NAME
Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)
SYNOPSIS
use Bio::Tools::ECnumber;
# Creation of ECnumber objects
my $EC1 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.1" );
my $EC2 = Bio::Tools::ECnumber->new( -ec_string => "EC 1.1.1.1" );
my $EC3 = Bio::Tools::ECnumber->new();
# Copying
my $EC4 = $EC1->copy();
# Modification/canonicalization of ECnumber objects
print $EC3->EC_string( "1.01.01.001" ); # Prints "1.1.1.1".
# Stringify
print $EC3->EC_string();
# or
print $EC3->to_string();
# Test for equality
# -- Against ECnumber object:
if ( $EC3->is_equal( $EC2 ) ) { # Prints "equal".
print "equal";
}
# -- Against string representation of EC number:
if ( ! $EC3->is_equal( "1.1.1.-" ) ) { # Prints "not equal".
print "not equal";
}
# Test for membership
my $EC5 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.-" );
# -- Against ECnumber object.
if ( $EC1->is_member( $EC5 ) ) { # Prints "member".
print "member";
}
# -- Against string representation of EC number.
if ( ! $EC1->is_member( "4.3.1.-" ) ) { # Prints "not member".
print "not member";
}DESCRIPTION
Bio::Tools::ECnumber is a representation of EC numbers, the numerical heirarchy for Enzyme Classification.
See http://www.chem.qmul.ac.uk/iubmb/enzyme/ for more details.
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 listsSupport
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting 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
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
Address:
Genomics Institute of the Novartis Research Foundation
10675 John Jay Hopkins Drive
San Diego, CA 92121APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $EC1 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.1" );
or
$EC2 = Bio::Tools::ECnumber->new( -ec_string => "4.3.2.2",
-comment => "Is EC 4.3.2.2" );
or
$EC3 = Bio::Tools::ECnumber->new(); # EC3 is now "-.-.-.-"
Function: Creates a new ECnumber object.
Parses a EC number from "x.x.x.x", "EC x.x.x.x",
"ECx.x.x.x", or "EC:x.x.x.x";
x being either a positive integer or a "-".
Returns : A new ECnumber object.
Args : A string representing a EC number, e.g. "4.3.2.1"
or "EC 4.3.2.1" or "1.-.-.-".init
Title : init()
Usage : $EC1->init(); # EC1 is now "-.-.-.-"
Function: Initializes this ECnumber to default values.
Returns :
Args :copy
Title : copy()
Usage : $EC2 = $EC1->copy();
Function: Creates a new ECnumber object which is an exact copy
of this ECnumber.
Returns : A copy of this ECnumber.
Args :EC_string
Title : EC_string
Usage : $EC3->EC_string( "1.1.1.-" );
or
print $EC3->EC_string();
Function: Set/get for string representations of EC numbers.
Parses a EC number from "x.x.x.x", "EC x.x.x.x",
"ECx.x.x.x", or "EC:x.x.x.x";
x being either a positive integer or a "-".
Returns : A string representations of a EC number.
Args : A string representations of a EC number.to_string
Title : to_string()
Usage : print $EC3->to_string();
Function: To string method for EC numbers
(equals the "get" functionality of "EC_string").
Returns : A string representations of a EC number.
Args :is_equal
Title : is_equal
Usage : if ( $EC3->is_equal( $EC2 ) )
or
if ( $EC3->is_equal( "1.1.1.-" ) )
Function: Checks whether this ECnumber is equal to the argument
EC number (please note: "1.1.1.1" != "1.1.1.-").
Returns : True (1) or false (0).
Args : A ECnumber object or a string representation of a EC number.is_member
Title : is_member
Usage : if ( $EC1->is_member( $EC5 ) )
or
if ( $EC1->is_member( "4.3.-.-" ) )
Function: Checks whether this ECnumber is a member of the (incomplete)
argument EC number (e.g. "1.1.1.1" is a member of "1.1.1.-"
but not of "1.1.1.2").
Returns : True (1) or false (0).
Args : A ECnumber object or a string representation of a EC number.enzyme_class
Title : enzyme_class
Usage : $EC1->enzyme_class( 1 );
or
print $EC1->enzyme_class();
Function: Set/get for the enzyme class number of ECnumbers.
Returns : The enzyme class number of this ECnumber.
Args : A positive integer or "-".sub_class
Title : sub_class
Usage : $EC1->sub_class( 4 );
or
print $EC1->sub_class();
Function: Set/get for the enzyme sub class number of ECnumbers.
Returns : The enzyme sub class number of this ECnumber.
Args : A positive integer or "-".sub_sub_class
Title : sub_sub_class
Usage : $EC1->sub_sub_class( 12 );
or
print $EC1->sub_sub_class();
Function: Set/get for the enzyme sub sub class number of ECnumbers.
Returns : The enzyme sub sub class number of this ECnumber.
Args : A positive integer or "-".serial_number
Title : serial_number
Usage : $EC1->serial_number( 482 );
or
print $EC1->serial_number();
Function: Set/get for the serial number of ECnumbers.
Returns : The serial number of this ECnumber.
Args : A positive integer or "-".comment
Title : comment
Usage : $EC1->comment( "deprecated" );
or
print $EC1->comment();
Function: Set/get for a arbitrary comment.
Returns : A comment [scalar].
Args : A comment [scalar].