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.
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force_rmdir(dir)
Recursive 'rm -r' using fileutils.force_remove |
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transform_structure(st,
u,
x)
perform in-place transformation |
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standardize(old_ct,
rename,
reorder)
Convert non-standard residue names to standard forms where possible
(e.g. |
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list of _SkaData
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pairwise_align_ct(query,
templist,
keywords=None,
log=None,
debug=False,
save_props=False,
std_res=False,
reorder=False)
Wrapper for a series of pairwise ska jobs with CTs as input. |
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_SkaData
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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. |
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list of _SkaData
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pairwise_align_pdb(query,
templist,
keywords=None,
log=None,
debug=False,
std_res=False,
reorder=False)
Wrapper for a series of pairwise ska jobs with PDB files as input. |
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_SkaData
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multiple_align_pdb(query,
templist,
keywords=None,
log=None,
debug=False,
std_res=False,
reorder=False)
Wrapper for a single multiple-alignment ska job with PDB files as
input. |
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_SkaData
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run_align(structs,
keywords,
log=None,
debug=False)
Core driver routine, equivalent to $SCHRODINGER/ska with
all top-level input options specified in keywords . |
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