)
line = f.readline()
natoms = int(line.split()[0])
# write .xyz header
fxyz.write("%d\nGenerated from %s\n" % (natoms, txtfile))
for i in range(natoms):
# write the atomic symbol and coordinates
line = f.readline()
atnum = int(line.split()[1])
x, y, z = [float(x) for x in line.split()[2:5]]
if ob3:
fxyz.write("%s\t%f\t%f\t%f\n" %
(openbabel.GetSymbol(atnum), x, y, z))
else:
fxyz.write("%s\t%f\t%f\t%f\n" %
(etab.GetSymbol(atnum), x, y, z))
# store the parameters
qv, epsv, sigv = [float(x) for x in line.split()[5:]]
q.append(qv)
eps.append(epsv)
sig.append(sigv)
fxyz.close()
# read filel to a mol, remove temp and return
mol = pybel.readfile("xyz", temp_path).__next__()
os.remove(temp_path)
return mol, q, eps, sig
def get_mol_info(mol):
# table to convert atomic number to symbols
if not ob3:
etab = openbabel.OBElementTable()
q_atoms = []
q_all = []
for atom in mol:
if ob3:
q_atoms.append(openbabel.GetSymbol(atom.atomicnum))
else:
q_atoms.append(etab.GetSymbol(atom.atomicnum))
q_all.append(atom.coords)
return np.asarray(q_atoms), np.asarray(q_all)
def itp_from_params(mol, q, eps, sig, dfrBonds, dfrAngles, dfrDihedrals,
dfrImpDih):
# table to convert atomic number to symbols
if not ob3:
etab = openbabel.OBElementTable()
# !!! units are converted as the reverse of: http://chembytes.wikidot.com/oplsaagro2tnk and based on GROMACS manual
# write header
fcontent = """
;
; Generated by dice2gromacs
; https://github.com/hmcezar/dicetools
;
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
"""
# write the atomtypes
for i, atom in enumerate(mol.atoms):
if ob3:
fcontent += "att_%03d %s%03d %7.4f 0.000 A %.5e %.5e\n" % (
i + 1, openbabel.GetSymbol(atom.atomicnum), i + 1,
atom.atomicmass, a2nm(sig[i]), cal2j(eps[i]))
else:
fcontent += "att_%03d %s%03d %7.4f 0.000 A %.5e %.5e\n" % (
i + 1, etab.GetSymbol(atom.atomicnum), i + 1, atom.atomicmass,
a2nm(sig[i]), cal2j(eps[i]))
fcontent += """
[ moleculetype ]
;name nrexcl
UNL 3
[ atoms ]
; nr type resi res atom cgnr charge mass
"""
# write the atoms
for i, atom in enumerate(mol.atoms):
if ob3:
fcontent += "%6d att_%03d 1 UNL %s%03d 1 %.4f %7.4f\n" % (
i + 1, i + 1, openbabel.GetSymbol(
atom.atomicnum), i + 1, q[i], atom.atomicmass)
else:
fcontent += "%6d att_%03d 1 UNL %s%03d 1 %.4f %7.4f\n" % (
i + 1, i + 1, etab.GetSymbol(
atom.atomicnum), i + 1, q[i], atom.atomicmass)
# write the bonds
fcontent += """
[ bonds ]
; ai aj funct r k
"""
for bnd in dfrBonds:
ai, aj = [int(x) for x in bnd.split()]
fcontent += "%6d %6d 1 %.4f %.4f\n" % (
ai, aj, a2nm(dfrBonds[bnd][1]), cal2j(dfrBonds[bnd][0]) * 200.0)
# write the angles
fcontent += """
[ angles ]
; ai aj ak funct theta cth
"""
for ang in dfrAngles:
ai, aj, ak = [int(x) for x in ang.split()]
fcontent += "%6d %6d %6d 1 %.4f %.4f\n" % (
ai, aj, ak, dfrAngles[ang][1], cal2j(dfrAngles[ang][0]) * 2.0)
# write the proper dihedrals
fcontent += """
[ dihedrals ]
; proper dihedrals - converted to the RB form from Fourier type if OPLS
; ai aj ak al func params
"""
fimp = ""
for dih in dfrDihedrals:
ai, aj, ak, al = [int(x) for x in dih.split()]
if dfrDihedrals[dih][0].lower() == "amber":
# check if it's a proper or improper dihedral
bondIterator = openbabel.OBMolBondIter(mol.OBMol)
cnt = 0
for bond in bondIterator:
if ((ai == bond.GetBeginAtom().GetId() + 1) and
(aj == bond.GetEndAtom().GetId() + 1)) or (
(aj == bond.GetBeginAtom().GetId() + 1) and
(ai == bond.GetEndAtom().GetId() + 1)):
cnt += 1
elif ((aj == bond.GetBeginAtom().GetId() + 1) and
(ak == bond.GetEndAtom().GetId() + 1)) or (
(ak == bond.GetBeginAtom().GetId() + 1) and
(aj == bond.GetEndAtom().GetId() + 1)):
cnt += 1
elif ((ak == bond.GetBeginAtom().GetId() + 1) and
(al == bond.GetEndAtom().GetId() + 1)) or (
(al == bond.GetBeginAtom().GetId() + 1) and
(ak == bond.GetEndAtom().GetId() + 1)):
cnt += 1
if cnt == 3:
func = 9
fparam = [
cal2j(float(x)) / 2.0 for x in dfrDihedrals[dih][1:4]
]
for i, term in enumerate(fparam, 1):
if term != 0.0:
fcontent += "%6d %6d %6d %6d %1d %6.2f %9.5f %d\n" % (
ai, aj, ak, al, func,
float(dfrDihedrals[dih][i + 3]), term, i)
else:
func = 4
fparam = [
cal2j(float(x)) / 2.0 for x in dfrDihedrals[dih][1:4]
]
for i, term in enumerate(fparam, 1):
if term != 0.0:
fimp += "%6d %6d %6d %6d %1d %6.2f %9.5f %d\n" % (
ai, aj, ak, al, func,
float(dfrDihedrals[dih][i + 3]), term, i)
elif dfrDihedrals[dih][0].lower() == "opls":
fparam = [cal2j(float(x)) for x in dfrDihedrals[dih][1:4]]
c0 = fparam[1] + 0.5 * (fparam[0] + fparam[2])
c1 = 0.5 * (-fparam[0] + 3.0 * fparam[2])
c2 = -fparam[1]
c3 = -2.0 * fparam[2]
c4 = 0.0
c5 = 0.0
fcontent += "%6d %6d %6d %6d 3 %9.5f %9.5f %9.5f %9.5f %9.5f %9.5f\n" % (
ai, aj, ak, al, c0, c1, c2, c3, c4, c5)
else:
print(
"Error: Dihedral type (%s) found for dihedral %s in .dfr is not valid."
