Minor fixes to accommodate the changes introduced to the PDBXwriter r…

…un (atom lines) methods.
bartongroup · Sep 6, 2017 · 92973e5 · 92973e5
1 parent 1a988b4
commit 92973e5
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/prointvar/dssp.py b/prointvar/dssp.py
@@ -442,7 +442,8 @@ def _run(self, dssp_bin, run_unbound=False, override=False, save_new_input=False
                         w = PDBXwriter(inputfile=None, outputfile=outputpdb)
                         try:
                             w.run(data=data, chain=(chain,), res=None, atom=None,
-                                  lines=('ATOM',), override=override, format_type="pdb")
+                                  lines=('ATOM',), override=override, format_type="pdb",
+                                  category=category)
                         except ValueError:
                             # skipping only HETATM chains or (generally) empty tables
                             continue
@@ -483,7 +484,7 @@ def write(self, **kwargs):
         return self.run(**kwargs)
 
     def run(self, run_unbound=False, override=False, save_new_input=False,
-            clean_output=True):
+            clean_output=True, category='label'):
 
         # generate outputfile if missing
         if not self.outputfile:
@@ -497,7 +498,8 @@ def run(self, run_unbound=False, override=False, save_new_input=False,
 
             # run dssp and generate output
             self._run(dssp_bin, run_unbound=run_unbound, override=override,
-                      save_new_input=save_new_input, clean_output=clean_output)
+                      save_new_input=save_new_input, clean_output=clean_output,
+                      category=category)
         else:
             logger.info("DSSP for %s already available...", self.outputfile)
         return

diff --git a/prointvar/merger.py b/prointvar/merger.py
@@ -387,7 +387,7 @@ def table_generator(uniprot_id=None, pdb_id=None, chain=None, res=None,
 
                 if not os.path.isfile(outputdssp_unb) or override:
                     w = DSSPrunner(inputcif, outputdssp_unb)
-                    w.run(override=override, run_unbound=dssp_unbound)
+                    w.run(override=override, run_unbound=dssp_unbound, category="auth")
                 if os.path.exists(outputdssp_unb):
                     r = DSSPreader(outputdssp_unb)
                     dssp_unb_table = r.residues(add_ss_reduced=True, add_rsa_class=True,