NAME

Bio::Metabolic::Reaction - Perl extension for biochemical reactions

SYNOPSIS

  use Bio::Metabolic::Reaction;

  my $r1 = Bio::Metabolic::Reaction->new('r1',[$sub1,$sub2],[$sub3,$sub4]);

  $r1->kinetics('linear');

DESCRIPTION

This class implements objects representing a biochemical reaction. A biochemical reaction in this context is defined by its input and its output substrates, i.e. by two Bio::Metabolic::Network::Cluster objects. Further, every instance of this class is associated with a mathematical expression which determines the dynamical behaviour of the reaction, i.e. the reaction rate.

EXPORT

None

OVERLOADED OPERATORS

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

  Equality
    if ($reaction1 == $reaction2)
    if ($reaction1 != $reaction2)

AUTHOR

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

SEE ALSO

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

METHODS

Constructor new

There are three ways to call the constructor method:

1.) $r = Bio::Metabolic::Reaction->new($name, $inlist, $outlist);

    Here, the first argument must hold the name. The following two arguments 
    provide arrayrefs of Bio::Metabolic::Substrate objects, defining the input and 
    output substrates of the biochemical reaction.
    If a reactant occurs twice (e.g. X + X -> Y), it has to appear twice in the
    corresponding list.

2.) $r = Bio::Metabolic::Reaction->new($name, $substrates, $coefficients)

    The first argument must specify the name. The second argument can be an 
    arrayref of Bio::Metabolic::Substrate objects or a Bio::Metabolic::Substrate::Cluster
    object, defining all participating reactants.
    The third argument must hold numbers specifying the multiplicity of the 
    reactants in the same order as the reactants have been specified.

    Example: Let $X and $Y be Bio::Metabolic::Substrate objects defining the
        reactants X and Y. The reaction X + X -> Y can be defined either by

            $r1 = Bio::Metabolic::Reaction->new('r1', [$X,$X], [$Y]);

        or by

            $r2 = Bio::Metabolic::Reaction->new('r2', [$X,$Y], [-2,1]);

3.) The constructor can be called as an object method, using another reaction as template: $r2 = $r1->new().

Method copy

  copy() is exactly the same as $r2 = $r1->new();

Method name

Optional argument: sets the object's name. Returns the object's name.

Method substrates

Returns all participating compounds as a Bio::Metabolic::Substrate::Cluster object. Optional argument: sets the substrates.

Method stoichiometry

Returns a hashref. Keys are the substrate names, values the stoichiometric coefficients (negative for input substrates, positive for output substrates). It the absolute value differs from one, the corresponding substrate is consumed/produced more than once. Optional argument: sets the stoichiometries.

Method st_coefficient

Argument must be a substrate. Returns the stoichiometric coefficient (cf. method stoichiometry()) of the specified substrate.

Method in

Returns the input substrates as a Bio::Metabolic::Substrate::Cluster object.

Method out

Returns the output substrates as a Bio::Metabolic::Substrate::Cluster object.

Method dir

Take one parameter which must be -1 or 1. Returns the input or output substrates, respectively.

Method get_substrate_list

Returns input and output substrates as one list.

Method equals()

compares two Bio::Metabolic::Reaction objects. Returns 1 if all substrates occur with the same stoichiometric coefficient, 0 otherwise.

cpanm Bio::Metabolic

perl -MCPAN -e shell
install Bio::Metabolic