% (dfrDihedrals[dih][0], dih))
sys.exit(0)
# write the improper dihedrals
if fimp or dfrImpDih:
fcontent += """
[ dihedrals ]
; improper dihedrals
; ai aj ak al func params
"""
if fimp:
fcontent += fimp
for idih in dfrImpDih:
ai, aj, ak, al = [int(x) for x in idih.split()]
fcontent += "%6d %6d %6d %6d 4 %6.2f %9.5f %d\n" % (
ai, aj, ak, al, float(
dfrImpDih[idih][1]), cal2j(float(dfrImpDih[idih][0])), 2)
# write the pairs
fcontent += """
[ pairs ]
"""
pairs = get_pairs(mol)
for pair in pairs:
ai, aj = [int(x) for x in pair.split()]
fcontent += "%6d %6d 1\n" % (ai, aj)
return fcontent
def parse_mol_info(fname, fcharges, axis, buffa, buffo, pbcbonds, printdih,
ignorebonds, ignoreimproper):
iaxis = {"x": 0, "y": 1, "z": 2}
if axis in iaxis:
repaxis = iaxis[axis]
else:
print("Error: invalid axis")
sys.exit(0)
if fcharges:
chargesLabel = {}
with open(fcharges, "r") as f:
for line in f:
chargesLabel[line.split()[0]] = float(line.split()[1])
# set openbabel file format
base, ext = os.path.splitext(fname)
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats(ext[1:], "xyz")
# trick to disable ring perception and make the ReadFile waaaay faster
# Source: https://sourceforge.net/p/openbabel/mailman/openbabel-discuss/thread/56e1812d-396a-db7c-096d-d378a077853f%40ipcms.unistra.fr/#msg36225392
obConversion.AddOption("b", openbabel.OBConversion.INOPTIONS)
# read molecule to OBMol object
mol = openbabel.OBMol()
obConversion.ReadFile(mol, fname)
mol.ConnectTheDots() # necessary because of the 'b' INOPTION
# split the molecules
molecules = mol.Separate()
# detect the molecules types
mTypes = {}
mapmTypes = {}
atomIdToMol = {}
nty = 0
for i, submol in enumerate(molecules, start=1):
atomiter = openbabel.OBMolAtomIter(submol)
atlist = []
for at in atomiter:
atlist.append(at.GetAtomicNum())
atomIdToMol[at.GetId()] = i
foundType = None
for ty in mTypes:
# check if there's already a molecule of this type
if atlist == mTypes[ty]:
foundType = ty
# if not, create a new type
if not foundType:
nty += 1
foundType = nty
mTypes[nty] = atlist
mapmTypes[i] = foundType
# get atomic labels from pdb
idToAtomicLabel = {}
if ext[1:] == "pdb":
for res in openbabel.OBResidueIter(mol):
for atom in openbabel.OBResidueAtomIter(res):
if (atomIdToMol[atom.GetId()] > 1) and (len(mTypes) > 1):
idToAtomicLabel[
atom.GetId()] = res.GetAtomID(atom).strip() + str(
mapmTypes[atomIdToMol[atom.GetId()]])
else:
idToAtomicLabel[atom.GetId()] = res.GetAtomID(atom).strip()
else:
if not ob3:
etab = openbabel.OBElementTable()
for atom in openbabel.OBMolAtomIter(mol):
if (atomIdToMol[atom.GetId()] > 1) and (len(mTypes) > 1):
if ob3:
idToAtomicLabel[atom.GetId()] = openbabel.GetSymbol(
atom.GetAtomicNum()) + str(
mapmTypes[atomIdToMol[atom.GetId()]])
else:
idToAtomicLabel[atom.GetId()] = etab.GetSymbol(
atom.GetAtomicNum()) + str(
mapmTypes[atomIdToMol[atom.GetId()]])
else:
if ob3:
idToAtomicLabel[atom.GetId()] = openbabel.GetSymbol(
atom.GetAtomicNum())
else:
idToAtomicLabel[atom.GetId()] = etab.GetSymbol(
atom.GetAtomicNum())
# print(idToAtomicLabel)
# identify atom types and get masses
outMasses = "Masses\n\n"
massTypes = {}
mapTypes = {}
nmassTypes = 0
atomIterator = openbabel.OBMolAtomIter(mol)
for atom in atomIterator:
i = atom.GetId()
if idToAtomicLabel[i] not in massTypes:
nmassTypes += 1
mapTypes[nmassTypes] = idToAtomicLabel[i]
massTypes[idToAtomicLabel[i]] = nmassTypes
outMasses += "\t%d\t%.3f\t# %s\n" % (
nmassTypes, atom.GetAtomicMass(), idToAtomicLabel[i])
# create atoms list
outAtoms = "Atoms # full\n\n"
xmin = float("inf")
xmax = float("-inf")
ymin = float("inf")
ymax = float("-inf")
zmin = float("inf")
zmax = float("-inf")
natoms = 0
acoords = []
for mnum, imol in enumerate(molecules, start=1):
atomIterator = openbabel.OBMolAtomIter(imol)
for atom in sorted(atomIterator, key=lambda x: x.GetId()):
natoms += 1
i = atom.GetId()
apos = (atom.GetX(), atom.GetY(), atom.GetZ())
acoords.append(Atom(atom.GetAtomicNum(), apos))
# look for the maximum and minimum x for the box (improve later with numpy and all coordinates)
if apos[0] > xmax:
xmax = apos[0]
if apos[0] < xmin:
xmin = apos[0]
if apos[1] > ymax:
ymax = apos[1]
if apos[1] < ymin:
ymin = apos[1]
if apos[2] > zmax:
zmax = apos[2]
if apos[2] < zmin:
zmin = apos[2]
if fcharges:
outAtoms += "\t%d\t%d\t%d\t%.6f\t%.4f\t%.4f\t%.4f\t# %s\n" % (
i + 1, mnum, massTypes[idToAtomicLabel[i]],
chargesLabel[idToAtomicLabel[i]], atom.GetX(), atom.GetY(),
atom.GetZ(), idToAtomicLabel[i])
else:
