#
# BioPerl module for Bio::Tools::pICalculator
#
# Copyright (c) 2002, Merck & Co. Inc. All Rights Reserved.
#
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::pICalculator - calculate the isoelectric point of a protein
=head1 DESCRIPTION
Calculates the isoelectric point of a protein, the pH at which there
is no overall charge on the protein. Calculates the charge on a protein
at a given pH. Can use built-in sets of pK values or custom pK sets.
=head1 SYNOPSIS
use Bio::Tools::pICalculator;
use Bio::SeqIO;
my $in = Bio::SeqIO->new( -fh => \*STDIN ,
-format => 'Fasta' );
my $calc = Bio::Tools::pICalculator->new(-places => 2,
-pKset => 'EMBOSS');
while ( my $seq = $in->next_seq ) {
$calc->seq($seq);
my $iep = $calc->iep;
print sprintf( "%s\t%s\t%.2f\n",
$seq->id,
$iep,
$calc->charge_at_pH($iep) );
for( my $i = 0; $i <= 14; $i += 0.5 ){
print sprintf( "pH = %.2f\tCharge = %.2f\n",
$i,
$calc->charge_at_pH($i) );
}
}
=head1 SEE ALSO
http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf
http://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html
http://us.expasy.org/tools/pi_tool.html
=head1 LIMITATIONS
There are various sources for the pK values of the amino acids.
The set of pK values chosen will affect the pI reported.
The charge state of each residue is assumed to be independent of
the others. Protein modifications (such as a phosphate group) that
have a charge are ignored.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions
preferably to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Mark Southern (mark_southern@merck.com). From an algorithm by David
Tabb found at http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf.
Modification for Bioperl, additional documentation by Brian Osborne.
=head1 COPYRIGHT
Copyright (c) 2002, Merck & Co. Inc. All Rights Reserved. This module is
free software. It may be used, redistributed and/or modified under the terms
of the Perl Artistic License (see http://www.perl.com/perl/misc/Artistic.html)
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Private methods are usually preceded by a _.
=cut
# Let the code begin...
package Bio::Tools::pICalculator;
use strict;
use base qw(Bio::Root::Root);
# pK values from the DTASelect program from Scripps
# http://fields.scripps.edu/DTASelect
my $DTASelect_pK = { N_term => 8.0,
K => 10.0, # Lys
R => 12.0, # Arg
H => 6.5, # His
D => 4.4, # Asp
E => 4.4, # Glu
C => 8.5, # Cys
Y => 10.0, # Tyr
C_term => 3.1
};
# pK values from the iep program from EMBOSS
# http://emboss.sourceforge.net/apps/cvs/emboss/apps/iep.html
my $Emboss_pK = { N_term => 8.6,
K => 10.8, # Lys
R => 12.5, # Arg
H => 6.5, # His
D => 3.9, # Asp
E => 4.1, # Glu
C => 8.5, # Cys
Y => 10.1, # Tyr
C_term => 3.6
};
=head2 desc
Title : new
Usage : Bio::Tools::pICalculator->new
Function: Instantiates the Bio::Tools::pICalculator object
Example : $calc = Bio::Tools::pICalculator->new( -pKset => \%pKvalues,
# a Bio::Seq object
-seq => $seq,
-places => 2 );
or:
$calc = Bio::Tools::pICalculator->new( -pKset => 'string',
# a Bio::Seq object
-seq => $seq,
-places => 1 );
Constructs a new pICalculator. Arguments are a flattened hash.
Valid, optional keys are:
pKset - A reference to a hash with key value pairs for the
pK values of the charged amino acids. Required keys
are:
N_term C_term K R H D E C Y
pKset - A string ( 'DTASelect' or 'EMBOSS' ) that will
specify an internal set of pK values to be used. The
default is 'EMBOSS'
seq - A Bio::Seq sequence object to analyze
places - The number of decimal places to use in the
isoelectric point calculation. The default is 2.
