bio::tools::picalculator(3pm) [debian man page]

Bio::Tools::pICalculator(3pm)				User Contributed Perl Documentation			     Bio::Tools::pICalculator(3pm)

NAME

       Bio::Tools::pICalculator - calculate the isoelectric point of a protein

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.

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	%s	%.2f
",
			   $seq->id,
			   $iep,
			   $calc->charge_at_pH($iep) );

	    for( my $i = 0; $i <= 14; $i += 0.5 ){
	       print sprintf( "pH = %.2f	Charge = %.2f
",
			      $i,
			      $calc->charge_at_pH($i) );
	    }
	 }

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

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.

FEEDBACK

   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

   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/

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.

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)

APPENDIX

       The rest of the documentation details each of the object methods.  Private methods are usually preceded by a _.

   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

   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

   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'

   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

   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

perl v5.14.2							    2012-03-02					     Bio::Tools::pICalculator(3pm)