outAtoms += "\t%d\t%d\t%d\tX.XXXXXX\t%.4f\t%.4f\t%.4f\t# %s\n" % (
i + 1, mnum, massTypes[idToAtomicLabel[i]], atom.GetX(),
atom.GetY(), atom.GetZ(), idToAtomicLabel[i])
# define box shape and size
try:
fromBounds = False
rcell = mol.GetData(12)
cell = openbabel.toUnitCell(rcell)
v1 = [
cell.GetCellVectors()[0].GetX(),
cell.GetCellVectors()[0].GetY(),
cell.GetCellVectors()[0].GetZ()
]
v2 = [
cell.GetCellVectors()[1].GetX(),
cell.GetCellVectors()[1].GetY(),
cell.GetCellVectors()[1].GetZ()
]
v3 = [
cell.GetCellVectors()[2].GetX(),
cell.GetCellVectors()[2].GetY(),
cell.GetCellVectors()[2].GetZ()
]
boxinfo = [v1, v2, v3]
orthogonal = True
for i, array in enumerate(boxinfo):
for j in range(3):
if i == j:
continue
if not math.isclose(0., array[j], abs_tol=1e-6):
orthogonal = False
except:
fromBounds = True
v1 = [xmax - xmin, 0., 0.]
v2 = [0., ymax - ymin, 0.]
v3 = [0., 0., zmax - zmin]
orthogonal = True
# add buffer
if orthogonal:
buf = []
boxinfo = [v1, v2, v3]
for i, val in enumerate(boxinfo[repaxis]):
if i == repaxis:
buf.append(val + buffa)
else:
buf.append(val)
boxinfo[repaxis] = buf
for i in range(3):
if i == repaxis:
continue
buf = []
for j, val in enumerate(boxinfo[i]):
if j == i:
buf.append(val + buffo)
else:
buf.append(val)
boxinfo[i] = buf
# print(boxinfo)
# Duplicate to get the bonds in the PBC. Taken from (method _crd2bond):
# https://github.com/tongzhugroup/mddatasetbuilder/blob/66eb0f15e972be0f5534dcda27af253cd8891ff2/mddatasetbuilder/detect.py#L213
if pbcbonds:
acoords = Atoms(acoords, cell=boxinfo, pbc=True)
repatoms = acoords.repeat(
2
)[natoms:] # repeat the unit cell in each direction (len(repatoms) = 7*natoms)
tree = cKDTree(acoords.get_positions())
d = tree.query(repatoms.get_positions(), k=1)[0]
nearest = d < 8.
ghost_atoms = repatoms[nearest]
realnumber = np.where(nearest)[0] % natoms
acoords += ghost_atoms
write("replicated.xyz",
acoords) # write the structure with the replicated atoms
# write new mol with new bonds
nmol = openbabel.OBMol()
nmol.BeginModify()
for idx, (num, position) in enumerate(
zip(acoords.get_atomic_numbers(), acoords.positions)):
a = nmol.NewAtom(idx)
a.SetAtomicNum(int(num))
a.SetVector(*position)
nmol.ConnectTheDots()
# nmol.PerceiveBondOrders() # super slow becauses it looks for rings
nmol.EndModify()
else:
acoords = Atoms(acoords, cell=boxinfo, pbc=False)
nmol = openbabel.OBMol()
nmol.BeginModify()
for idx, (num, position) in enumerate(
zip(acoords.get_atomic_numbers(), acoords.positions)):
a = nmol.NewAtom(idx)
a.SetAtomicNum(int(num))
a.SetVector(*position)
nmol.ConnectTheDots()
# nmol.PerceiveBondOrders() # super slow becauses it looks for rings
nmol.EndModify()
# identify bond types and create bond list
outBonds = "Bonds # harmonic\n\n"
bondTypes = {}
mapbTypes = {}
nbondTypes = 0
nbonds = 0
bondsToDelete = []
bondIterators = []
if ignorebonds:
sepmols = nmol.Separate()
for smol in sepmols[1:]:
bondIterators.append(openbabel.OBMolBondIter(smol))
else:
bondIterators.append(openbabel.OBMolBondIter(nmol))
lastidx = 1
for iterator in bondIterators:
for i, bond in enumerate(iterator, lastidx):
b1 = bond.GetBeginAtom().GetId()
b2 = bond.GetEndAtom().GetId()
# check if its a bond of the replica only
if (b1 >= natoms) and (b2 >= natoms):
bondsToDelete.append(bond)
continue
# remap to a real atom if needed
if b1 >= natoms:
b1 = realnumber[b1 - natoms]
if b2 >= natoms:
b2 = realnumber[b2 - natoms]
# identify bond type
btype1 = "%s - %s" % (idToAtomicLabel[b1], idToAtomicLabel[b2])
btype2 = "%s - %s" % (idToAtomicLabel[b2], idToAtomicLabel[b1])
if btype1 in bondTypes:
bondid = bondTypes[btype1]
bstring = btype1
elif btype2 in bondTypes:
bondid = bondTypes[btype2]
bstring = btype2
else:
nbondTypes += 1
mapbTypes[nbondTypes] = btype1
bondid = nbondTypes
bondTypes[btype1] = nbondTypes
bstring = btype1
nbonds += 1
outBonds += "\t%d\t%d\t%d\t%d\t# %s\n" % (nbonds, bondid, b1 + 1,
b2 + 1, bstring)
lastidx = i
# delete the bonds of atoms from other replicas
for bond in bondsToDelete:
nmol.DeleteBond(bond)
# identify angle types and create angle list
angleTypes = {}
mapaTypes = {}
nangleTypes = 0
nangles = 0
angleIterators = []
if ignorebonds:
sepmols = nmol.Separate()
for smol in sepmols[1:]:
smol.FindAngles()
angleIterators.append(openbabel.OBMolAngleIter(smol))
prevnumatoms = sepmols[0].NumAtoms()
else:
nmol.FindAngles()
angleIterators.append(openbabel.OBMolAngleIter(nmol))
outAngles = "Angles # harmonic\n\n"
lastidx = 1
for j, iterator in enumerate(angleIterators, 1):
for i, angle in enumerate(iterator, lastidx):
