The Perl Toolchain Summit needs more sponsors. If your company depends on Perl, please support this very important event.
 / 
SmotifTF-0.09
River stage zero No dependents
++
/ EnumerateSmotifCombinations

NAME

EnumerateSmotifCombinations

VERSION

Version 0.01

SYNOPSIS

    Module for enumerating combinations of Smotifs to generate full protein models

    Usage:

    use EnumerateSmotifCombinations;

    EnumerateSmotifCombinations($pdbcode,$mot,$havestructure);

EXPORT

    enumerate
    full_enum
    prepare_for_enumeration
    pre_gen_list
    gen_list

prepare_for_enumeration

This subroutine prepares all the files needed for enumeration

pre_gen_list

Subroutine to generate the input list for enumeration

gen_list

Subroutine to generate the input list for enumeration

enumerate

This subroutine builds a full enumeration of combinations of given smotifs (stored in a file) and calculates 4 scoring component values: radius of gyration, statistical pairwise contact potential, implicit solvation potential, and long range H bond potential.

INPUTS 1. pdbcode - the 4-character name of the folder to store input and output data 2. mot1 - an underscore-delimited set of characters outlining which subset of smotifs to enumerate. Example: If there are 4 putative smotifs, each with 5 candidates, _0_2_3 will take the first candidate for smotif1, the third candidate for smotif2, the fourth candidate for smotif3, and then enumerate through all the candidates for smotif4, resulting in 5 structures total. For the same set, _1 will take the second candidate for smotif1, and enumerate all combinations for the following three smotifs, resulting in 5x5x5=125 candidates. 3. havestructure - either 0 or 1 0 indicate there is no solved structure for comparison 1 indicate solved structure exists in the input folder. If 1, the RMSD of each enumerated structure (as compared to the solved structure) will be output, as well as GDT_TS scores for thos structures with RMSD < 10A. If the no structure option is selected (0), the RMSD and GDT_TS columns of the output will contain zeros.

REQUIRED FILES (all to be found in the "pdbcode" directory) "pdbcode".out - file containing a list of start and end points of smotifs in the query protein, as well as secondary structure and loop lengths. This is one of the standard output files of the generate_shift_files.pl script.

  "pdbcode"_motifs_best.csv - file containing a list of candidates for each putative smotif. 
                   This is one of the standard output files of the findranks.pl script.

OUTPUT (to screen) For each enumerated structure without excessive steric clashes (# backbone atoms within 2A < number of smotifs), tab-delimited information about the constituent smotifs and the overall structure scoring components is printed to the screen.

Sample line for a structure with 4 smotifs 1.437 0.740 1.867 8.377 224162 148918 54194 127698 1.7483 0.9973 0.9616 1.2306 8.8294 58.8240 12 0 0 0 0

Explanation: 1.437 0.740 1.867 8.377 : RMSDs of the 4 smotif components individually 224162 148918 54194 127698 : Nids of the 4 smotif components 1.7483 : Per-residue radius of gyration z-score 0.9973 : Per-residue pairwise contact potential z-score 0.9616 : Per-residue solvation potential z-score 1.2306 : Long-range H-bond potential z-score 8.8294 : Overall structure RMSD (from solved structure) 58.8250 : Overall structure GDT_TS score 12 0 0 0: List of indices of smotifs, as found in the <pdbcode>_motifs_best.csv file 0 : Number of steric clashes

full_enum

Subroutine to recursively run full enumeration

in_array

Subroutine to check if a scalar element is in an array

get_dd_info

Subroutine to get dynamic database entry details from smotif nid

AUTHORS

Fiserlab Members , <andras at fiserlab.org>

BUGS

Please report any bugs or feature requests to bug-. at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=..

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc EnumerateSmotifCombinations

LICENSE AND COPYRIGHT

Copyright 2015 Fiserlab Members .

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.