Bio::Tools pICalculator
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Summary
Bio::Tools::pICalculator - calculate the isoelectric point of a protein
Package variables
Privates (from "my" definitions)
$DTASelect_pK = { N_term => 8.0, K => 10.0, R => 12.0, H => 6.5, D => 4.4, E => 4.4, C => 8.5, Y => 10.0, C_term => 3.1 }
$Emboss_pK = { N_term => 8.6, K => 10.8, R => 12.5, H => 6.5, D => 3.9, E => 4.1, C => 8.5, Y => 10.1, C_term => 3.6 }
Inherit
Bio::Root::Root
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) ); } }
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.
Methods
new
No description
Code
seqDescriptionCode
pKsetDescriptionCode
places
No description
Code
iepDescriptionCode
charge_at_pHDescriptionCode
count_charged_residues
No description
Code
_calculate_iep
No description
Code
_calculate_charge_at_pH
No description
Code
_partial_charge
No description
Code
Methods description
seqcode    nextTop
 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
pKsetcodeprevnextTop
 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'
iepcodeprevnextTop
 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
charge_at_pHcodeprevnextTop
 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
Methods code
newdescriptionprevnextTop
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;
}
seqdescriptionprevnextTop
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};
}
pKsetdescriptionprevnextTop
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};
}
placesdescriptionprevnextTop
sub places {
   my $this = shift;
   $this->{-places} = shift if @_;
   return $this->{-places};
}
iepdescriptionprevnextTop
sub iep {
   my $this = shift;
   return _calculate_iep($this->{-pKset},
	    		 $this->{-places},
			 $this->{-seq},
			 $this->{-count}
		        );
}
charge_at_pHdescriptionprevnextTop
sub charge_at_pH {
   my $this = shift;
   return _calculate_charge_at_pH( shift, $this->{-pKset},
				  $this->{-count} );
}
count_charged_residuesdescriptionprevnextTop
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;
}
_calculate_iepdescriptionprevnextTop
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!
}
_calculate_charge_at_pHdescriptionprevnextTop
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
}
_partial_chargedescriptionprevnextTop
sub _partial_charge {
   my $cr = 10 ** ( $_[0] - $_[1] );
   return $cr / ( $cr + 1 );
} 1; __END__
}
General documentation
SEE ALSOTop
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
LIMITATIONSTop
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.
FEEDBACKTop
Mailing ListsTop
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
BugsTop
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/
AUTHORTop
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.
COPYRIGHTTop
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)
APPENDIXTop
The rest of the documentation details each of the object methods.
Private methods are usually preceded by a _.
descTop
 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