Alexandre Masselot
and 1 contributors

NAME

InSilicoSpectro::InSilico::CleavEnzyme Basic enzyme object.

SYNOPSIS

  # Reads all cleavage enzyme definition in the default file(s) ({phenyx.config.cleavenzymes})
  InSilicoSpectro::InSilico::CleavEnzyme::init();

  # Prints all the modifications
  foreach (InSilicoSpectro::InSilico::Enzyme::getList()){
    print;
  }

DESCRIPTION

Cleavage enzyme object that comprises a description of the enzyme and basic methods for reading XML configuration file(s) and printing. A dictionary is created at the package level to store all the read enzymes from the configuration file(s).

FUNCTIONS

Initialization

init([$filename])

Opens the given file, or file ${phenyx.config.cleavenzymes} if no parameter was given, and stores all the modif in the dictionnary.

getFromDico($name)

This function retrieves and returns an enzyme from the dictionary based on its name.

getList()

Returns a sorted list of all the enzyme names in the dictionary.

METHODS

new([$h])

Creates (constructor) a new object enzyme. $h contains a reference to a hash or is a hash itself. The hash lists object attributes with their values and it is used to initialize the newly created object.

name([$str])

Sets the enzyme name if an argument is given, otherwise returns the name value.

regexp([$restr])

Sets a regular expression for enzymatic digestion (use looking (back|for)wards) if an argument is given, otherwise returns the regexp (compiled).

terminus([$t])

Sets the terminus side (trypsin is C-term) of the enzyme if an argument (either 'C' or 'T') is given, otherwise returns terminus either 'N' or 'C'.

CTermGain([$g])

Sets the atoms gained at the peptide C-terminal site after digestion (normally OH) if an argument is given, otherwise returns the atoms gained.

NTermGain([$g])

Sets the atoms gained at the peptide N-terminal site after digestion (normally H) if an argument is given, otherwise returns the atoms gained.

CTermModif([$g])

Sets the name of the modification induced by the enzyme at the peptide C-terminus if an argument is given, otherwise returns the modification name.

NTermModif([$g])

Sets the name of the modification induced by the enzyme at the peptide N-terminus if an argument is given, otherwise returns the modification name.

print

overloaded "" operator

EXAMPLES

See t/InSilico/testCleavEnzyme.pl.

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 Jacques Colinge, Upper Austria University of Applied Science at Hagenberg