Merge branch 'development'

Author: Sebastian Salentin

CHANGES.txt

@@ -2,6 +2,8 @@ Changelog
 ---------
 
 ### 1.3.2
+* __Processing of protein-peptide interactions via --peptides__
+* option to keep modified residues as ligands (--keepmod)
 * Improved code for reports
 * Smart ordering of ligand in composite compounds
 * Fixes handling and visualization of DNA/RNA

DOCUMENTATION.md

@@ -118,6 +118,17 @@ PLIP will create subdirectories for each given structure in the output folder.
 If in PDB ID mode (`i`), the folder structure will be nested and based on the two middle characters of the PDB ID.
 The structure 1vsn in batch processing will have its output files in <outputfolder>/vs/1vsn .
 
+### Detection of protein-peptide interactions
+For the detection of ligands, PLIP relies on the separation of ATOM and HETATM entries in the PDB file.
+The latter are searched for suitable ligands when running in normal mode.
+Peptide ligands, however, are usually deposited as ATOM entries in a separate chain.
+PLIP can not detect these entities automatically.
+To switch into protein-peptide interaction mode, start PLIP with the option `--peptide`, followed by the peptide chain of interest, e.g.:
+
+```bash
+plip -i 5hi4 --peptides I -vx
+```
+
 ## Changing detection thresholds
 The PLIP algorithm uses a rule-based detection to report non-covalent interaction between proteins and their partners.
 The current settings are based on literature values and have been refined based on extensive testing with independent cases from mainly crystallography journals, covering a broad range of structure resolutions.
@@ -150,10 +161,11 @@ PLIP offers further command line options which enables you to switch advanced se
 * Do not discard alternate locations (`--altlocation`)
 * Set debug mode (`--debug`)
 * Turn off automatic fixing of errors in PDB files (`--nofix`)
+* Keep modified residues as ligands (`--keepmod`)
 
 ## Web Service
 A web service for analysis of protein-ligand complexes using PLIP is available at
-http://projects.biotec.tu-dresden.de/plip-web
+http://plip.biotec.tu-dresden.de/
 The web site offers advanced functions to search for specific entries from PDB and lists the interaction results in the browser.
 Additionally, the service used the BioLiP database to annotate biologically relevant ligands.
 The option to change threshold, ligand filtering, and batch processing is only available in the command line tool and with the Python modules.

README.md

@@ -77,7 +77,7 @@ Joachim Haupt joachim.haupt (at) biotec.tu-dresden.de | https://github.com/vjhau
 Melissa F. Adasme Mora melissa.adasme (at) biotec.tu-dresden.de
 
 ## PLIP Web Server
-Visit our PLIP Web Server on http://projects.biotec.tu-dresden.de/plip-web
+Visit our PLIP Web Server on http://plip.biotec.tu-dresden.de/
 
 ## Contact Me
 Do you have feature requests, found a bug or want to use `PLIP` in your project?

plip/modules/config.py

@@ -30,6 +30,7 @@
 PLUGIN_MODE = False  # Special mode for PLIP in Plugins (e.g. PyMOL)
 NOFIX = False  # Turn off fixing of errors in PDB files
 PEPTIDES = []  # Definition which chains should be considered as peptide ligands
+KEEPMOD = False
 
 # Configuration file for Protein-Ligand Interaction Profiler (PLIP)
 # Set thresholds for detection of interactions

plip/modules/detection.py

@@ -372,8 +372,9 @@ def metal_complexation(metals, metal_binding_lig, metal_binding_bs):
                     final_geom, final_coo, = next_total.geometry, next_total.coordination
                     rms, excluded = next_total.rms, next_total.excluded
                     break
-                elif i == len(all_total) - 1:
-                    final_geom, final_coo, rms, excluded = "NA", "NA", 0.0, []
+                elif i == len(all_total) - 2:
+                    final_geom, final_coo, rms, excluded = "NA", "NA", float('nan'), []
+                    break
 
         # Record all contact pairing, excluding those with targets superfluous for chosen geometry
         only_water = set([x[0].location for x in contact_pairs]) == {'water'}

plip/modules/preparation.py

@@ -333,7 +333,10 @@ def filter_for_ligands(self):
 
         water = [o for o in pybel.ob.OBResidueIter(self.proteincomplex.OBMol) if o.GetResidueProperty(9)]
         # Filter out non-ligands
-        candidates2 = [a for a in candidates1 if is_lig(a.GetName()) and a.GetName() not in self.modresidues]
+        if not config.KEEPMOD:  # Keep modified residues as ligands
+            candidates2 = [a for a in candidates1 if is_lig(a.GetName()) and a.GetName() not in self.modresidues]
+        else:
+            candidates2 = [a for a in candidates1 if is_lig(a.GetName())]
         write_message("%i ligand(s) after first filtering step.\n" % len(candidates2), mtype='debug')
 
         ############################################

plip/modules/visualize.py

@@ -99,7 +99,7 @@ def visualize_in_pymol(plcomplex):
         for member in lig_members:
            resid, chain, resnr = member[0], member[1], str(member[2])
            cmd.select(ligname, '%s or (resn %s and chain %s and resi %s)' % (ligname, resid, chain, resnr))
-    
+
     cmd.show('sticks', ligname)
     cmd.color('myblue')
     cmd.color('myorange', ligname)

plip/plipcmd

@@ -209,6 +209,9 @@ if __name__ == '__main__':
     parser.add_argument("--peptides", dest="peptides", default=[],
                         help="Allows to define one or multiple chains as peptide ligands",
                         nargs="+")
+    parser.add_argument("--keepmod", dest="keepmod", default=False,
+                        help="Keep modified residues as ligands",
+                        action="store_true")
     # Optional threshold arguments, not shown in help
     thr = namedtuple('threshold', 'name type')
     thresholds = [thr(name='aromatic_planarity', type='angle'),
@@ -241,6 +244,7 @@ if __name__ == '__main__':
     config.ALTLOC = arguments.altlocation
     config.PEPTIDES =arguments.peptides
     config.NOFIX = arguments.nofix
+    config.KEEPMOD = arguments.keepmod
     # Assign values to global thresholds
     for t in thresholds:
         tvalue = getattr(arguments, t.name)