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Bio::Tools::ECnumber.3pm

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 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:

   http://bugzilla.open-bio.org/
 
 

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].