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SmotifCS-0.07
River stage zero No dependents
++
/ GenerateShiftFiles

NAME

GenerateShiftFiles

VERSION

Version 0.01

SYNOPSIS

This script runs TALOS+ on the chemical shift input file in order to determine the secondary structure elements of the unknown protein

INPUT ARGUMENTS: 1) $pdb : pdb code (the chemical shift file should be in the subdirectory identified by the pdb code e.g. 1ptf/pdb1ptfshifts.dat) 2) $chain : chain ID (default = A)

INPUT FILES: In the <pdbcode> folder: 1) pdb<pdbcode>shifts.dat : BMRB-format file with chemical shift data

OUTPUT FILES: In the <pdbcode> folder: 1) pred<pdbcode>.tab : File with Residue number, name, and estimates for phi and psi angles 2) <pdbcode>.out :File with smotif information: Protein code, Chain, Smotif type, Smotif start residue, Loop length, Length of first secondary structure, Length of second secondary structure, Sequence 3) pdb<pdbcode>_shiftsXXX.dat : Set of files containing chemical shift data for residues in each smotif

    Usage: 

    use GenerateShiftFiles;

    GenerateShiftFiles($pdb,$chain);

SUBROUTINES

        run_and_analyze_talos
        count_smotifs
        split_ss_string
        translate

run_and_analyze_talos

        SUBROUTINE to identify smotifs from TALOS+ determination of secondary structures using chemical shift data

split_ss_string

        SUBROUTINE to convert a series of secondary structure types to a list of 
    start and end points for smotifs

    Input 1: $ss - a string of secondary structure types, 
             where H=alpha helix and E=strand e.g. (HHHHLLLLEEEE)
        
    Input 2: $startpos - residue at which first smotif begins
        
    Output  : Array containing Smotif definitions

Subroutine to count the number of Smotifs in a given Smotif definition file (typically $pdb/$pdb.out). Input : Filename with Smotif definition Output: Returns the number of Smotifs in the given file

Subroutine to count the number of Smotifs in a given Smotif definition file (typically $pdb/$pdb.out). Input : Filename with Smotif definition Output: Returns the number of Smotifs in the given file

SUBROUTINE to convert 3-letter amino acids into single-letter codes Input: 3-letter amino acid code Output: Corresponding 1-letter amino acid code

AUTHOR

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=.. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

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

    perldoc GenerateShiftFiles

You can also look for information at:

ACKNOWLEDGEMENTS

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.