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#!/usr/bin/env python3
"""
Add minimal ModelCIF-related tables to an mmCIF file.
Given any mmCIF file as input, this script will add any missing
ModelCIF-related tables and write out a new file that is minimally compliant
with the ModelCIF dictionary.
This is done by simply reading in the original file with python-modelcif and
then writing it out again, so
a) any data in the input file that is not understood by python-modelcif
will be lost on output; and
b) input files that aren't compliant with the PDBx dictionary, or that
contain syntax errors or other problems, may crash or otherwise confuse
python-modelcif.
While a best effort is made, it is not guaranteed that the output file is
valid. It is recommended that it is run through a validator such as
examples/validate_mmcif.py and any errors corrected or reported as
issues.
"""
import modelcif.reader
import modelcif.dumper
import modelcif.model
import ihm.util
import os
import argparse
def add_modelcif_info(s):
if not s.title:
s.title = 'Auto-generated system'
if not s.protocols:
default_protocol = modelcif.protocol.Protocol()
step = modelcif.protocol.ModelingStep(
name='modeling', input_data=None, output_data=None)
default_protocol.steps.append(step)
s.protocols.append(default_protocol)
for model_group in s.model_groups:
for model in model_group:
# Entity description is also used by python-modelcif for
# ma_data.name, which is mandatory, so it cannot be unknown/?
for asym in model.assembly:
if asym.entity.description is ihm.unknown:
asym.entity.description = "target"
model.not_modeled_residue_ranges.extend(
_get_not_modeled_residues(model))
return s
def _get_not_modeled_residues(model):
"""Yield NotModeledResidueRange objects for all residue ranges in the
Model that are not referenced by Atom objects"""
for assem in model.assembly:
asym = assem.asym if hasattr(assem, 'asym') else assem
if not asym.entity.is_polymeric():
continue
# Make a set of all residue indices of this asym "handled"
# by being modeled with Atom objects
handled_residues = set()
for atom in model._atoms:
if atom.asym_unit is asym:
handled_residues.add(atom.seq_id)
# Convert set to a list of residue ranges
handled_residues = ihm.util._make_range_from_list(
sorted(handled_residues))
# Return not-modeled for each non-handled range
for r in ihm.util._invert_ranges(handled_residues,
end=assem.seq_id_range[1],
start=assem.seq_id_range[0]):
yield modelcif.model.NotModeledResidueRange(asym, r[0], r[1])
def get_args():
p = argparse.ArgumentParser(
description="Add minimal ModelCIF-related tables to an mmCIF file.")
p.add_argument("input", metavar="input.cif", help="input mmCIF file name")
p.add_argument("output", metavar="output.cif",
help="output mmCIF file name",
default="output.cif", nargs="?")
return p.parse_args()
def main():
args = get_args()
if (os.path.exists(args.input) and os.path.exists(args.output)
and os.path.samefile(args.input, args.output)):
raise ValueError("Input and output are the same file")
with open(args.input) as fh:
with open(args.output, 'w') as fhout:
modelcif.dumper.write(
fhout,
[add_modelcif_info(s) for s in modelcif.reader.read(fh)])
if __name__ == '__main__':
main()
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