NAME

Bio::Metabolic::Substrate - Perl extension for the description of biochemical substrates

SYNOPSIS

use Bio::Metabolic::Substrate;

my $sub1 = Bio::Metabolic::Substrate->new('Water');

my $sub2 = Bio::Metabolic::Substrate->new('Oxygen', {o => 2});

DESCRIPTION

This class implements the object class representing Biochemical Compounds (Substrates) occurring in biochemical reactions. Substrates must contain a name and arbitrary many attributes.

EXPORT

None

OVERLOADED OPERATORS

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

Equality
  if ($sub1 == $sub2)
  if ($sub1 != $sub2)

Lexical comparison
  $cmp = $sub1 cmp $sub2;
  

AUTHOR

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

SEE ALSO

Bio::Metabolic.

METHODS

Constructor new

First argument must specify the name. Second argument is a hash reference of key-value pairs defining the object attributes. Attributes are optional.

Upon creation, each substrate object gets associated with a variable (Math::Symbolic::Variable object) which is accessible by the accessor method var(). The purpose for this is the automatic creation of ordinary differential equation systems describing the dynamic behaviour of a metabolic system.

Returns a Bio::Metabolic::Substrate.

Method copy

copy() returns a copy of the object. Attributes are cloned. The variable associated with the substrate (see var() below) is new defined and the value (if existing) is not copied.

Method name

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

Method attributes

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

Method var

Optional argument: sets the object's variable. Returns the object's variable (Math::Symbolic::Variable object).

Method fix

Sets the value of the object's variable, thus fixing the substrate's concentration.

Method release

Sets the value of the object's variable to undef, thus releasing the substrate's concentration.

Method get_attribute

Argument specifies the attribute name. Returns the attribute value or undef if such an attribute does not exist.

Method substrate_to_string

Returns a readable string. The string consists of the object's attributes listed in braces. If the object does not have any attributes, the string consists of the object's name in square brackets.

Method equals

Compares two substrates. If one of the substrates has attributes the set of attributes is compared. If both objects are without attributes, the names are compared. Returns 1 upon equality, 0 otherwise.

Method not_equals

Compares two substrates. If one of the substrates has attributes the set of attributes is compared. If both objects are without attributes, the names are compared. Returns 0 upon equality, 1 otherwise.

Method is_empty

returns 1 if the object does not have any attributes

Method compare_names

Lexical comparison of the object names or optionally strings.

cpanm Bio::Metabolic

perl -MCPAN -e shell
install Bio::Metabolic