diff options
Diffstat (limited to 'plip')
| -rw-r--r-- | plip/basic/config.py | 2 | ||||
| -rw-r--r-- | plip/exchange/report.py | 6 | ||||
| -rw-r--r-- | plip/plipcmd.py | 13 | ||||
| -rw-r--r-- | plip/structure/preparation.py | 17 | ||||
| -rw-r--r-- | plip/test/test_command_line.py | 6 | ||||
| -rw-r--r-- | plip/test/test_hydrogen_bonds.py | 2 |
6 files changed, 24 insertions, 22 deletions
diff --git a/plip/basic/config.py b/plip/basic/config.py index a7468cf..4eee215 100644 --- a/plip/basic/config.py +++ b/plip/basic/config.py @@ -1,4 +1,4 @@ -__version__ = '2.1.0-beta' +__version__ = '2.1.3' __maintainer__ = 'PharmAI GmbH (2020) - www.pharm.ai - hello@pharm.ai' import logging diff --git a/plip/exchange/report.py b/plip/exchange/report.py index a559bf8..20f281e 100644 --- a/plip/exchange/report.py +++ b/plip/exchange/report.py @@ -97,9 +97,7 @@ class StructureReport: xml_declaration=True) else: output = et.tostring(self.xmlreport, pretty_print=True) - if config.RAWSTRING: - output = repr(output) - print(output) + print(output.decode('utf8')) def write_txt(self, as_string=False): """Write the TXT report""" @@ -108,8 +106,6 @@ class StructureReport: [f.write(textline + '\n') for textline in self.txtreport] else: output = '\n'.join(self.txtreport) - if config.RAWSTRING: - output = repr(output) print(output) diff --git a/plip/plipcmd.py b/plip/plipcmd.py index e4c0815..f7dffab 100644 --- a/plip/plipcmd.py +++ b/plip/plipcmd.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python3 +#! /usr/bin/env python """ Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files. plipcmd.py - Main script for PLIP command line execution. @@ -166,7 +166,7 @@ def run_analysis(inputstructs, inputpdbids): logger.info(f'finished analysis, find the result files in {config.BASEPATH}') -if __name__ == '__main__': +def main(): """Parse command line arguments and start main script for analysis.""" parser = ArgumentParser(prog="PLIP", description=description) pdbstructure = parser.add_mutually_exclusive_group(required=True) # Needs either PDB ID or file @@ -178,7 +178,7 @@ if __name__ == '__main__': outputgroup.add_argument("-O", "--stdout", dest="stdout", action="store_true", default=False, help="Write to stdout instead of file") parser.add_argument("--rawstring", dest="use_raw_string", default=False, action="store_true", - help="Use Python raw strings for stdout and stdin") + help="Use Python raw strings for stdin") parser.add_argument("-v", "--verbose", dest="verbose", default=False, help="Turn on verbose mode", action="store_true") parser.add_argument("-q", "--quiet", dest="quiet", default=False, help="Turn on quiet mode", action="store_true") @@ -240,9 +240,7 @@ if __name__ == '__main__': for t in thresholds: parser.add_argument('--%s' % t.name, dest=t.name, type=lambda val: threshold_limiter(parser, val), help=argparse.SUPPRESS) - arguments = parser.parse_args() - # configure log levels config.VERBOSE = True if arguments.verbose else False config.QUIET = True if arguments.quiet else False @@ -255,7 +253,6 @@ if __name__ == '__main__': logger.setLevel(logging.CRITICAL) else: logger.setLevel(config.DEFAULT_LOG_LEVEL) - config.MAXTHREADS = arguments.maxthreads config.XML = arguments.xml config.TXT = arguments.txt @@ -308,3 +305,7 @@ if __name__ == '__main__': parser.error("The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle") expanded_path = tilde_expansion(arguments.input) if arguments.input is not None else None run_analysis(expanded_path, arguments.pdbid) # Start main script + + +if __name__ == '__main__': + main() diff --git a/plip/structure/preparation.py b/plip/structure/preparation.py index 6b63d63..c2631d3 100644 --- a/plip/structure/preparation.py +++ b/plip/structure/preparation.py @@ -290,20 +290,19 @@ class LigandFinder: ligtype = classify_by_name(names) logger.debug(f'ligand classified as {ligtype}') - hetatoms = set() + hetatoms = dict() for obresidue in kmer: - hetatoms_res = set([(obatom.GetIdx(), obatom) for obatom in pybel.ob.OBResidueAtomIter(obresidue) - if obatom.GetAtomicNum() != 1]) - + cur_hetatoms = {obatom.GetIdx(): obatom for obatom in pybel.ob.OBResidueAtomIter(obresidue) if + obatom.GetAtomicNum() != 1} if not config.ALTLOC: # Remove alternative conformations (standard -> True) - hetatoms_res = set([atm for atm in hetatoms_res - if not self.mapper.mapid(atm[0], mtype='protein', - to='internal') in self.altconformations]) - hetatoms.update(hetatoms_res) + ids_to_remove = [atom_id for atom_id in hetatoms.keys() if + self.mapper.mapid(atom_id, mtype='protein', to='internal') in self.altconformations] + for atom_id in ids_to_remove: + del cur_hetatoms[atom_id] + hetatoms.update(cur_hetatoms) logger.debug(f'hetero atoms determined (n={len(hetatoms)})') - hetatoms = dict(hetatoms) # make it a dict with idx as key and OBAtom as value lig = pybel.ob.OBMol() # new ligand mol neighbours = dict() for obatom in hetatoms.values(): # iterate over atom objects diff --git a/plip/test/test_command_line.py b/plip/test/test_command_line.py index 5d8e8e5..d3ab332 100644 --- a/plip/test/test_command_line.py +++ b/plip/test/test_command_line.py @@ -46,3 +46,9 @@ class CommandLineTest(unittest.TestCase): shell=True) self.assertEqual(len(os.listdir(self.tmp_dir.name)), 2) self.assertEqual(exitcode, 0) + + def test_stdout(self): + """A PDB ID with no valid PDB record is provided.""" + exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O', shell=True) + self.assertEqual(exitcode, 0) + diff --git a/plip/test/test_hydrogen_bonds.py b/plip/test/test_hydrogen_bonds.py index 9d68532..75cae6c 100644 --- a/plip/test/test_hydrogen_bonds.py +++ b/plip/test/test_hydrogen_bonds.py @@ -35,4 +35,4 @@ class HydrogenBondTestCase(unittest.TestCase): self.assertEqual(len(interactions1.hbonds_ldon), 0) config.NOHYDRO = False interactions2 = characterize_complex('./pdb/1x0n_state_1.pdb', 'DTF:A:174') - self.assertEqual(len(interactions2.hbonds_ldon), 1) + self.assertEqual(len(interactions2.hbonds_ldon), 1)
\ No newline at end of file |