ECnumber - representation of EC numbers 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 of ECnumber objects # -------------------------------- print $EC3->EC_string( "1.01.01.001" ); # Prints "1.1.1.1". # To string # --------- 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"; } ECnumber is a representation of EC numbers [http://www.chem.qmul.ac.uk/iubmb/enzyme/].

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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Christian M. Zmasek Email: czmasek@gnf.org or cmzmasek@yahoo.com WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 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].