CHANGES.txt

 Changelog
 ---------
 
+# 1.4.2
+* Adds "--name" option to change name of output files
+* Adds "--nopdbcanmap" option to skip calculation of canonical->PDB mapping which can lead to segfaults with OpenBabel
+* Improved handling of ligand names
+
 # 1.4.1
 * Improved import of modules
 * Corrections for README and documentation

README.md

@@ -33,7 +33,7 @@ pymol 1VSN_NFT_A_283.pse
 In your terminal, add the PLIP repository to your PYTHONPATH variable.
 For our example, we also download a PDB file for testing.
 ```bash
-export PYTHONPATH=~/pliptool/plip:${PYTHONPATH}
+export PYTHONPATH=~/pliptool:${PYTHONPATH}
 cd /tmp && wget http://files.rcsb.org/download/1EVE.pdb
 python
 ```

debian/changelog

+plip (1.4.2+dfsg-1) unstable; urgency=medium
+
+  * New upstream version 1.4.2+dfsg
+
+ -- Alexandre Mestiashvili <mestia@debian.org>  Thu, 07 Jun 2018 20:05:34 +0200
+
 plip (1.4.1+dfsg-1) unstable; urgency=medium
 
   * New upstream version 1.4.1+dfsg

plip/modules/config.py

@@ -23,6 +23,8 @@ PEPTIDES = []  # Definition which chains should be considered as peptide ligands
 INTRA = None
 KEEPMOD = False
 DNARECEPTOR = False
+OUTPUTFILENAME = "report" # Naming for the TXT and XML report files
+NOPDBCANMAP = False # Skip calculation of mapping canonical atom order: PDB atom order
 
 # Configuration file for Protein-Ligand Interaction Profiler (PLIP)
 # Set thresholds for detection of interactions

plip/modules/plipxml.py

@@ -53,10 +53,10 @@ class Interaction(XMLStorage):
     def __init__(self, interaction_part):
         self.id = interaction_part.get('id')
         self.resnr = self.getdata(interaction_part, 'resnr')
-        self.restype = self.getdata(interaction_part, 'restype')
+        self.restype = self.getdata(interaction_part, 'restype', force_string=True)
         self.reschain = self.getdata(interaction_part, 'reschain', force_string=True)
         self.resnr_lig = self.getdata(interaction_part, 'resnr_lig')
-        self.restype_lig = self.getdata(interaction_part, 'restype_lig')
+        self.restype_lig = self.getdata(interaction_part, 'restype_lig', force_string=True)
         self.reschain_lig = self.getdata(interaction_part, 'reschain_lig', force_string=True)
         self.ligcoo = self.getcoordinates(interaction_part, 'ligcoo')
         self.protcoo = self.getcoordinates(interaction_part, 'protcoo')
@@ -87,8 +87,8 @@ class HydrogenBond(Interaction):
         self.protisdon = self.getdata(hbond_part, 'protisdon')
         self.donoridx = self.getdata(hbond_part, 'donoridx')
         self.acceptoridx = self.getdata(hbond_part, 'acceptoridx')
-        self.donortype = self.getdata(hbond_part, 'donortype')
-        self.acceptortype = self.getdata(hbond_part, 'acceptortype')
+        self.donortype = self.getdata(hbond_part, 'donortype', force_string=True)
+        self.acceptortype = self.getdata(hbond_part, 'acceptortype', force_string=True)
 
 
 class WaterBridge(Interaction):
@@ -105,8 +105,8 @@ class WaterBridge(Interaction):
 
         self.donor_idx = self.getdata(wbridge_part, 'donor_idx')
         self.acceptor_idx = self.getdata(wbridge_part, 'acceptor_idx')
-        self.donortype = self.getdata(wbridge_part, 'donortype')
-        self.acceptortype = self.getdata(wbridge_part, 'acceptortype')
+        self.donortype = self.getdata(wbridge_part, 'donortype', force_string=True)
+        self.acceptortype = self.getdata(wbridge_part, 'acceptortype', force_string=True)
         self.water_idx = self.getdata(wbridge_part, 'water_idx')
         self.watercoo = self.getcoordinates(wbridge_part, 'watercoo')
 
@@ -118,7 +118,7 @@ class SaltBridge(Interaction):
         Interaction.__init__(self, sbridge_part)
         self.dist =  self.getdata(sbridge_part, 'dist')
         self.protispos = self.getdata(sbridge_part, 'protispos')
-        self.lig_group = self.getdata(sbridge_part, 'lig_group')
+        self.lig_group = self.getdata(sbridge_part, 'lig_group', force_string=True)
         self.lig_idx_list = [int(tagpart.text) for tagpart in
                              sbridge_part.xpath('lig_idx_list/idx')]
 
