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choderalab / ensembler

Automated omics-scale protein modeling and simulation setup.
http://ensembler.readthedocs.io/
GNU General Public License v2.0
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Skip template loop modeling for templates not missing any loops #63

Open jchodera opened 8 years ago

jchodera commented 8 years ago 
mski1776:ensembler-test choderaj$ ensembler quickmodel --target_uniprot_entry_name ABL1_HUMAN --uniprot_domain_regex '^Protein kinase' --template_pdbids 2SRC
WARNING: /opt/anaconda1anaconda2anaconda3 not found.
Ignoring mpi4py.
Using mpi4py on OS X with Anaconda currently requires that /opt/anaconda1anaconda2anaconda3 points to your Anaconda installation.
As a workaround, you can create a symlink, e.g. "sudo ln -s ~/anaconda /opt/anaconda1anaconda2anaconda3
Done.
Querying UniProt web server...
Number of entries returned from initial UniProt search: 2

Set of unique domain names returned from the initial UniProt search using the query string 'mnemonic:ABL1_HUMAN':
set(['SH2', 'SH3', 'Protein kinase'])

Unique domain names selected after searching with the case-sensitive regex string '^Protein kinase':
set(['Protein kinase'])

Done.
Downloading PDB file for: 2SRC
Downloading sifts file for: 2SRC
1 PDB chains selected.
Extracting residues from PDB chains...
1 templates selected.

Writing template structures...
Done.
MPI rank 0 pdbfixer error for template SRC_HUMAN_D0_2SRC_A - see logfile
Modeling missing loops for template SRC_HUMAN_D0_2SRC_A
Traceback (most recent call last):
  File "/Users/choderaj/miniconda/bin/ensembler", line 6, in <module>
    sys.exit(main())
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/cli.py", line 40, in main
    command.dispatch(args)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/cli_commands/quickmodel.py", line 106, in dispatch
    QuickModel(targetid=args['--targetid'], templateids=templateids, target_uniprot_entry_name=args['--target_uniprot_entry_name'], uniprot_domain_regex=args['--uniprot_domain_regex'], pdbids=pdbids, chainids=chainids_dict, template_uniprot_query=args['--template_uniprot_query'], template_seqid_cutoff=template_seqid_cutoff, loopmodel=not args['--no-loopmodel'], package_for_fah=args['--package_for_fah'], nfahclones=nfahclones, structure_dirs=structure_paths)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/tools/quick_model.py", line 95, in __init__
    self._model(self.targetid, self.templateids, loopmodel=self.loopmodel, package_for_fah=self.package_for_fah, nfahclones=self.nfahclones)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/tools/quick_model.py", line 138, in _model
    ensembler.modeling.model_template_loops(process_only_these_templates=templateids)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/utils.py", line 37, in print_done
    fn(*args, **kwargs)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/modeling.py", line 74, in model_template_loops
    loopmodel_templates(templates_resolved_seq, missing_residues_list, process_only_these_templates=process_only_these_templates, overwrite_structures=overwrite_structures)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/modeling.py", line 221, in loopmodel_templates
    loopmodel_template(template, missing_residues[template_index], overwrite_structures=overwrite_structures)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/modeling.py", line 234, in loopmodel_template
    write_loop_file(template, missing_residues)
  File "/Users/choderaj/miniconda/lib/python2.7/site-packages/ensembler/modeling.py", line 259, in write_loop_file
    loop_residues_data = [(key[1], len(residues)) for key, residues in missing_residues.iteritems()]
AttributeError: 'NoneType' object has no attribute 'iteritems'