Returns : The description
Args : The description or none
=cut
sub new {
my( $class, %opts ) = @_;
my $self = $class->SUPER::new(%opts);
$self = bless {}, ref $self || $self;
$self->seq( $opts{-seq} ) if exists $opts{-seq};
$self->pKset( $opts{-pKset} || 'EMBOSS' );
exists $opts{-places} ? $self->places( $opts{-places} ) :
$self->places(2);
return $self;
}
=head2 seq
Title : seq
Usage : $calc->seq($seqobj)
Function: Sets or returns the Bio::Seq used in the calculation
Example : $seqobj = Bio::Seq->new(-seq=>"gghhhmmm",-id=>"GHM");
$calc = Bio::Tools::pICalculator->new;
$calc->seq($seqobj);
Returns : Bio::Seq object
Args : Bio::Seq object or none
=cut
sub seq {
my( $this, $seq ) = @_;
unless( defined $seq && UNIVERSAL::isa($seq,'Bio::Seq') ){
$this->throw("$seq is not a valid Bio::Seq object");
}
$this->{-seq} = $seq;
$this->{-count} = count_charged_residues( $seq );
return $this->{-seq};
}
=head2 pKset
Title : pKset
Usage : $pkSet = $calc->pKSet(\%pKSet)
Function: Sets or returns the hash of pK values used in the calculation
Example : $calc->pKset('emboss')
Returns : reference to pKset hash
Args : The reference to a pKset hash, a string, or none. Examples:
pKset - A reference to a hash with key value pairs for the
pK values of the charged amino acids. Required keys
are:
N_term C_term K R H D E C Y
pKset - A valid string ( 'DTASelect' or 'EMBOSS' ) that will
specify an internal set of pK values to be used. The
default is 'EMBOSS'
=cut
sub pKset {
my ( $this, $pKset ) = @_;
if( ref $pKset eq 'HASH' ){ # user defined pK values
$this->{-pKset} = $pKset;
}elsif( $pKset =~ /^emboss$/i ){ # from EMBOSS's iep program
$this->{-pKset} = $Emboss_pK;
}elsif( $pKset =~ /^dtaselect$/i ){ # from DTASelect (scripps)
$this->{-pKset} = $DTASelect_pK;
}else{ # default to EMBOSS
$this->{-pKset} = $Emboss_pK;
}
return $this->{-pKset};
}
sub places {
my $this = shift;
$this->{-places} = shift if @_;
return $this->{-places};
}
=head2 iep
Title : iep
Usage : $calc->iep
Function: Returns the isoelectric point
Example : $calc = Bio::Tools::pICalculator->new(-places => 2);
$calc->seq($seqobj);
$iep = $calc->iep;
Returns : The isoelectric point of the sequence in the Bio::Seq object
Args : None
=cut
sub iep {
my $this = shift;
return _calculate_iep($this->{-pKset},
$this->{-places},
$this->{-seq},
$this->{-count}
);
}
=head2 charge_at_pH
Title : charge_at_pH
Usage : $charge = $calc->charge_at_pH($pH)
Function: Sets or gets the description of the sequence
Example : $calc = Bio::Tools::pICalculator->new(-places => 2);
$calc->seq($seqobj);
$charge = $calc->charge_at_ph("7");
Returns : The predicted charge at the given pH
Args : pH
=cut
sub charge_at_pH {
my $this = shift;
return _calculate_charge_at_pH( shift, $this->{-pKset},
$this->{-count} );
}
sub count_charged_residues {
my $seq = shift;
my $sequence = $seq->seq;
my $count;
for ( qw( K R H D E C Y ) ){ # charged AA's
$count->{$_}++ while $sequence =~ /$_/ig;
}
return $count;
}
sub _calculate_iep {
my( $pK, $places, $seq, $count ) = @_;
my $pH = 7.0;
my $step = 3.5;
my $last_charge = 0.0;
my $format = "%.${places}f";
unless( defined $count ){
$count = count_charged_residues($seq);
}
while(1){
my $charge = _calculate_charge_at_pH( $pH, $pK, $count );
last if sprintf($format,$charge) ==
sprintf($format,$last_charge);
$charge > 0 ? ( $pH += $step ) : ( $pH -= $step );
$step /= 2.0;
$last_charge = $charge;
}
return sprintf( $format, $pH );
}
# it's the sum of all the partial charges for the
# termini and all of the charged aa's!
sub _calculate_charge_at_pH {
no warnings; # don't complain if a given key doesn't exist
my( $pH, $pK, $count ) = @_;
my $charge = _partial_charge( $pK->{N_term}, $pH )
+ $count->{K} * _partial_charge( $pK->{K}, $pH )
+ $count->{R} * _partial_charge( $pK->{R}, $pH )
+ $count->{H} * _partial_charge( $pK->{H}, $pH )
- $count->{D} * _partial_charge( $pH, $pK->{D} )
- $count->{E} * _partial_charge( $pH, $pK->{E} )
- $count->{C} * _partial_charge( $pH, $pK->{C} )
- $count->{Y} * _partial_charge( $pH, $pK->{Y} )
- _partial_charge( $pH, $pK->{C_term} );
return $charge;
}
# Concentration Ratio is 10**(pK - pH) for positive groups
# and 10**(pH - pK) for negative groups
sub _partial_charge {
my $cr = 10 ** ( $_[0] - $_[1] );
return $cr / ( $cr + 1 );
}
1;
__END__