if ignorebonds:
a1 = angle[1] + prevnumatoms
a2 = angle[0] + prevnumatoms
a3 = angle[2] + prevnumatoms
else:
a1 = angle[1]
a2 = angle[0]
a3 = angle[2]
# remap to a real atom if needed
if a1 >= natoms:
a1 = realnumber[a1 - natoms]
if a2 >= natoms:
a2 = realnumber[a2 - natoms]
if a3 >= natoms:
a3 = realnumber[a3 - natoms]
atype1 = "%s - %s - %s" % (
idToAtomicLabel[a1], idToAtomicLabel[a2], idToAtomicLabel[a3])
atype2 = "%s - %s - %s" % (
idToAtomicLabel[a3], idToAtomicLabel[a2], idToAtomicLabel[a1])
if atype1 in angleTypes:
angleid = angleTypes[atype1]
astring = atype1
elif atype2 in angleTypes:
angleid = angleTypes[atype2]
astring = atype2
else:
nangleTypes += 1
mapaTypes[nangleTypes] = atype1
angleid = nangleTypes
angleTypes[atype1] = nangleTypes
astring = atype1
nangles += 1
outAngles += "\t%d\t%d\t%d\t%d\t%d\t# %s\n" % (
nangles, angleid, a1 + 1, a2 + 1, a3 + 1, astring)
lastidx = i
if ignorebonds:
prevnumatoms += sepmols[j].NumAtoms()
# identify dihedral types and create dihedral list
if printdih:
dihedralTypes = {}
mapdTypes = {}
ndihedralTypes = 0
ndihedrals = 0
dihedralIterators = []
if ignorebonds:
sepmols = nmol.Separate()
for smol in sepmols[1:]:
smol.FindTorsions()
dihedralIterators.append(openbabel.OBMolTorsionIter(smol))
else:
nmol.FindTorsions()
dihedralIterators.append(openbabel.OBMolTorsionIter(nmol))
outDihedrals = "Dihedrals # charmmfsw\n\n"
lastidx = 1
for iterator in dihedralIterators:
for i, dihedral in enumerate(iterator, lastidx):
a1 = dihedral[0]
a2 = dihedral[1]
a3 = dihedral[2]
a4 = dihedral[3]
# remap to a real atom if needed
if a1 >= natoms:
a1 = realnumber[a1 - natoms]
if a2 >= natoms:
a2 = realnumber[a2 - natoms]
if a3 >= natoms:
a3 = realnumber[a3 - natoms]
if a4 >= natoms:
a4 = realnumber[a4 - natoms]
dtype1 = "%s - %s - %s - %s" % (
idToAtomicLabel[a1], idToAtomicLabel[a2],
idToAtomicLabel[a3], idToAtomicLabel[a4])
dtype2 = "%s - %s - %s - %s" % (
idToAtomicLabel[a4], idToAtomicLabel[a3],
idToAtomicLabel[a2], idToAtomicLabel[a1])
if dtype1 in dihedralTypes:
dihedralid = dihedralTypes[dtype1]
dstring = dtype1
elif dtype2 in dihedralTypes:
dihedralid = dihedralTypes[dtype2]
dstring = dtype2
else:
ndihedralTypes += 1
mapdTypes[ndihedralTypes] = dtype1
dihedralid = ndihedralTypes
dihedralTypes[dtype1] = ndihedralTypes
dstring = dtype1
ndihedrals += 1
outDihedrals += "\t%d\t%d\t%d\t%d\t%d\t%d\t# %s\n" % (
ndihedrals, dihedralid, a1 + 1, a2 + 1, a3 + 1, a4 + 1,
dstring)
lastidx = i
if not ignoreimproper:
# look for the improper dihedrals
improperDihedralTypes = {}
mapiDTypes = {}
niDihedralTypes = 0
niDihedrals = 0
mollist = []
if ignorebonds:
sepmols = nmol.Separate()
for smol in sepmols[1:]:
smol.PerceiveBondOrders()
mollist.append(smol)
else:
nmol.PerceiveBondOrders()
mollist.append(nmol)
outImpropers = "Impropers # harmonic\n\n"
for imol in mollist:
atomIterator = openbabel.OBMolAtomIter(imol)
for atom in atomIterator:
try:
# print(atom.GetHyb(), atom.GetAtomicNum(), atom.GetValence())
expDegree = atom.GetValence()
except:
# print(atom.GetHyb(), atom.GetAtomicNum(), atom.GetExplicitDegree())
expDegree = atom.GetExplicitDegree()
# returns impropers for atoms with connected to other 3 atoms and SP2 hybridization
if atom.GetHyb() == 2 and expDegree == 3:
connectedAtoms = []
for atom2, depth in openbabel.OBMolAtomBFSIter(
imol,
atom.GetId() + 1):
if depth == 2:
connectedAtoms.append(atom2)
torsional = [
atom.GetId() + 1, connectedAtoms[0].GetId() + 1,
connectedAtoms[1].GetId() + 1,
connectedAtoms[2].GetId() + 1
]
a1 = torsional[0] - 1
a2 = torsional[1] - 1
a3 = torsional[2] - 1
a4 = torsional[3] - 1
# remap to a real atom if needed
if a1 >= natoms:
a1 = realnumber[a1 - natoms]
if a2 >= natoms:
a2 = realnumber[a2 - natoms]
if a3 >= natoms:
a3 = realnumber[a3 - natoms]
if a4 >= natoms:
a4 = realnumber[a4 - natoms]
dtype1 = "%s - %s - %s - %s" % (
idToAtomicLabel[a1], idToAtomicLabel[a2],
idToAtomicLabel[a3], idToAtomicLabel[a4])
dtype2 = "%s - %s - %s - %s" % (
idToAtomicLabel[a4], idToAtomicLabel[a3],
idToAtomicLabel[a2], idToAtomicLabel[a1])
if dtype1 in improperDihedralTypes:
idihedralid = improperDihedralTypes[dtype1]
dstring = dtype1
elif dtype2 in improperDihedralTypes:
idihedralid = improperDihedralTypes[dtype2]
dstring = dtype2
else:
niDihedralTypes += 1
mapiDTypes[niDihedralTypes] = dtype1
idihedralid = niDihedralTypes
improperDihedralTypes[dtype1] = niDihedralTypes
dstring = dtype1
niDihedrals += 1
outImpropers += "\t%d\t%d\t%d\t%d\t%d\t%d\t# %s\n" % (
