Merge pull request #145 from pharmai/development

Version 2.3.0

.github/workflows/action.yml

@@ -1,7 +1,7 @@
 name: PLIP Build
 
 on:
-  push
+  [push, pull_request]
 
 jobs:
   docker-hub:
@@ -16,4 +16,4 @@ jobs:
           password: ${{ secrets.DOCKER_HUB_TOKEN }}
           repository: pharmai/plip
           tag_with_ref: true
-          push: ${{ startsWith(github.ref, 'refs/tags/') }}
+          push: ${{ startsWith(github.ref, 'refs/tags/') }}

CHANGES.txt

@@ -1,5 +1,10 @@
 Changelog
 ---------
+# 2.3.0
+* fixes an issue that caused encoding errors to be thrown
+* salt bridge interaction improved
+* minor bugs fixed
+
 # 2.2.2
 * fixes an issue that caused encoding errors to be thrown
 

README.md

@@ -69,7 +69,7 @@ If you cannot use the containerized bundle or want to use PLIP sources, make sur
 - Python >= 3.6.9
 - [OpenBabel](#Installing-OpenBabel) >= 3.0.0 with [Python bindings](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html)
 - PyMOL >= 2.3.0 with Python bindings (optional, for visualization only)
-- ImageMagick >= 6.9 (optional)
+- ImageMagick >= 7.0 (optional)
 
 **Python:** If you are on a system where Python 3 is executed using `python3` instead of just `python`, replace the `python` and `pip` commands in the following steps with `python3` and `pip3` accordingly.
 
@@ -164,7 +164,7 @@ Using PLIP in your commercial or non-commercial project is generally possible wh
 If you are using PLIP in your work, please cite
 > Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA.
 > Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
- 
+
 or
 
 > Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler.

plip/basic/config.py

@@ -1,4 +1,4 @@
-__version__ = '2.2.2'
+__version__ = '2.3.0'
 __maintainer__ = 'PharmAI GmbH (2020-2021) - www.pharm.ai - hello@pharm.ai'
 __citation_information__ = "Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. " \
                            "Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294"

plip/basic/supplemental.py

@@ -298,7 +298,6 @@ def sort_members_by_importance(members):
     main = [x for x in members if x[0] not in config.METAL_IONS]
     ion = [x for x in members if x[0] in config.METAL_IONS]
     sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
-    sorted_main = sorted(main, key=lambda x: (x[1], x[2]))
     sorted_ion = sorted(ion, key=lambda x: (x[1], x[2]))
     return sorted_main + sorted_ion
 

plip/structure/preparation.py

@@ -51,14 +51,16 @@ def parse_pdb(self):
         alt = []
         previous_ter = False
 
-        model_dict = {1: list()}
+        model_dict = {0: list()}
 
         # Standard without fixing
         if not config.NOFIX:
             if not config.PLUGIN_MODE:
                 lastnum = 0  # Atom numbering (has to be consecutive)
                 other_models = False
-                current_model = 1
+                # Model 0 stores header and similar additional data
+                # or the full file if no MODEL entries exist in the file
+                current_model = 0
                 for line in fil:
                     corrected_line, newnum = self.fix_pdbline(line, lastnum)
                     if corrected_line is not None:
@@ -81,8 +83,11 @@ def parse_pdb(self):
                 try:
                     if other_models:
                         logger.info(f'selecting model {config.MODEL} for analysis')
-                    corrected_pdb = ''.join(model_dict[config.MODEL])
-                    corrected_lines = model_dict[config.MODEL]
+                    corrected_pdb = ''.join(model_dict[0])
+                    corrected_lines = model_dict[0]
+                    if current_model > 0:
+                        corrected_pdb += ''.join(model_dict[config.MODEL])
+                        corrected_lines += model_dict[config.MODEL]
                 except KeyError:
                     corrected_pdb = ''.join(model_dict[1])
                     corrected_lines = model_dict[1]
@@ -924,6 +929,7 @@ def find_hal(self, atoms):
 
     def find_charged(self, mol):
         """Looks for positive charges in arginine, histidine or lysine, for negative in aspartic and glutamic acid."""
+        """If nucleic acids are part of the receptor, looks for negative charges in phosphate backbone"""
         data = namedtuple('pcharge', 'atoms atoms_orig_idx type center restype resnr reschain')
         a_set = []
         # Iterate through all residue, exclude those in chains defined as peptides
@@ -961,6 +967,17 @@ def find_charged(self, mol):
                                       restype=res.GetName(),
                                       resnr=res.GetNum(),
                                       reschain=res.GetChain()))
+            if res.GetName() in config.DNA + config.RNA and config.DNARECEPTOR: # nucleic acids have negative charge in sugar phosphate
+                for a in pybel.ob.OBResidueAtomIter(res):
+                    if a.GetType().startswith('P') and res.GetAtomProperty(a, 9) \
+                            and not self.Mapper.mapid(a.GetIdx(), mtype='protein') in self.altconf:
+                        a_contributing.append(pybel.Atom(a))
+                        a_contributing_orig_idx.append(self.Mapper.mapid(a.GetIdx(), mtype='protein'))
+                if not len(a_contributing) == 0:
+                    a_set.append(data(atoms=a_contributing,atoms_orig_idx=a_contributing_orig_idx, type='negative', 
+                                      center=centroid([ac.coords for ac in a_contributing]), restype=res.GetName(),
+                                      resnr=res.GetNum(),
+                                      reschain=res.GetChain()))
         return a_set
 
     def find_metal_binding(self, mol):
@@ -1365,7 +1382,7 @@ def load_pdb(self, pdbpath, as_string=False):
 
         if not as_string:
             self.sourcefiles['filename'] = os.path.basename(self.sourcefiles['pdbcomplex'])
-        self.protcomplex, self.filetype = read_pdb(self.corrected_pdb, as_string=True)
+        self.protcomplex, self.filetype = read_pdb(self.corrected_pdb, as_string= (self.corrected_pdb != pdbpath)) # self.corrected_pdb may fallback to pdbpath
 
         # Update the model in the Mapper class instance
         self.Mapper.original_structure = self.protcomplex.OBMol