Oliver Ebenhöh

NAME

Bio::Metabolic::Network - Perl extension for biochemical reaction networks

SYNOPSIS

  use Bio::Metabolic::Network;

  my $net = Bio::Metabolic::Network->new($reaction1, $reaction2, ... );

DESCRIPTION

This class implements objects representing biochemical reaction networks. A reaction network is defined a number of biochemical reactions.

EXPORT

None

OVERLOADED OPERATORS

  String Conversion
    $string = "$network";
    print "\$network = '$network'\n";

  Comparison
    if ($network1 <= $network2)...

AUTHOR

Oliver Ebenhoeh, oliver.ebenhoeh@rz.hu-berlin.de

SEE ALSO

Bio::Metabolic Bio::Metabolic::Substrate Bio::Metabolic::Substrate::Cluster Bio::Metabolic::Reaction.

METHODS

Constructor new

Returns a new Bio::Metabolic::Network object. Passed arguments must be Bio::Metabolic::Reaction objects.

Every network object is associated with a matrx, the stoichiometric matrix. This matrix is defined by the reactions and gets determined upon creation.

Method copy

Returns a clone of the network. However, the references to the reactions point to exactly the same reactions. If one gets modified, it effects all networks with that reaction.

Method reactions

Returns an arrayref of the reactions.

Method has_reaction

Argument is a reaction. Returns 1 if the network contains the raction, 0 otherwise.

Method add_reaction

Argument is a Bio::Metabolic::Reaction. Alters the object in-line, adding the reaction to the list.

Method remove_reaction

Argument is a Bio::Metabolic::Reaction. Altering the object in-line, removeing the reaction from the network. Return undef if network did not have the reaction, 1 on success.

Method network_to_string

Returns a string representation of the network

Method add_networks

Adds an arbitrary number of networks, returning a new object containing all reactions that are contained at least present in one of the networks.

Method is_in

$net1->is_in($net2) Returns 1 if all reactions in $net1 also occur in $net2, i.e. if $net1 is a subnetwork of $net2.

Method dist

Provides a distance measure between networks. Returns the number of reactions that are different in the two networks.

Method substrates

Returns a Bio::Metabolic::Substrate::Cluster containing all substrates participating in at least one reaction.

Method matrix

Returns the stoichiometric matrix of the network as a PD::Matrix object.

Method new_matrix

determines the stoichiometric matrix of the network defined by its reactions.

Method print_matrix

Prints the matrix in a way that describes which substrates are associated with which rows and which reactions with which columns.