niDihedrals, idihedralid, a1 + 1, a2 + 1, a3 + 1,
a4 + 1, dstring)
# print header
if printdih and (ndihedrals > 0):
if ignoreimproper or (niDihedrals == 0):
header = "LAMMPS topology created from %s using pdb2lmp.py - By Henrique Musseli Cezar, 2020\n\n\t%d atoms\n\t%d bonds\n\t%d angles\n\t%d dihedrals\n\n\t%d atom types\n\t%d bond types\n\t%d angle types\n\t%d dihedral types\n\n" % (
fname, natoms, nbonds, nangles, ndihedrals, nmassTypes,
nbondTypes, nangleTypes, ndihedralTypes)
else:
header = "LAMMPS topology created from %s using pdb2lmp.py - By Henrique Musseli Cezar, 2020\n\n\t%d atoms\n\t%d bonds\n\t%d angles\n\t%d dihedrals\n\t%d impropers\n\n\t%d atom types\n\t%d bond types\n\t%d angle types\n\t%d dihedral types\n\t%d improper types\n\n" % (
fname, natoms, nbonds, nangles, ndihedrals, niDihedrals,
nmassTypes, nbondTypes, nangleTypes, ndihedralTypes,
niDihedralTypes)
else:
header = "LAMMPS topology created from %s using pdb2lmp.py - By Henrique Musseli Cezar, 2020\n\n\t%d atoms\n\t%d bonds\n\t%d angles\n\n\t%d atom types\n\t%d bond types\n\t%d angle types\n\n" % (
fname, natoms, nbonds, nangles, nmassTypes, nbondTypes,
nangleTypes)
# add box info
if fromBounds:
boxsize = [(xmin, xmax), (ymin, ymax), (zmin, zmax)]
boxsize[repaxis] = (boxsize[repaxis][0] - buffa / 2.,
boxsize[repaxis][1] + buffa / 2.)
for i in range(3):
if i == repaxis:
continue
boxsize[i] = (boxsize[i][0] - buffo / 2.,
boxsize[i][1] + buffo / 2.)
header += "\t%.8f\t%.8f\t xlo xhi\n\t%.8f\t%.8f\t ylo yhi\n\t%.8f\t%.8f\t zlo zhi\n" % (
boxsize[0][0], boxsize[0][1], boxsize[1][0], boxsize[1][1],
boxsize[2][0], boxsize[2][1])
else:
if orthogonal:
header += "\t%.8f\t%.8f\t xlo xhi\n\t%.8f\t%.8f\t ylo yhi\n\t%.8f\t%.8f\t zlo zhi\n" % (
0., boxinfo[0][0], 0., boxinfo[1][1], 0., boxinfo[2][2])
else:
header += "\t%.8f\t%.8f\t xlo xhi\n\t%.8f\t%.8f\t ylo yhi\n\t%.8f\t%.8f\t zlo zhi\n\t%.8f\t%.8f\t%.8f\t xy xz yz\n" % (
0., boxinfo[0][0], 0., boxinfo[1][1], 0., boxinfo[2][2],
boxinfo[1][0], boxinfo[2][0], boxinfo[2][1])
# print Coeffs
outCoeffs = "Pair Coeffs\n\n"
for i in range(1, nmassTypes + 1):
outCoeffs += "\t%d\teps\tsig\t# %s\n" % (i, mapTypes[i])
outCoeffs += "\nBond Coeffs\n\n"
for i in range(1, nbondTypes + 1):
outCoeffs += "\t%d\tK\tr_0\t# %s\n" % (i, mapbTypes[i])
outCoeffs += "\nAngle Coeffs\n\n"
for i in range(1, nangleTypes + 1):
outCoeffs += "\t%d\tK\ttetha_0 (deg)\t# %s\n" % (i, mapaTypes[i])
if printdih and (ndihedrals > 0):
outCoeffs += "\nDihedral Coeffs\n\n"
for i in range(1, ndihedralTypes + 1):
outCoeffs += "\t%d\tK\tn\tphi_0 (deg)\tw\t# %s\n" % (i,
mapdTypes[i])
if not ignoreimproper and (niDihedralTypes > 0):
outCoeffs += "\nImproper Coeffs\n\n"
for i in range(1, niDihedralTypes + 1):
outCoeffs += "\t%d\tK\txi_0 (deg)\t# %s\n" % (i, mapiDTypes[i])
if printdih and (ndihedrals > 0):
if ignoreimproper or (niDihedralTypes == 0):
return header + "\n" + outMasses + "\n" + outCoeffs + "\n" + outAtoms + "\n" + outBonds + "\n" + outAngles + "\n" + outDihedrals
else:
return header + "\n" + outMasses + "\n" + outCoeffs + "\n" + outAtoms + "\n" + outBonds + "\n" + outAngles + "\n" + outDihedrals + "\n" + outImpropers
else:
return header + "\n" + outMasses + "\n" + outCoeffs + "\n" + outAtoms + "\n" + outBonds + "\n" + outAngles
def top2dfr(topfile, geomfile, flexfrag, eqgeom, savefrags, topcharges, ffname,
path):
if "amber" in ffname:
potname = "AMBER"
else:
potname = "OPLS"
# get the atomic positions from the geometry file
base, ext = os.path.splitext(geomfile)
if not ob3:
etab = openbabel.OBElementTable()
mol = pybel.readfile(ext[1:], geomfile).__next__()
molxyzinfo = {}
for i, atom in enumerate(mol, 1):
if ob3:
molxyzinfo[i] = [openbabel.GetSymbol(atom.atomicnum), atom.coords]
else:
molxyzinfo[i] = [etab.GetSymbol(atom.atomicnum), atom.coords]
# first pass through the topology file to get the data into a dictionary
tdata = {}
tdata["[ improper ]"] = []
with open(topfile) as f:
while True:
line = f.readline()
if not line:
break
if line.strip().startswith(";") or line.strip().startswith(
"#") or len(line.strip()) == 0:
continue
if strip_comment(line).startswith("[ "):
if strip_comment(line) not in tdata:
key = strip_comment(line)
tdata[key] = []
else:
# remove comments from the line
if "improper" not in line:
line = strip_comment(line)
if "improper" in line:
tdata["[ improper ]"].append(line)
else:
try:
tdata[key].append(line)
except:
print(
"You have a line (%s) of data before assigning a type of entry (such as [ atoms ], [ bonds ] ...)"
