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SmotifCS-0.07
River stage zero No dependents
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/ Compare_shifts_torsion

NAME

Compare_shifts_torsion

VERSION

Version 0.01

SYNOPSIS

Script to compare experimental chemical shift data from a query protein against the database of smotifs with theoretical chemical shifts. The comparison consists of summing the weighted squared difference between the chemical shifts of the loop residues and up to 3 flanking secondary structure residues

INPUT ARGUMENTS 1) $pdb : 4-letter name of the folder where the experimental chemical shift data is stored 2) $havestructure : 0=no solved structure for RMSD comparison, 1=solved structure exists for RMSD comparison 3) $motnum : which smotif of the protein to compare (0=1st smotif, 1=2nd smotif, and so on)

INPUT FILES In the shift_weights/ folder: 1) tworanges.csv : A tab-delimited file containing the 5%-95% range of values for chemical shifts for each residue and atom type 2) A set of paired amino acid files (20x20=400 total, ranging from AA to YY) each containing the relative frequency that a given chemical shift value corresponds to an alpha-helical, beta-strand, or "other" configuration. Each of these files has a separate distribution for each of the six atom types.

In the <pdbcode> folder: 1) pred<pdbcode>.tab : Standard output file from TALOS+ with estimates of backbone torsion angles 2) <pdbcode>.out : Standard output file from generate_shifts.pl with information about each smotif

OUTPUT FILES In the <pdbcode> folder: 1) shiftcands<pdbcode><motnum>_<looplength><smotif type>.csv : File containing results of comparing the query smotif against the database. Includes the number of residues compared, the chemical shift difference value, the RMSD (if structure is included), the loop length, the smotif NID, the secondary structure RMSD, secondary structure lengths, and loop structural signatures for the query and database motif and their overlap.

test_motif

        Subroutine to compare chemical shifts and torsion angles between a query Smotif and 
        a library Smotif

        test_motif($pdb,$havestructure,$motnum);

        Input arguments
        my $pdb=$ARGV[0];               #folder where the data is stored
        my $havestructure=$ARGV[1];     #1=solved structure exists (for RMSD comparison), 0=no solved structure
        my $motnum=$ARGV[2];            #smotif number to compare

get_acc_list

        Subroutine to convert phi-psi angles to a set of 11 structural 
        features (used by Narcis when generating the smotif database

read_file

        Subroutine to read chemical shifts from the file

comp_shifts

        Subroutine to compare two sets of chemical shifts 
        by calculating the average weighted sum of squared differences

match_in_array

        Subroutine to find if a scalar element appears in an array

rand_coil

        Subroutine to generate a hash with the random coil 
        values for backbone atoms (data from NMRPipe)

read_ranges

        Subroutine to read values for the ranges for chemical 
        shift values for each atom- and residue-type (from a file)

weight_table

        Subroutine to read values for the frequencies of 
        chemical shift values in alpha-, beta-, or other configurations (from a file)

bin

        Subroutine to bin a value based on an increment

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 Compare_shifts_torsion

You can also look for information at:

ACKNOWLEDGEMENTS

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.