Manual Reference Pages - CHEMISTRY::MACROMOL (3)
Chemistry::MacroMol - Perl module for macromolecules
my $mol = Chemistry::MacroMol->new(name => my big molecule);
$mol->new_domain(name => "ASP"); # see Chemistry::Domain for details
my @domains = $mol->domains;
For the purposes of this module, a macromolecule is just a molecule that
consists of several domains. For example, a protein consists of aminoacid
residues, or a nucleic acid consists of bases. Therefore Chemistry::MacroMol
is derived from Chemistry::Mol, with additional methods to handle the domains.
The way things are currently structured, an atom in a macromolecule belong
both to the MacroMol object and to a Domain object. This way you can get all the
atoms in $protein via $protein->atoms, or to the atoms in residue 123 via
Remember that this class inherits all the methods from Chemistry::Mol. They
wont be repeated here.
Chemistry::MacroMol->new(name => value, ...)
Create a new MacroMol object with the specified attributes. You can use the
same attributes as for Chemistry::Mol->new.
Add one or more Domain objects to the molecule. Returns the last domain added.
Returns the domain class that a macromolecule class expects to use by default.
Chemistry::MacroMol objects return Chemistry::Domain, but subclasses will
likely override this method.
$mol->new_domain(name => value, ...)
Shorthand for $mol->add_domain($mol->domain_class->new(parent => $mol, name => value, ...));
Returns the domains with the given indices, or all by default. NOTE:
the indices start from one (1), not from zero.
Ivan Tubert, <email@example.com>
COPYRIGHT AND LICENSE
Copyright 2004 by Ivan Tubert
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
|perl v5.20.3 ||MACROMOL (3) ||2004-07-03 |
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