InSilicoSpectro::InSilico::CleavEnzyme Basic enzyme object.

  # 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;
  }

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).

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

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

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

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.

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

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

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'.

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

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

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.

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.

See t/InSilico/testCleavEnzyme.pl.

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 Jacques Colinge, Upper Austria University of Applied Science at Hagenberg