using PLIP v2.1.3

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