@@ -157,8 +157,8 @@ class HalogenBond(Interaction):
         self.dist = self.getdata(halogen_part, 'dist')
         self.don_angle = self.getdata(halogen_part, 'don_angle')
         self.acc_angle = self.getdata(halogen_part, 'acc_angle')
-        self.donortype = self.getdata(halogen_part, 'donortype')
-        self.acceptortype = self.getdata(halogen_part, 'acceptortype')
+        self.donortype = self.getdata(halogen_part, 'donortype', force_string=True)
+        self.acceptortype = self.getdata(halogen_part, 'acceptortype', force_string=True)
         self.don_idx = self.getdata(halogen_part, 'don_idx')
         self.acc_idx = self.getdata(halogen_part, 'acc_idx')
         self.sidechain = self.getdata(halogen_part, 'sidechain')
@@ -170,14 +170,14 @@ class MetalComplex(Interaction):
     def __init__(self, metalcomplex_part):
         Interaction.__init__(self, metalcomplex_part)
         self.metal_idx = self.getdata(metalcomplex_part, 'metal_idx')
-        self.metal_type = self.getdata(metalcomplex_part, 'metal_type')
+        self.metal_type = self.getdata(metalcomplex_part, 'metal_type', force_string=True)
         self.target_idx = self.getdata(metalcomplex_part, 'target_idx')
-        self.target_type = self.getdata(metalcomplex_part, 'target_type')
+        self.target_type = self.getdata(metalcomplex_part, 'target_type', force_string=True)
         self.coordination = self.getdata(metalcomplex_part, 'coordination')
         self.dist = self.getdata(metalcomplex_part, 'dist')
-        self.location = self.getdata(metalcomplex_part, 'location')
+        self.location = self.getdata(metalcomplex_part, 'location', force_string=True)
         self.rms = self.getdata(metalcomplex_part, 'rms')
-        self.geometry = self.getdata(metalcomplex_part, 'geometry')
+        self.geometry = self.getdata(metalcomplex_part, 'geometry', force_string=True)
         self.complexnum = self.getdata(metalcomplex_part, 'complexnum')
         self.targetcoo = self.getcoordinates(metalcomplex_part, 'targetcoo')
         self.metalcoo = self.getcoordinates(metalcomplex_part, 'metalcoo')
@@ -190,13 +190,13 @@ class BSite(XMLStorage):
         self.pdbid = pdbid
         self.bsid = ":".join(bindingsite.xpath('identifiers/*/text()')[2:5])
         self.uniqueid = ":".join([self.pdbid, self.bsid])
-        self.hetid = self.getdata(bindingsite, 'identifiers/hetid')
-        self.longname = self.getdata(bindingsite, 'identifiers/longname')
-        self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype')
-        self.smiles = self.getdata(bindingsite, 'identifiers/smiles')
-        self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey')
+        self.hetid = self.getdata(bindingsite, 'identifiers/hetid', force_string=True)
+        self.longname = self.getdata(bindingsite, 'identifiers/longname', force_string=True)
+        self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype', force_string=True)
+        self.smiles = self.getdata(bindingsite, 'identifiers/smiles', force_string=True)
+        self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey', force_string=True)
         self.position = self.getdata(bindingsite, 'identifiers/position')
-        self.chain = self.getdata(bindingsite, 'identifiers/chain')
+        self.chain = self.getdata(bindingsite, 'identifiers/chain', force_string=True)
 
         # Information on binding site members
         self.members = []

plip/modules/preparation.py

@@ -340,7 +340,10 @@ class LigandFinder:
 
         write_message("Renumerated molecule generated\n", mtype='debug')
 
+        if not config.NOPDBCANMAP:
             atomorder = canonicalize(lig)
+        else:
+            atomorder =  None
 
         can_to_pdb = {}
         if atomorder is not None:

plip/modules/report.py

@@ -19,17 +19,18 @@ from . import config
 # External libraries
 import lxml.etree as et
 
-__version__ = '1.4.1'
+__version__ = '1.4.2'
 
 class StructureReport:
     """Creates reports (xml or txt) for one structure/"""
-    def __init__(self, mol):
+    def __init__(self, mol, outputprefix='report'):
         self.mol = mol
         self.excluded = self.mol.excluded
         self.xmlreport = self.construct_xml_tree()
         self.txtreport = self.construct_txt_file()
         self.get_bindingsite_data()
         self.outpath = mol.output_path
+        self.outputprefix = outputprefix
 
