NAME

InSilicoSpectro::InSilico::RetentionTimer - A base class for implementing a peptide retention time predictor

SYNOPSIS

  use InSilicoSpectro::InSilico::RetentionTimer;

  # create a retention time predictor
  my $rt = InSilicoSpectro::InSilico::RetentionTimer->new;

  # predict retention time for a peptide
  $rt->predict( peptide=>'ACFGDMKWVTFISLLRPLLFSSAYSRGVFRRDTHKSEIAHRFKDLGE' );

  # calibrate the predictor
  $rt->calibrate( data=>{calseqs=>\@calseqs,caltimes=>\@caltimes,calmodifs=>\@calmodifs},calibrator=>$ec );

DESCRIPTION

InSilicoSpectro::InSilico::RetentionTimer is a base class for predictors of peptides retention time in HPLC. It gives also a method for calibration of the predictor.

FUNCTIONS

count_aa()

This function counts the number of ocurrences of each amino acid in a given sequence and returns a reference to an array with the count sorted by the one-letter symbol: ACDEFGHIKLMNPQRSTVWY.

  my $count = count_aa( 'AAK' );
  print "Found $count[0] Alanines and $count[1] Cysteines\n";

METHODS

my $rt=InSilicoSpectro::InSilico::RetentionTimer->new($h)

$h contains a hash with parameters.

$rt->predict($point)

Predict the retention time.

$rt->calibrate(%h)

Calibrate the predictor.

$rt->write_cal( calfile=>$file );

Save current calibrator.

$rt->read_cal ( calfile=>$file );

Retrieve a previously saved calibrator.

$rt->set($name, $val)

Set an instance parameter.

$rt->get($name)

Get an instance parameter.

EXAMPLES

SEE ALSO

InSilicoSpectro::InSilico::RetentionTime::Hodges

InSilicoSpectro::InSilico::RetentionTime::Petritis

InSilicoSpectro::InSilico::ExpCalibrator

InSilicoSpectro::InSilico::IsoelPoint

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

Pablo Carbonell, Alexandre Masselot, www.genebio.com