From 92973e5afc88f76512abd1871967aad76583cc1c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fa=CC=81bio=20Madeira?= Date: Wed, 6 Sep 2017 17:29:06 +0100 Subject: [PATCH] Minor fixes to accommodate the changes introduced to the PDBXwriter run (atom lines) methods. --- prointvar/dssp.py | 8 +++++--- prointvar/merger.py | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/prointvar/dssp.py b/prointvar/dssp.py index 9600a84..975a3e2 100644 --- 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 index 42cc005..54e9b7e 100644 --- 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,