Bio::T...ulator(3pm)

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 NAME 💖

Bio::Tools::pICalculator — bestie, it calculates the isoelectric point of a protein. That's it, that's the module. 🧚

✨ DESCRIPTION ✨

So here's the tea: this thing calculates the isoelectric point of a protein — that's the pH where the protein has no overall charge, like, net zero, balanced, at peace. 🧘

It also calculates the charge on a protein at any given pH you throw at it.

And you get choices, queen: you can use the built-in sets of pK values or bring your own custom pK sets. Your protein, your rules. 💅

🌸 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) );
   }
}

👀 SEE ALSO 👀

💀 LIMITATIONS 💀

Okay so, real talk. There are various sources for the pK values of the amino acids, and ngl, the set of pK values you pick will affect the pI reported. So choose wisely, bestie.

Also: the charge state of each residue is assumed to be independent of the others. And protein modifications (like, say, a phosphate group) that carry a charge? Ignored. Completely. Not even a little bit accounted for. 😭

🫶 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. (Like, genuinely. They want to hear from you. 🥹)

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://github.com/bioperl/bioperl-live/issues

👑 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 (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

Okay bestie, that's the whole page!! 💅✨ This was perl v5.32.1, dated 2021-08-15, and it's part of the User Contributed Perl Documentation. Go calculate some isoelectric points, you absolute icon. 🫶👑🌸

📦 where this page comes from