NAME
InSilicoSpectro::InSilico::ModRes Residue modifications package
SYNOPSIS
#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($_)->get('name')."\n";
}DESCRIPTION
Manage all what is related to residue modifications (masses, positions, SwissProt annotations...)
FUNCTIONS
Initialization
init([$files, [$files, [...]]])
Opens the given files or try to locate the file ${phenyx.config.modres} and stores all the modif in the dictionnary
getFromDico(name)
A dictionnary holds all the enzymes, based on their key
getList()
Returns a list of all the enzymes, sorted by name
registerModResHandler([\&sub])
get/set a subroutine to be called whenever a new modres is instanciated (for example, register into MassCalaculator
METHODS
my $mr=InSilicoSpectro::InSilico::ModRes->new([$h])
$h contains a pointer to a hash for definition
$mr->name([$str])
Set the name if an argument is given.
Returns the name value
$mr->regexp([$str]);
Set the modif regular expression from a string (or return this regular expression if no argument is given)
$mr->cTerm([$val]); =head3 $mr->nTerm([$val]);
Set if the modif is peptide C/N terminus (or just returns the current status is no value is passed to the function)
$mr->protCTerm([$val]); =head3 $mr->protNTerm([$val]);
Set if the modif is protein C/N terminus (or just returns the current status is no value is passed to the function)
$mr->seq2pos($seq);
returns an array of position where the modif can appear on sequence $seq.
This array contains
- [-1] if it can be attributed nterm
- [length $seq] if it can be attributer cterm
- else, a list of indices, starting at 0 for the first AA of the sequence
$mr->set($name, $val)
Set an instance paramter.
$mr->get($name)
Get an instance parameter.
$mr->getXMLTwigElt()
return an XML::Twig::Elt object containing the modres
EXAMPLES
see t/InSilico/tesModRes.pl script
SEE ALSO
Phenyx::Config::GlobalParam
COPYRIGHT
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
AUTHORS
Alexandre Masselot, www.genebio.com