InSilicoSpectro::InSilico::ModRes Residue modifications package
#read all modres definitions in the default file ({phenyx.config.modres}) InSilicoSpectro::InSilico::ModRes::init(); #or, if the ohenyx system is not installed InSilicoSpectro::InSilico::ModRes::init("some/path/to/defatultdef.xml"); #print all the modifications foreach (InSilicoSpectro::InSilico::ModRes::getList()){ $_->print(); } #given a swissprot FT valkue, return the related modres foreach ('PHOSPHORYLATION', 'ACETYLATION (IN ISOFORM SHORT))', 'PHOSPHORYLATION', 'ACETYLATION', 'SULFATION'){ print "$_ => ".InSilicoSpectro::InSilico::ModRes::getModifFromSprotFT($_)->get('name')."\n"; }
Manage all what is related to residue modifications (masses, positions, SwissProt annotations...)
Opens the given files or try to locate the file ${phenyx.config.modres} and stores all the modif in the dictionnary
A dictionnary holds all the enzymes, based on their key
Returns a list of all the enzymes, sorted by name
get/set a subroutine to be called whenever a new modres is instanciated (for example, register into MassCalaculator
$h contains a pointer to a hash for definition
Set the name if an argument is given.
Returns the name value
Set the modif regular expression from a string (or return this regular expression if no argument is given)
Set if the modif is peptide C/N terminus (or just returns the current status is no value is passed to the function)
Set if the modif is protein C/N terminus (or just returns the current status is no value is passed to the function)
returns an array of position where the modif can appear on sequence $seq.
This array contains
Set an instance paramter.
Get an instance parameter.
return an XML::Twig::Elt object containing the modres
see t/InSilico/tesModRes.pl script
Phenyx::Config::GlobalParam
Copyright (C) 2004-2005 Geneva Bioinformatics www.genebio.com
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Alexandre Masselot, www.genebio.com
To install InSilicoSpectro, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro
For more information on module installation, please visit the detailed CPAN module installation guide.