def write_merged_bioassembly(inpath, outdir, outname, force_rerun=False):
"""Utility to take as input a bioassembly file and merge all its models into multiple chains in a single model.
Args:
infile (str): Path to input PDB file with multiple models that represent an oligomeric form of a structure.
outdir (str): Path to output directory
outname (str): New filename of structure file
force_rerun (bool): If a new PDB should be written if the file exists
Returns:
str: Path to newly written PDB file.
"""
outpath = outfile = op.join(outdir, outname + '.pdb')
if ssbio.utils.force_rerun(flag=force_rerun,
outfile=op.join(outdir, outname + '.pdb')):
s = StructProp('Model merging', structure_path=inpath, file_type='pdb')
ss = s.parse_structure()
merge_all_models_into_first_model(ss.structure)
outpath = ss.write_pdb(custom_name=outname,
out_dir=outdir,
force_rerun=force_rerun)
else:
return outpath
def get_metalpdb_info(metalpdb_lig_file):
"""Parse a MetalPDB .lig file and return a tuple of the chain ID it represents, along with metal binding information.
Args:
metalpdb_lig_file (str): Path to .lig file
Returns:
tuple: (str, dict) of the chain ID and the parsed metal binding site information
"""
pdb_metals = [
'CU', 'ZN', 'MN', 'FE', 'MG', 'CO', 'SE', 'YB', 'SF4', 'FES', 'F3S',
'NI', 'FE2'
]
# Information to collect
coordination_number = 0
endogenous_ligands = []
exogenous_ligands = []
# Load the structure
ss = StructProp(ident='metalpdb',
structure_path=metalpdb_lig_file,
file_type='pdb')
# This lig file should just be for one chain
chain_id = op.basename(metalpdb_lig_file)[5]
metal_id = (op.basename(metalpdb_lig_file).split('_')[2],
op.basename(metalpdb_lig_file).split('_')[3])
for r in ss.parse_structure().first_model.get_residues():
return_id = (r.get_id(), r.get_resname())
# print(r.resname)
# Binding partners
## check if residue is a normal one (not a HETATM, WAT, or the metal that is identified)
if r.get_id()[0] != ' ':
if not r.resname.strip() in pdb_metals and r.resname != 'HOH':
# print('appended', r.resname)
exogenous_ligands.append(return_id)
else:
endogenous_ligands.append(return_id)
# Coordination number
for a in r.get_atom():
if not a.element in pdb_metals:
coordination_number += 1
infodict = {
metal_id: {
'endogenous_ligands': endogenous_ligands,
'exogenous_ligands': exogenous_ligands,
'coordination_number': coordination_number
}
}
return chain_id, infodict