BioPHP - Chemical groups of aminoacids in protein

Original code submitted by joseba
Code bellow is covered by GNU GPL v2 license.

Description

Last change: 2010/10/18 17:04 | Edit description | Recent Changes | Original description

Translates peptide sequence to checmical groups.
Chemical groups/aminoacids: 
   L/GAVLI
   H/ST
   M/NQ
   R/FYW
   S/CM
   I/P
   A/DE
   C/KRH
   */*
   X/X

Code

Last change: 2010/10/18 17:04 | Edit Code | Recent Changes | Download | Original code

function chemgrp($amino_seq){
        $chemgrp_seq = "";
        $ctr = 0;
        while(1)
                {
                $amino_letter = substr($amino_seq, $ctr, 1);
                if ($amino_letter == "") break;
                if (strpos(" GAVLI", $amino_letter)>0) $chemgrp_seq .= "L";
                elseif (($amino_letter == "S") or ($amino_letter == "T")) $chemgrp_seq .= "H";
                elseif (($amino_letter == "N") or ($amino_letter == "Q")) $chemgrp_seq .= "M";
                elseif (strpos(" FYW", $amino_letter)>0) $chemgrp_seq .= "R";
                elseif (($amino_letter == "C") or ($amino_letter == "M")) $chemgrp_seq .= "S";
                elseif ($amino_letter == "P") $chemgrp_seq .= "I";
                elseif (($amino_letter == "D") or ($amino_letter == "E")) $chemgrp_seq .= "A";
                elseif (($amino_letter == "K") or ($amino_letter == "R") or ($amino_letter == "H"))
                        $chemgrp_seq .= "C";
                elseif ($amino_letter == "*") $chemgrp_seq .= "*";
                elseif ($amino_letter == "X" or $amino_letter == "N") $chemgrp_seq .= "X";
                else die("Invalid amino acid symbol in input sequence.");
                $ctr++;
                }
        return $chemgrp_seq;
}