def fixResidueSeqNumbers(mol):
curr_seq_no = 0
res_start = 0
res_end = 0
num_atoms = mol.getNumAtoms()
old_res_seq_nos = []
old_to_new_seq_no_map = {}
for atom in mol.atoms:
old_res_seq_nos.append(Biomol.getResidueSequenceNumber(atom))
while res_start < num_atoms:
while res_end < num_atoms and (old_res_seq_nos[res_start]
== old_res_seq_nos[res_end]):
res_end += 1
if not old_res_seq_nos[res_start] in old_to_new_seq_no_map:
old_to_new_seq_no_map[old_res_seq_nos[res_start]] = curr_seq_no
while res_start < res_end:
Biomol.setResidueSequenceNumber(mol.getAtom(res_start),
curr_seq_no)
res_start += 1
curr_seq_no += 1
return old_res_seq_nos, old_to_new_seq_no_map
def setResidueSeqNumbers(mol, seq_nos):
i = 0
while i < len(seq_nos):
Biomol.setResidueSequenceNumber(mol.getAtom(i), seq_nos[i])
i += 1
def process():
if len(sys.argv) < 4:
print >> sys.stderr, 'Usage:', sys.argv[
0], '[input topology-file] [input coordinates-file] [output CDF-file]'
sys.exit(2)
print >> sys.stderr, '- Processing topology-file', sys.argv[
1], 'and coordinates-file', sys.argv[2], '...'
u = MDAnalysis.Universe(sys.argv[1], sys.argv[2])
cdf_mol = Chem.BasicMolecule()
cdf_mol.reserveMemoryForAtoms(len(u.atoms))
cdf_mol.reserveMemoryForBonds(len(u.bonds))
print >> sys.stderr, '- Num. atoms:', len(u.atoms)
print >> sys.stderr, '- Num. bonds:', len(u.bonds)
num_frames = len(u.trajectory)
print >> sys.stderr, '- Num. frames:', num_frames
# construct atoms
print >> sys.stderr, '- Building atoms ...'
waters = {}
i = 0
for md_atom in u.atoms:
atom = cdf_mol.addAtom()
sym = MDAnalysis.topology.guessers.guess_atom_element(md_atom.name)
Chem.setSymbol(atom, sym.title())
Chem.setImplicitHydrogenCount(atom, 0)
Biomol.setChainID(atom, md_atom.segid)
if md_atom.resname == 'WAT':
Biomol.setResidueCode(atom, 'HOH')
else:
Biomol.setResidueCode(atom, md_atom.resname)
if Biomol.getResidueCode(atom) == 'HOH':
if md_atom.resid in waters:
waters[md_atom.resid].append(i)
else:
waters[md_atom.resid] = [i]
Biomol.setResidueSequenceNumber(atom, int(md_atom.resid))
Biomol.setResidueAtomName(atom, md_atom.name)
# fix positive charge on arginin nitrogen
if md_atom.resname == 'ARG' and md_atom.name == 'NH2':
Chem.setFormalCharge(atom, 1)
coords = []
for coord in md_atom.position:
coords.append(float(coord))
Chem.set3DCoordinates(atom, coords)
coords_array = Math.Vector3DArray()
coords_array.reserve(num_frames)
Chem.set3DCoordinatesArray(atom, coords_array)
Chem.setPEOECharge(atom, float(md_atom.charge))
i += 1
Chem.setAtomTypesFromSymbols(cdf_mol, True)
# construct bonds
print >> sys.stderr, '- Building bonds ...'
for md_bond in u.bonds:
cdf_mol.addBond(int(md_bond.atoms[0].index),
int(md_bond.atoms[1].index))
print >> sys.stderr, '- Building water atom bonds ...'
for water in waters.values():
if len(water) < 2:
continue
for atom_idx in water:
if Chem.getType(cdf_mol.atoms[atom_idx]) == Chem.AtomType.O:
if atom.numBonds > 1:
break
for atom_idx2 in water:
if Chem.getType(
cdf_mol.atoms[atom_idx2]) == Chem.AtomType.H:
cdf_mol.addBond(atom_idx, atom_idx2)
break
# make sane biomolecule
Chem.perceiveSSSR(cdf_mol, True)
Chem.setRingFlags(cdf_mol, True)
Chem.perceiveBondOrders(cdf_mol, True)
Chem.perceiveHybridizationStates(cdf_mol, True)
Chem.setAromaticityFlags(cdf_mol, True)
Chem.calcFormalCharges(cdf_mol, True)
# read timsteps and write cdf
print >> sys.stderr, '- Importing coordinates ...'
i = 0
traj_coords = []
atom_coords = Math.Vector3D()
for ts in u.trajectory:
print >> sys.stderr, '- Processing time step', i, '...'
for md_atom in u.atoms:
del traj_coords[:]
for coord in md_atom.position:
traj_coords.append(float(coord))
coords_array = Chem.get3DCoordinatesArray(
cdf_mol.getAtom(int(md_atom.index)))
atom_coords[0] = traj_coords[0]
atom_coords[1] = traj_coords[1]
atom_coords[2] = traj_coords[2]
coords_array.addElement(atom_coords)
i += 1
print >> sys.stderr, '- Writing output file:'
if not Chem.FileCDFMolecularGraphWriter(sys.argv[3]).write(cdf_mol):
print >> sys.stderr, '!! Could not write output file'
sys.exit(2)