% (line))
sys.exit(0)
# check if atoms were found
if "[ atoms ]" not in tdata:
print(
"The [ atoms ] section was not found in your topology, make sure you're using a single file without #include"
)
sys.exit(0)
# get the atoms and its positions and parameters in a dictionary
atoms = OrderedDict()
rdfs = {}
atom_num = 1
rdf_label = 1
for line in tdata["[ atoms ]"]:
atomlbl = line.split()[0]
atoms[atomlbl] = []
fromatomtype = True
# if atomtypes are in the topology, use them. Otherwise get from ffnonbonded.itp
ffline = ""
if "[ atomtypes ]" in tdata:
ffline = lookup_ljparam_ifile(line.split()[1],
tdata["[ atomtypes ]"])
# get the data from the ffnonbonded.itp
if not ffline:
fromatomtype = False
ffline = lookup_ljparam(line.split()[1], path)
# if the atomtype was not found, stop
if not ffline:
print(
"Atom type %s was not found neither in the .itp or the force field directory"
% (line.split()[1]))
sys.exit(0)
# append the data to the list in the same order it will be written in the .dfr
atoms[atomlbl].append(str(atom_num))
atom_num += 1
if "amber" in ffname:
atomsp = ffline.split()[1]
else:
atomsp = ffline.split()[2]
if atomsp not in rdfs:
rdfs[atomsp] = str(rdf_label)
rdf_label += 1
atoms[atomlbl].append(rdfs[atomsp])
if "[ atomtypes ]" in tdata:
atoms[atomlbl].append(mol.atoms[int(atomlbl) - 1].atomicnum)
else:
atoms[atomlbl].append(atomsp)
x, y, z = molxyzinfo[int(atomlbl)][1]
atoms[atomlbl].append(str(x))
atoms[atomlbl].append(str(y))
atoms[atomlbl].append(str(z))
if ("amber" in ffname) or fromatomtype:
if topcharges:
atoms[atomlbl].append(line.split()[6])
else:
atoms[atomlbl].append(ffline.split()[-4])
atoms[atomlbl].append(str(j2cal(float(ffline.split()[-1]))))
atoms[atomlbl].append(str(nm2a(float(ffline.split()[-2]))))
# the last one will not be printed but is needed to retrieve the force constants
if ("[ atomtypes ]" in tdata) and ("opls" in ffname):
atoms[atomlbl].append(ffline.split()[1])
else:
atoms[atomlbl].append(ffline.split()[0])
else:
if topcharges:
atoms[atomlbl].append(line.split()[6])
else:
atoms[atomlbl].append(ffline.split()[4])
atoms[atomlbl].append(str(j2cal(float(ffline.split()[7]))))
atoms[atomlbl].append(str(nm2a(float(ffline.split()[6]))))
# the last one will not be printed but is needed to retrieve the opls-aa force constants
atoms[atomlbl].append(ffline.split()[1])
# print(atoms[atomlbl])
# now create the fragment connection list from this file and store it in fraginfo
# creates a temporary xyz using mkstemp (https://www.logilab.org/blogentry/17873)
# this file will be used to get the fragment data
fd, temp_path = tempfile.mkstemp(suffix=".xyz")
fxyz = os.fdopen(fd, 'w')
fxyz.write(mol.write("xyz"))
fxyz.close()
generate_fragfile(temp_path, "header")
base, ext = os.path.splitext(temp_path)
fraginfo = []
with open(base + ".dfr") as f:
while True:
line = f.readline()
if line.strip() != "$atoms fragments":
continue
else:
while line.strip() != "$end fragment connection":
if flexfrag:
fraginfo.append(line.replace("R", "M"))
else:
fraginfo.append(line)
line = f.readline()
fraginfo.append(line)
break
# remove the files
os.remove(temp_path)
os.remove(base + ".dfr")
os.remove(base + ".txt")
if savefrags:
shutil.move(
base + "_fragments",
os.path.join(
os.path.dirname(os.path.abspath(geomfile)),
os.path.splitext(os.path.basename(topfile))[0] + "_fragments"))
else:
shutil.rmtree(base + "_fragments")
