Package schrodinger :: Package application :: Module ska

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.

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

Classes

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_SkaData
Data structure for named backend return values...

Functions

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transform_structure(st, u, x)
perform in-place transformation

_standardize(old_ct, rename, reorder)
Return the standardized version of the input structure, without modifying the input CT.

list of _SkaData

pairwise_align_ct(query, templist, keywords=None, log=None, debug=False, save_props=False, std_res=False, reorder=False, asl=None)
Wrapper for a series of pairwise ska jobs with CTs as input.

_SkaData

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.

_SkaData

run_align(structs, keywords, log=None, debug=False)
Core driver routine, equivalent to $SCHRODINGER/ska with all top-level input options specified in keywords.

Variables

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_true_val = re.compile(r'(?i)^(1|TRUE|YES)$')

_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]

_standardize(old_ct, rename, reorder)

Return the standardized version of the input structure, without modifying the input CT.

Parameters:

rename (bool) - Whether to convert the non-standard residue names to standard forms where possible (e.g. HID -> HIS).
reorder (bool) - Whether to re-order the residues by sequence.
If both options are False, will return the original input structure, without making a copy.

pairwise_align_ct(query, templist, keywords=None, log=None, debug=False, save_props=False, std_res=False, reorder=False, asl=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 substructure to align (applied to all structures)

Returns: list of _SkaData

list of alignments corresponding to templist

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: _SkaData: a single multiple alignment

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 of Structures) - 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: _SkaData

a single multiple alignment

Variables Details

[hide private]

_atom_rec

Value:

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