updates citation info

- citation record for text report updated
- help text updated for command line

plip/exchange/report.py

@@ -68,8 +68,7 @@ def construct_txt_file(self):
         textlines.append("=" * len(textlines[0]))
         textlines.append('Created on %s using PLIP v%s\n' % (time.strftime("%Y/%m/%d"), __version__))
         textlines.append('If you are using PLIP in your work, please cite:')
-        textlines.append('Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.')
-        textlines.append('Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi: 10.1093/nar/gkv315\n')
+        textlines.append(config.__citation_information__)
         if len(self.excluded) != 0:
             textlines.append('Excluded molecules as ligands: %s\n' % ','.join([lig for lig in self.excluded]))
         if config.DNARECEPTOR:

plip/plipcmd.py

@@ -25,11 +25,10 @@
 from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
 from plip.structure.preparation import tilde_expansion, PDBComplex
 
-description = f"The Protein-Ligand Interaction Profiler (PLIP) {__version__}" \
+description = f"The Protein-Ligand Interaction Profiler (PLIP) Version {__version__} " \
               "is a command-line based tool to analyze interactions in a protein-ligand complex. " \
               "If you are using PLIP in your work, please cite: " \
-              "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
-              "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315" \
+              f"{config.__citation_information__} " \
               f"Supported and maintained by: {config.__maintainer__}"
 
 

plip/test/test_command_line.py

@@ -57,3 +57,8 @@ def test_stdout(self):
         exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -t -f ./pdb/1eve.pdb -O', shell=True)
         self.assertEqual(exitcode, 0)
 
+    def test_help(self):
+        """A PDB ID with no valid PDB record is provided."""
+        exitcode = subprocess.call(f'{sys.executable} ../plipcmd.py -h', shell=True)
+        self.assertEqual(exitcode, 0)
+