# !!! units should be converted as in: http://chembytes.wikidot.com/oplsaagro2tnk !!!
# get the bond info
bonds = []
for line in tdata["[ bonds ]"]:
# get parameters from user's .itp
if (len(line.split()) == 5):
if eqgeom:
bonds.append(
line.split()[0] + " " + line.split()[1] + " \t" +
str(round(j2cal(float(line.split()[4])) / (200.0), 4)) +
"\t" + str(
round(
mol.OBMol.GetBond(int(line.split(
)[0]), int(line.split()[1])).GetLength(), 4)) +
"\n")
else:
bonds.append(
line.split()[0] + " " + line.split()[1] + " \t" +
str(round(j2cal(float(line.split()[4])) / (200.0), 4)) +
"\t" + str(nm2a(float(line.split()[3]))) + "\n")
# get parameters from ffbonded.itp
else:
ffline = lookup_ffbond(atoms[line.split()[0]][9],
atoms[line.split()[1]][9], path)
if ffline == "not found":
bonds.append(
line.split()[0] + " " + line.split()[1] + " \tXXX\t" +
str(
round(
mol.OBMol.GetBond(int(line.split(
)[0]), int(line.split()[1])).GetLength(), 4)) +
"\n")
elif eqgeom:
bonds.append(
line.split()[0] + " " + line.split()[1] + " \t" +
str(round(j2cal(float(ffline.split()[4])) / (200.0), 4)) +
"\t" + str(
round(
mol.OBMol.GetBond(int(line.split(
)[0]), int(line.split()[1])).GetLength(), 4)) +
"\n")
else:
bonds.append(
line.split()[0] + " " + line.split()[1] + " \t" +
str(round(j2cal(float(ffline.split()[4])) / (200.0), 4)) +
"\t" + str(nm2a(float(ffline.split()[3]))) + "\n")
# get the angle info
angles = []
for line in tdata["[ angles ]"]:
# get parameters from user's .itp
if (len(line.split()) == 6):
if eqgeom:
angles.append(
line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " \tharmonic\t" +
str(j2cal(float(line.split()[5])) / (2.0)) + "\t" + str(
round(
mol.OBMol.GetAngle(
mol.OBMol.GetAtom(int(line.split()[0])),
mol.OBMol.GetAtom(int(line.split()[1])),
mol.OBMol.GetAtom(int(line.split()[2]))), 4)) +
"\n")
else:
angles.append(line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " \tharmonic\t" +
str(j2cal(float(line.split()[5])) / (2.0)) +
"\t" + str(float(line.split()[4])) + "\n")
# get parameters from ffbonded.itp
else:
ffline = lookup_ffangle(atoms[line.split()[0]][9],
atoms[line.split()[1]][9],
atoms[line.split()[2]][9], path)
if ffline == "not found":
angles.append(
line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " \tharmonic\tXXX\t" + str(
round(
mol.OBMol.GetAngle(
mol.OBMol.GetAtom(int(line.split()[0])),
mol.OBMol.GetAtom(int(line.split()[1])),
mol.OBMol.GetAtom(int(line.split()[2]))), 4)) +
"\n")
elif eqgeom:
angles.append(
line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " \tharmonic\t" +
str(j2cal(float(ffline.split()[5])) / (2.0)) + "\t" + str(
round(
mol.OBMol.GetAngle(
mol.OBMol.GetAtom(int(line.split()[0])),
mol.OBMol.GetAtom(int(line.split()[1])),
mol.OBMol.GetAtom(int(line.split()[2]))), 4)) +
"\n")
else:
angles.append(line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " \tharmonic\t" +
str(j2cal(float(ffline.split()[5])) /
(2.0)) + "\t" + ffline.split()[4] + "\n")
# get the dihedrals info
dihedrals = []
pline = {}
ipline = {}
dih9 = False
dih4 = False
for rline in tdata["[ dihedrals ]"]:
line = strip_comment(rline)
ffline = ""
# get parameters from user's .itp
if (len(line.split()) == 11 and line.split()[4] == '3'):
V3 = round(-j2cal(float(line.split()[8]) / 2.0), 3)
V2 = round(-j2cal(float(line.split()[7])), 3)
V1 = round(-2.0 * j2cal(float(line.split()[6])) + 3.0 * V3, 3)
dihedrals.append(line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " " + line.split()[3] +
" \t" + potname + "\t" + str(V1) + "\t" +
str(V2) + "\t" + str(V3) + "\t0.0\t0.0\t0.0\n")
elif (len(line.split()) == 8 and line.split()[4] == '9'):
dih9 = True
dihline = "%s %s %s %s" % (line.split()[0], line.split()[1],
line.split()[2], line.split()[3])
if dihline in pline:
pline[dihline].append(line)
else:
pline[dihline] = [line]
elif (len(line.split()) == 8
and (line.split()[4] == '4' or line.split()[4] == '1')):
dih4 = True
dihline = "%s %s %s %s" % (line.split()[0], line.split()[1],
line.split()[2], line.split()[3])
if dihline in ipline:
ipline[dihline].append(line)
else:
ipline[dihline] = [line]
# get parameters from ffbonded.itp
elif len(line.split()) == 5:
ffline = lookup_ffdihedral(atoms[line.split()[0]][9],
atoms[line.split()[1]][9],
atoms[line.split()[2]][9],
atoms[line.split()[3]][9],
int(line.split()[4]), ffname, path)
else:
print(
"Error: something is wrong in dihedral line (%s) maybe the number of parameters?"
% (line))
sys.exit(0)
# parameters from ffbonded.itp need to be converted and stored
if ffline:
if ffline == "not found":
dihedrals.append(line.split()[0] + " " + line.split()[1] +
" " + line.split()[2] + " " +
line.split()[3] + " \t" + potname +
"\tXXX\tXXX\tXXX" + "\t0.0\t0.0\t0.0\n")
continue
if "amber" in ffname:
# parameters are already of Fourier type, just need to convert to cal
if float(ffline.split()[8]) == 0.:
dihedrals.append(
line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " " + line.split()[3] + " \t" +
potname + "\t" + str(j2cal(float(ffline.split()[5]))) +
"\t" + str(j2cal(float(ffline.split()[6]))) + "\t" +
str(j2cal(float(ffline.split()[7]))) + "\t" +
str(round(float(ffline.split()[9]), 1)) + "\t" +
str(round(float(ffline.split()[10]), 1)) + "\t" +
str(round(float(ffline.split()[11]), 1)) + "\n")
else:
dihedrals.append(
line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " " + line.split()[3] + " \t" +
potname + "\t" + str(j2cal(float(ffline.split()[5]))) +
"\t" + str(j2cal(float(ffline.split()[6]))) + "\t" +
str(j2cal(float(ffline.split()[7]))) + "\t" +
str(j2cal(float(ffline.split()[8]))) + "\t" +
str(round(float(ffline.split()[9]), 1)) + "\t" +
str(round(float(ffline.split()[10]), 1)) + "\t" +
str(round(float(ffline.split()[11]), 1)) + "\t" +
str(round(float(ffline.split()[12]), 1)) + "\n")
else:
if float(ffline.split()[9]) != 0.0 or float(
ffline.split()[10]) != 0.0:
print(
"Parameters for %s - %s - %s - %s dihedrals are undefined, please treat by hand!"