     def construct_xml_tree(self):
         """Construct the basic XML tree"""
@@ -95,7 +96,7 @@ class StructureReport:
     def write_xml(self, as_string=False):
         """Write the XML report"""
         if not as_string:
-            et.ElementTree(self.xmlreport).write('%s/report.xml' % self.outpath, pretty_print=True, xml_declaration=True)
+            et.ElementTree(self.xmlreport).write('{}/{}.xml'.format(self.outpath, self.outputprefix), pretty_print=True, xml_declaration=True)
         else:
             output = et.tostring(self.xmlreport, pretty_print=True)
             if config.RAWSTRING:
@@ -105,7 +106,7 @@ class StructureReport:
     def write_txt(self, as_string=False):
         """Write the TXT report"""
         if not as_string:
-            with open('%s/report.txt' % self.outpath, 'w') as f:
+            with open('{}/{}.txt'.format(self.outpath, self.outputprefix), 'w') as f:
                 [f.write(textline + '\n') for textline in self.txtreport]
         else:
             output = '\n'.join(self.txtreport)

plip/plipcmd

@@ -44,7 +44,7 @@ def threshold_limiter(aparser, arg):
 
 
 
-def process_pdb(pdbfile, outpath, as_string=False):
+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:
         startmessage = '\nStarting analysis of %s\n' % pdbfile.split('/')[-1]
@@ -62,7 +62,7 @@ def process_pdb(pdbfile, outpath, as_string=False):
     create_folder_if_not_exists(outpath)
 
     # Generate the report files
-    streport = StructureReport(mol)
+    streport = StructureReport(mol, outputprefix=outputprefix)
 
     config.MAXTHREADS = min(config.MAXTHREADS, len(mol.interaction_sets))
 
@@ -127,6 +127,7 @@ def main(inputstructs, inputpdbids):
     write_message('\n' + '*' * len(title) + '\n')
     write_message(title)
     write_message('\n' + '*' * len(title) + '\n\n')
+    outputprefix = config.OUTPUTFILENAME
 
     if inputstructs is not None:  # Process PDB file(s)
         num_structures = len(inputstructs)
@@ -147,7 +148,8 @@ def main(inputstructs, inputpdbids):
                 if num_structures > 1:
                     basename = inputstruct.split('.')[-2].split('/')[-1]
                     config.OUTPATH = '/'.join([config.BASEPATH, basename])
-            process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin)
+                    outputprefix = 'report'
+            process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin, outputprefix=outputprefix)
     else:  # Try to fetch the current PDB structure(s) directly from the RCBS server
         num_pdbids = len(inputpdbids)
         inputpdbids =remove_duplicates(inputpdbids)
@@ -155,7 +157,8 @@ def main(inputstructs, inputpdbids):
             pdbpath, pdbid = download_structure(inputpdbid)
             if num_pdbids > 1:
                 config.OUTPATH = '/'.join([config.BASEPATH, pdbid[1:3].upper(), pdbid.upper()])
-            process_pdb(pdbpath, config.OUTPATH)
+                outputprefix = 'report'
+            process_pdb(pdbpath, config.OUTPATH, outputprefix=outputprefix)
 
     if (pdbid is not None or inputstructs is not None) and config.BASEPATH is not None:
         if config.BASEPATH in ['.', './']:
@@ -204,9 +207,14 @@ if __name__ == '__main__':
     parser.add_argument("--nofixfile", dest="nofixfile", default=False,
                         help="Turns off writing files for fixed PDB files.",
                         action="store_true")
+    parser.add_argument("--nopdbcanmap", dest="nopdbcanmap", default=False,
+                        help="Turns off calculation of mapping between canonical and PDB atom order for ligands.",
+                        action="store_true")
     parser.add_argument("--dnareceptor", dest="dnareceptor", default=False,
                         help="Uses the DNA instead of the protein as a receptor for interactions.",
                         action="store_true")
+    parser.add_argument("--name", dest="outputfilename", default="report",
+                        help="Set a filename for the report TXT and XML files. Will only work when processing single structures.")
     ligandtype = parser.add_mutually_exclusive_group()  # Either peptide/inter or intra mode
     ligandtype.add_argument("--peptides", "--inter", dest="peptides", default=[],
                         help="Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts",
@@ -251,8 +259,10 @@ if __name__ == '__main__':
     config.INTRA = arguments.intra
     config.NOFIX = arguments.nofix
     config.NOFIXFILE = arguments.nofixfile
+    config.NOPDBCANMAP = arguments.nopdbcanmap
     config.KEEPMOD = arguments.keepmod
     config.DNARECEPTOR = arguments.dnareceptor
+    config.OUTPUTFILENAME = arguments.outputfilename
     # Make sure we have pymol with --pics and --pymol
     if config.PICS or config.PYMOL:
         try:

setup.py

@@ -6,7 +6,7 @@ setup.py - Setup configuration file for pip, etc.
 from setuptools import setup
 
 setup(name='plip',
-      version='1.4.1',
+      version='1.4.2',
       description='PLIP - Fully automated protein-ligand interaction profiler',
       classifiers=[
           'Development Status :: 5 - Production/Stable',