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BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::ECnumber

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 hierarchy 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 lists

Support

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

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 92121

APPENDIX

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].