NAME

Chemistry::Mol - Molecule object toolkit

SYNOPSIS

use Chemistry::Mol;

$mol = Chemistry::Mol->new(id => "mol_id", name => "my molecule");
$c = $mol->new_atom(symbol => "C", coords => [0,0,0]); 
$o = $mol->new_atom(symbol => "O", coords => [0,0,1.23]); 
$mol->new_bond(atoms => [$c, $o], order => 3);

print $mol->print;

DESCRIPTION

This package, along with Chemistry::Atom and Chemistry::Bond, includes basic objects and methods to describe molecules.

The core methods try not to enforce a particular convention. This means that only a minimal set of attributes is provided by default, and some attributes have very loosely defined meaning. This is because each program and file type has different idea of what each concept (such as bond and atom type) means. Bonds are defined as a list of atoms (typically two) with an arbitrary type. Atoms are defined by a symbol and a Z, and may have 3D coordinates (2D and internal coming soon).

METHODS

See also Chemistry::Obj for generic attributes.

Chemistry::Mol->new(name => value, ...)

Create a new Mol object with the specified attributes.

$mol = Chemistry::Mol->new(id => 'm123', name => 'my mol')

is the same as

Chemistry::Mol->new()
$mol->id('m123')
$mol->name('my mol')

$mol->add_atom($atom, ...)

Add one or more Atom objects to the molecule. Returns the last atom added.

$mol->new_atom(name => value, ...)

Shorthand for $mol->add_atom(Chemistry::Atom->new(name => value, ...)); It has the disadvantage that it doesn't let you create a subclass of Chemistry::Atom.

$mol->add_bond($bond, ...)

Add one or more Bond objects to the molecule. Returns the last bond added.

$mol->new_bond(name => value, ...)

Shorthand for $mol->add_bond(Chemistry::Bond->new(name => value, ...)); It has the disadvantage that it doesn't let you create a subclass of Chemistry::Bond.

$mol->by_id($id)

Return the atom or bond object with the corresponding id.

$mol->atoms($n1, ...)

Returns the atoms with the given indices, or all by default. Indices start from one, not from zero.

$mol->atoms_by_name($name)

Returns the atoms with the given name (treated as an anchored regular expression).

$mol->bonds($n1, ...)

Returns the bonds with the given indices, or all by default. Indices start from one, not from zero.

$mol->print(option => value...)

Convert the molecule to a string representation. If no options are given, a default YAML-like format is used (this may change in the future). Otherwise, the format should be specified by using the format option.

$mol->parse($string, option => value...)

Parse the molecule encoded in $string. The format should be specified with the the format option; otherwise, it will be guessed.

Chemistry::Mol->read($fname, option => value ...)

Read a file and return a list of Mol objects, or croaks if there was a problem. The type of file will be guessed if not specified via the format option.

Note that only registered file readers will be used. Readers may be registered using register_type(); modules that include readers (such as Chemistry::File::PDB) usually register them automatically.

$mol->write($fname, option => value ...)

Write a molecule file, or croak if there was a problem. The type of file will be guessed if not specified via the format option.

Note that only registered file formats will be used.

Chemistry::Mol->register_format($name, $ref)

Register a file type. The identifier $name must be unique. $ref is either a class name (a package) or an object that complies with the Chemistry::File interface (e.g., a subclass of Chemistry::File). If $ref is omitted, the calling package is used automatically. More than one format can be registered at a time, but then $ref must be included for each format (e.g., Chemistry::Mol->register_format(format1 => "package1", format2 => package2).

The typical user doesn't have to care about this function. It is used automatically by molecule file I/O modules.

Chemistry::Mol->formats

Returns a list of the file formats that have been installed by register_type()

$mol->mass

Return the molar mass.

$mol->formula_hash

Returns a hash reference describing the molecular formula. For methane it would return { C => 1, H => 4 }.

$mol->formula($format)

Returns a string with the formula. The format can be specified as a printf-like string with the control sequences specified in the Chemistry::File::Formula documentation.

BUGS

Blatant memory leaks. Due to the use of circular references, Perl's current garbage collector never cleans up molecule, atom, and bond objects. A future version should address this.

SEE ALSO

Chemistry::Atom, Chemistry::Bond, Chemistry::File, Chemistry::Tutorial

AUTHOR

Ivan Tubert <itub@cpan.org>

COPYRIGHT

Copyright (c) 2003 Ivan Tubert. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.