def gen_itp(args):
# Import of Itp and FF files
force_field = load_library(args.name, args.lib, args.inpath)
# Generate the MetaMolecule
if args.seq:
monomers = split_seq_string(args.seq)
meta_molecule = MetaMolecule.from_monomer_seq_linear(
monomers=monomers, force_field=force_field, mol_name=args.name)
#ToDo
# fix too broad except
elif args.seq_file:
extension = args.seq_file.suffix.casefold()[1:]
try:
parser = getattr(MetaMolecule, 'from_{}'.format(extension))
meta_molecule = parser(json_file=args.seq_file,
force_field=force_field,
mol_name=args.name)
except AttributeError:
raise IOError(
"Cannot parse file with extension {}.".format(extension))
# Do transformationa and apply link
meta_molecule = MapToMolecule().run_molecule(meta_molecule)
meta_molecule = ApplyLinks().run_molecule(meta_molecule)
with open(args.outpath, 'w') as outpath:
vermouth.gmx.itp.write_molecule_itp(meta_molecule.molecule,
outpath,
moltype=args.name,
header=["polyply-itp"])
DeferredFileWriter().write()
def write_map(filename, cg_mol):
aa_nodes = {}
aa_to_cg = defaultdict(list)
for cg_idx in cg_mol:
bead = cg_mol.nodes[cg_idx]
aa_graph = bead['graph']
for aa_idx in aa_graph:
atom = aa_graph.nodes[aa_idx]
aa_nodes[aa_idx] = atom
aa_to_cg[aa_idx].append(cg_idx)
with open(filename, 'w') as file_out:
molname = cg_mol.meta['moltype']
file_out.write('[ molecule ]\n')
file_out.write(molname + '\n')
file_out.write('[ martini ]\n')
file_out.write(' '.join(cg_mol.nodes[idx]['atomname']
for idx in cg_mol) + '\n')
file_out.write('[ mapping ]\n')
file_out.write('<FORCE FIELD NAMES>\n')
file_out.write('[ atoms ]\n')
for aa_idx, atom in sorted(aa_nodes.items(),
key=lambda i: i[1].get('atomid', i[0])):
cg_idxs = aa_to_cg[aa_idx]
file_out.write('{} {} {}\n'.format(
atom.get('atomid', aa_idx), atom['atomname'],
' '.join(cg_mol.nodes[cg_idx]['atomname']
for cg_idx in cg_idxs)))
def write_ndx(filename, cg_mol, stepsize=10):
with open(filename, 'w') as file_out:
for bead_idx in cg_mol:
node = cg_mol.nodes[bead_idx]
at_idxs = list(node.get('graph', []))
file_out.write('[ {} ]\n'.format(node['atomname']))
for idx in range(0, len(at_idxs), stepsize):
idxs = (at_idx + 1 for at_idx in at_idxs[idx:idx + stepsize])
file_out.write(' '.join(map(str, idxs)) + '\n')
file_out.write('\n')
def write_itp(path, cg_mol):
with open(path, 'w') as out:
write_molecule_itp(cg_mol, out)
def write_pdb(path, cg_mol):
system = System()
system.add_molecule(cg_mol)
with open(path, 'w') as out:
out.write(write_pdb_string(system))