GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TOOLS::ECNUMBER (3)

.ds Aq ’

NAME

Bio::Tools::ECnumber - representation of EC numbers (Enzyme Classification)

CONTENTS

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:



  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].



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::TOOLS::ECNUMBER (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.