Bio::Metabolic::Network - Perl extension for biochemical reaction networks
use Bio::Metabolic::Network; my $net = Bio::Metabolic::Network->new($reaction1, $reaction2, ... );
This class implements objects representing biochemical reaction networks. A reaction network is defined a number of biochemical reactions.
String Conversion $string = "$network"; print "\$network = '$network'\n"; Comparison if ($network1 <= $network2)...
Oliver Ebenhoeh, email@example.com
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.
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.
Returns an arrayref of the reactions.
Argument is a reaction. Returns 1 if the network contains the raction, 0 otherwise.
Argument is a Bio::Metabolic::Reaction. Alters the object in-line, adding the reaction to the list.
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.
Returns a string representation of the network
Adds an arbitrary number of networks, returning a new object containing all reactions that are contained at least present in one of the networks.
$net1->is_in($net2) Returns 1 if all reactions in $net1 also occur in $net2, i.e. if $net1 is a subnetwork of $net2.
Provides a distance measure between networks. Returns the number of reactions that are different in the two networks.
Returns a Bio::Metabolic::Substrate::Cluster containing all substrates participating in at least one reaction.
Returns the stoichiometric matrix of the network as a PD::Matrix object.
determines the stoichiometric matrix of the network defined by its reactions.
Prints the matrix in a way that describes which substrates are associated with which rows and which reactions with which columns.