def process_pdb(model,
attribution_fn,
pdbfile,
outpath,
input_dim,
radius=12,
bs=16):
mol = PDBComplex()
mol.output_path = outpath
mol.load_pdb(pdbfile, as_string=False)
for ligand in mol.ligands:
mol.characterize_complex(ligand)
create_folder_if_not_exists(outpath)
complexes = [
VisualizerDataWithMolecularInfo(mol, site)
for site in sorted(mol.interaction_sets)
if not len(mol.interaction_sets[site].interacting_res) == 0
]
[
visualize_in_pymol(model,
attribution_fn=attribution_fn,
output_dir=outpath,
plcomplex=plcomplex,
input_dim=input_dim,
radius=radius,
bs=bs) for plcomplex in complexes
]
print()
def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
if not as_string:
pdb_file_name = pdbfile.split('/')[-1]
startmessage = f'starting analysis of {pdb_file_name}'
else:
startmessage = 'starting analysis from STDIN'
logger.info(startmessage)
mol = PDBComplex()
mol.output_path = outpath
mol.load_pdb(pdbfile, as_string=as_string)
# @todo Offers possibility for filter function from command line (by ligand chain, position, hetid)
for ligand in mol.ligands:
mol.characterize_complex(ligand)
create_folder_if_not_exists(outpath)
# Generate the report files
streport = StructureReport(mol, outputprefix=outputprefix)
config.MAXTHREADS = min(config.MAXTHREADS, len(mol.interaction_sets))
######################################
# PyMOL Visualization (parallelized) #
######################################
if config.PYMOL or config.PICS:
from plip.visualization.visualize import visualize_in_pymol
complexes = [
VisualizerData(mol, site) for site in sorted(mol.interaction_sets)
if not len(mol.interaction_sets[site].interacting_res) == 0
]
if config.MAXTHREADS > 1:
logger.info(
f'generating visualizations in parallel on {config.MAXTHREADS} cores'
)
parfn = parallel_fn(visualize_in_pymol)
parfn(complexes, processes=config.MAXTHREADS)
else:
[visualize_in_pymol(plcomplex) for plcomplex in complexes]
if config.XML: # Generate report in xml format
streport.write_xml(as_string=config.STDOUT)
if config.TXT: # Generate report in txt (rst) format
streport.write_txt(as_string=config.STDOUT)
