Package schrodinger :: Package application :: Module ska
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Module ska

Core routines for wrapping SKA backend.

This module provides direct access to the functionality used by the top-level ska program and structalign utility. The usual keyword-value options in the top-level input file are supplied as a python dict. Wrappers are supplied to provide PDB filenames as input as well as maestro CTs which are transformed in place.

Copyright Schrodinger, LLC. All rights reserved.

Classes [hide private]
  SkaData
Data structure for named backend return values...
Functions [hide private]
 
force_rmdir(dir)
Recursive 'rm -r' using fileutils.force_remove
 
transform_structure(st, u, x)
perform in-place transformation
list of SkaData
pairwise_align_ct(query, templist, keywords={'MODE': 'align'}, log=None, debug=False, save_props=False)
Wrapper for a series of pairwise ska jobs with CTs as input.
SkaData
multiple_align_ct(query, templist, keywords={'MODE': 'align'}, log=None, debug=False, save_props=False)
Wrapper for a single multiple-alignment ska job with CTs as input.
list of SkaData
pairwise_align_pdb(query, templist, keywords={'MODE': 'align'}, log=None, debug=False)
Wrapper for a series of pairwise ska jobs with PDB files as input.
SkaData
multiple_align_pdb(query, templist, keywords={'MODE': 'align'}, log=None, debug=False)
Wrapper for a single multiple-alignment ska job with PDB files as input.
SkaData
run_align(keywords, log=None, debug=False)
Core driver routine, equivalent to $SCHRODINGER/ska with all top-level input options specified in keywords.
Variables [hide private]
  _true_val = re.compile(r'(?i)^(1|TRUE|YES)$')
  _data_fmt = re.compile(r'^REMARK\s+([-\.\d]+)\s+([-\.\d]+)\s+(...
  _chain_fmt = re.compile(r'^REMARK Chain [A-Za-z]: tc_sse:(\S+)$')
  _atom_rec = re.compile(r'^((ATOM |HETATM).{24})([ -\.\d]{8})(...
  _winlen_vals = [2, 6, 9, 14, 17]
  _trolltop = None
hash(x)
  __package__ = 'schrodinger.application'
Function Details [hide private]

pairwise_align_ct(query, templist, keywords={'MODE': 'align'}, log=None, debug=False, save_props=False)

 

Wrapper for a series of pairwise ska jobs with CTs as input.

Parameters:
  • query ((seqname, ct) tuple) - fixed reference structure
  • templist (list of (seqname, ct) tuples) - one or more structures to be aligned
  • keywords (dict) - top-level keyword-value input options (other than QUERY_FILE and TEMPLATE)
  • log (logging.logger) - active logger for diagnostic messages
  • debug (bool) - debug flag passed to backend
  • save_props (bool) - True if output data included as CT properties
Returns: list of SkaData
list of alignments corresponding to templist

multiple_align_ct(query, templist, keywords={'MODE': 'align'}, log=None, debug=False, save_props=False)

 

Wrapper for a single multiple-alignment ska job with CTs as input.

Arguments are the same as in pairwise_align_ct above.

Returns: SkaData
a single multiple alignment

pairwise_align_pdb(query, templist, keywords={'MODE': 'align'}, log=None, debug=False)

 

Wrapper for a series of pairwise ska jobs with PDB files as input.

Parameters:
  • query (string) - fixed reference PDB file
  • templist (list of strings) - one or more PDB files to be aligned
  • keywords (dict) - top-level keyword-value input options (other than QUERY_FILE and TEMPLATE)
  • log (logging.logger) - active logger for diagnostic messages
  • debug (bool) - debug flag passed to backend
Returns: list of SkaData
list of alignments corresponding to templist

multiple_align_pdb(query, templist, keywords={'MODE': 'align'}, log=None, debug=False)

 

Wrapper for a single multiple-alignment ska job with PDB files as input.

Arguments are the same as in pairwise_align_pdb above.

Returns: SkaData
a single multiple alignment

run_align(keywords, log=None, debug=False)

 

Core driver routine, equivalent to $SCHRODINGER/ska with all top-level input options specified in keywords. Returns alignment, scores, and rotation matrices as well as backend stdout.

Parameters:
  • options (dict) - top-level keyword-value input options
  • log (logging.logger) - active logger for diagnostic messages
  • debug (bool) - debug flag passed to backend
Returns: SkaData
a single multiple alignment

Variables Details [hide private]

_data_fmt

Value:
re.compile(r'^REMARK\s+([-\.\d]+)\s+([-\.\d]+)\s+([-\.\d]+)$')

_atom_rec

Value:
re.compile(r'^((ATOM  |HETATM).{24})([ -\.\d]{8})([ -\.\d]{8})([ -\.\d\
]{8})(.*)$')