%
(atoms[line.split()[0]][9], atoms[line.split()[1]][9],
atoms[line.split()[2]][9], atoms[line.split()[3]][9]))
V3 = round(-j2cal(float(ffline.split()[8]) / 2.0), 3)
V2 = round(-j2cal(float(ffline.split()[7])), 3)
V1 = round(-2.0 * j2cal(float(ffline.split()[6])) + 3.0 * V3,
3)
dihedrals.append(line.split()[0] + " " + line.split()[1] +
" " + line.split()[2] + " " +
line.split()[3] + " \t" + potname + "\t" +
str(V1) + "\t" + str(V2) + "\t" + str(V3) +
"\t0.0\t0.0\t0.0\n")
# after reading all the dihedrals, if type 9 was used, we need to convert
if dih9:
for kdih in pline:
params = [0.0] * 6
for line in pline[kdih]:
n = int(line.split()[7])
# have to multiply by 2.0 since I use the 0.5*(...) version of the AMBER definition
params[n - 1] = 2.0 * float(line.split()[6])
params[n + 2] = float(line.split()[5])
retline = "%s\t%d\t%f\t%f\t%f\t%f\t%f\t%f" % (
kdih, 9, params[0], params[1], params[2], params[3], params[4],
params[5])
dihedrals.append(retline.split()[0] + " " + retline.split()[1] +
" " + retline.split()[2] + " " +
retline.split()[3] + " \t" + potname + "\t" +
str(j2cal(float(retline.split()[5]))) + "\t" +
str(j2cal(float(retline.split()[6]))) + "\t" +
str(j2cal(float(retline.split()[7]))) + "\t" +
retline.split()[8] + "\t" + retline.split()[9] +
"\t" + retline.split()[10] + "\n")
# finally, add the improper dihedrals described as proper dihedrals
if dih4:
for kdih in ipline:
params = [0.0] * 6
for line in ipline[kdih]:
n = int(line.split()[7])
# have to multiply by 2.0 since I use the 0.5*(...) version of the AMBER definition
params[n - 1] = 2.0 * float(line.split()[6])
params[n + 2] = float(line.split()[5])
retline = "%s\t%d\t%.3f\t%.3f\t%.3f\t%.2f\t%.2f\t%.2f" % (
kdih, 9, params[0], params[1], params[2], params[3], params[4],
params[5])
dihedrals.append(retline.split()[0] + " " + retline.split()[1] +
" " + retline.split()[2] + " " +
retline.split()[3] + " \t" + "AMBER" + "\t" +
str(j2cal(float(retline.split()[5]))) + "\t" +
str(j2cal(float(retline.split()[6]))) + "\t" +
str(j2cal(float(retline.split()[7]))) + "\t" +
retline.split()[8] + "\t" + retline.split()[9] +
"\t" + retline.split()[10] + "\n")
# get the improper dihedrals info
improper = []
for line in tdata["[ improper ]"]:
if len(strip_comment(line).split()) >= 7:
improper.append(line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " " + line.split()[3] + " \t" +
str(round(j2cal(float(line.split()[6])), 3)) +
"\t" + line.split()[5] + "\n")
else:
if "opls" in ffname:
ffline = lookup_ffimproper(line.split()[5], path)
improper.append(
line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " " + line.split()[3] + " \t" +
str(round(j2cal(float(ffline.split()[3])), 3)) + "\t" +
ffline.split()[2] + "\n")
else:
ffline = lookup_ffdihedral(atoms[line.split()[0]][9],
atoms[line.split()[1]][9],
atoms[line.split()[2]][9],
atoms[line.split()[3]][9], 4, path)
improper.append(line.split()[0] + " " + line.split()[1] + " " +
line.split()[2] + " " + line.split()[3] +
" \t" + "OPLS" + "\t" +
str(j2cal(float(ffline.split()[5]))) + "\t" +
str(j2cal(float(ffline.split()[6]))) + "\t" +
str(j2cal(float(ffline.split()[7]))) + "\t" +
ffline.split()[8] + "\t" + ffline.split()[9] +
"\t" + ffline.split()[10] + "\n")
# print everything to the output file
base, ext = os.path.splitext(geomfile)
with open(base + ".txt", "w") as f:
f.write("*\n1\n")
f.write(
str(len(atoms)) + " \t %s (generated with gromacs2dice)\n" %
(os.path.basename(base)))
for atom, data in atoms.items():
f.write(
"%2d %2d \t %7.4f \t %7.4f \t %7.4f \t %7.4f \t %7.4f \t %7.4f\n"
% (int(data[1]), int(data[2]), float(data[3]), float(
data[4]), float(data[5]), float(data[6]), float(
data[7]), float(data[8])))
f.write("$end\n")
with open(base + ".dfr", "w") as f:
for line in fraginfo:
f.write(line)
f.write("\n$bond\n")
for line in bonds:
f.write(line)
f.write("$end bond\n\n$angle\n")
for line in angles:
f.write(line)
f.write("$end angle\n\n$dihedral\n")
for line in dihedrals:
f.write(line)
if dih4:
for line in improper:
f.write(line)
f.write("$end dihedral\n")
if improper:
for line in improper:
print("\n$improper dihedral\n")
f.write(line)
f.write("$end improper dihedral\n")
if not flexfrag:
withoutba = clean_dofs(base + ".dfr")
with open(base + ".dfr", 'w') as f:
f.write(withoutba)
print("The files %s and %s were successfully generated." %
(base + ".txt", base + ".dfr"))
