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 gen_params(name, outpath, inpath=None, lib=None, seq=None, seq_file=None):
"""
Top level function for running the polyply parameter generation.
Parameters seq and seq_file are mutually exclusive. Set the other
to None. Of inpath and lib only one has to be given. Set the other
to None if not used.
Parameters
----------
name: str
name of the molecule in the itp file
outpath: :class:`pathlib.Path`
file path for output file
inpath: list[pathlib.Path]
list of paths to files with input definitions
library: str
name of the force field library to use
seq: list[str]
list of strings with format "resname:#monomers"
seqf: :class:`pathlib.Path`
file path to valid sequence file (.json/.fasta/.ig/.txt)
"""
# Import of Itp and FF files
LOGGER.info("reading input and library files", type="step")
force_field = load_library(name, lib, inpath)
# Generate the MetaMolecule
if seq:
LOGGER.info("reading sequence from command", type="step")
monomers = split_seq_string(seq)
meta_molecule = MetaMolecule.from_monomer_seq_linear(
monomers=monomers, force_field=force_field, mol_name=name)
elif seq_file:
LOGGER.info("reading sequence from file", type="step")
meta_molecule = MetaMolecule.from_sequence_file(
force_field, seq_file, name)
# Do transformationa and apply link
LOGGER.info("mapping sequence to molecule", type="step")
meta_molecule = MapToMolecule(force_field).run_molecule(meta_molecule)
LOGGER.info("applying links between residues", type="step")
meta_molecule = ApplyLinks().run_molecule(meta_molecule)
# Raise warning if molecule is disconnected
if not nx.is_connected(meta_molecule.molecule):
LOGGER.warning("Your molecule consists of disjoint parts."
"Perhaps links were not applied correctly.")
msg = "Missing link between residue {idxA} {resA} and residue {idxB} {resB}"
for missing in find_missing_edges(meta_molecule,
meta_molecule.molecule):
LOGGER.warning(msg, **missing)
with deferred_open(outpath, 'w') as outfile:
header = [' '.join(sys.argv) + "\n"]
header.append("Please cite the following papers:")
for citation in meta_molecule.molecule.citations:
cite_string = citation_formatter(
meta_molecule.molecule.force_field.citations[citation])
LOGGER.info("Please cite: " + cite_string)
header.append(cite_string)
vermouth.gmx.itp.write_molecule_itp(meta_molecule.molecule,
outfile,
moltype=name,
header=header)
DeferredFileWriter().write()