schrodinger.application.ska module

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.

For higher level API, use the schrodinger.structutils.structalign module.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.application.ska.get_ska_transformation_matrix(st)

Retrieves a transformation matrix from the given structure decorated with a ska alignment transformation.

Returns

4x4 transformation matrix

Return type

numpy.ndarray

schrodinger.application.ska.transform_structure(st, u, x)

perform in-place transformation

schrodinger.application.ska.pairwise_align_ct(query, templist, keywords=None, log=None, debug=False, save_props=False, std_res=False, reorder=False, asl=None, asl_mobile=None)

Wrapper for a series of pairwise ska jobs with CTs as input. NOTE: For higher-level API, use schrodinger.structutils.structalign module.

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

  • std_res (bool) – True if residue names are translated to standard forms

  • reorder (bool) – True if residues need to be reordered by connectivity

  • asl (str) – ASL for reference substructure to align

  • asl_mobile (str) – ASL for mobile substructures to align

Returns

list of alignments corresponding to templist

Return type

list of _SkaData

schrodinger.application.ska.multiple_align_ct(query, templist, keywords=None, log=None, debug=False, save_props=False, std_res=False, reorder=False)

Wrapper for a single multiple-alignment ska job with CTs as input. NOTE: For higher-level API, use schrodinger.structutils.structalign module.

Arguments are the same as in pairwise_align_ct above.

Returns

a single multiple alignment

Return type

_SkaData

schrodinger.application.ska.run_align(structs, 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.

NOTE: For higher-level API, use schrodinger.structutils.structalign module.

Parameters

  • structs (list(schrodinger.structure.Structure)) – structures to align. First in list is query; the rest of CTs will be aligned to it (templates).

  • keywords (dict) – top-level keyword-value input options

  • log (logging.logger) – active logger for diagnostic messages

  • debug (bool) – debug flag passed to backend

Returns

a single multiple alignment

Return type

_SkaData