Search results for "module:Chemistry::Mol"
Chemistry::Mol - Molecule object toolkit
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 defau...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::Obj - Abstract chemistry object
This module implements some generic methods that are used by Chemistry::Mol, Chemistry::Atom, Chemistry::Bond, Chemistry::File, etc. Common Attributes There are some common attributes that may be found in molecules, bonds, and atoms, such as id, name...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::Bond - Chemical bonds as objects in molecules
This module includes objects to describe chemical bonds. A bond is defined as a list of atoms (typically two), with some associated properties. Bond Attributes In addition to common attributes such as id, name, and type, bonds have the order attribut...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::File - Molecule file I/O base class
The main use of this module is as a base class for other molecule file I/O modules (for example, Chemistry::File::PDB). Such modules should override and extend the Chemistry::File methods as needed. You only need to care about the methods here if if ...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::Atom - Chemical atoms as objects in molecules
This module includes objects to describe chemical atoms. An atom is defined by its symbol and its coordinates, among other attributes. Atomic coordinates are described by a Math::VectorReal object, so that they can be easily used in vector operations...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::File::Dumper - Read and write molecules via Data::Dumper
This module hooks the Data::Dumper Perl core module to the Chemistry::File API, allowing you to dump and undump Chemistry::Mol objects easily. This module automatically registers the "dumper" format with Chemistry::Mol. For purposes of automatic file...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::File::Formula - Molecular formula reader/formatter
This module converts a molecule object to a string with the formula and back. It registers the 'formula' format with Chemistry::Mol. Besides its obvious use, it is included in the Chemistry::Mol distribution because it is a very simple example of a C...
MERKYS/Chemistry-Mol-0.39 - 13 Jul 2022 08:36:38 UTC
Chemistry::MacroMol - Perl module for macromolecules
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 Chemistr...
ITUB/Chemistry-MacroMol-0.06 - 03 Jul 2004 19:22:04 UTC
Chemistry::File::MDLMol - MDL molfile reader/writer
MDL Molfile (V2000) reader/writer. This module automatically registers the 'mdl' format with Chemistry::Mol. The first three lines of the molfile are stored as $mol->name, $mol->attr("mdlmol/line2"), and $mol->attr("mdlmol/comment"). This version onl...
MERKYS/Chemistry-File-MDLMol-0.24 - 03 Feb 2022 16:09:12 UTC
Chemistry::Domain - Class for domains in macromolecules
A domain is a substructure of a larger molecule. It is typically used to represent aminoacid residues within a protein, or bases within a nucleic acid, but you could use it for any arbitrary substructure such as functional groups and rings. A domain ...
ITUB/Chemistry-MacroMol-0.06 - 03 Jul 2004 19:22:04 UTC
Chemistry::File::SDF - MDL Structure Data File reader/writer
MDL SDF (V2000) reader. This module automatically registers the 'sdf' format with Chemistry::Mol. The parser returns a list of Chemistry::Mol objects. SDF data can be accessed by the $mol->attr method. Attribute names are stored as a hash ref at the ...
MERKYS/Chemistry-File-MDLMol-0.24 - 03 Feb 2022 16:09:12 UTC
Chemistry::Ring - Represent a ring as a substructure of a molecule
This module provides some basic methods for representing a ring. A ring is a subclass of molecule, because it has atoms and bonds. Besides that, it has some useful geometric methods for finding the centroid and the ring plane, and methods for aromati...
MERKYS/Chemistry-Ring-0.21 - 16 Dec 2022 08:35:04 UTC
Chemistry::Smiles - SMILES parser (deprecated)
NOTE: THIS MODULE IS DEPRECATED! Use Chemistry::File::SMILES instead. This object-oriented module parses a SMILES (Simplified Molecular Input Line Entry Specification) string. It can either return the molecule as a Chemistry::Mol object or be used vi...
ITUB/Chemistry-Smiles-0.13 - 27 Feb 2004 23:47:08 UTC
Chemistry::Mok - molecular awk interpreter
This module is the engine behind the mok program. See mok(1) for a detailed description of the language. Mok is part of the PerlMol project, <http://www.perlmol.org>....
ITUB/Chemistry-Mok-0.25 - 16 May 2005 21:55:57 UTC
Chemistry::SQL - Access Database Functions Module
This package provides the necessary functions to interact with the database. The methods implemented in this module are oriented to give users control of the database without knowing how to use SQL queries....
BREQUESEN/Chemistry-SQL-0.01 - 07 Dec 2005 08:59:28 UTC
Chemistry::Reaction - Explicit chemical reactions
This package, along with Chemistry::Pattern, provides an implementation of explicit chemical reactions. An explicit chemical reaction is a representation of the transformation that takes place in a given chemical reaction. In an explicit chemical rea...
ITUB/Chemistry-Reaction-0.02 - 26 Sep 2004 19:20:27 UTC
Chemistry::Pattern - Chemical substructure pattern matching
This module implements basic pattern matching for molecules. The Chemistry::Pattern class is a subclass of Chemistry::Mol, so patterns have all the properties of molecules and can come from reading the same file formats. Of course there are certain f...
ITUB/Chemistry-Pattern-0.27 - 10 May 2009 21:00:10 UTC
Chemistry::3DBuilder - Generate 3D coordinates from a connection table
This module generates a three-dimensional molecular structure from a connection table, such as that obtained by a 2D representation of the molecule or from a SMILES string. NOTE: this module is still at a very early stage of development so it has imp...
ITUB/Chemistry-3DBuilder-0.10 - 06 May 2005 22:37:42 UTC
Chemistry::PointGroup - Group theory for normal modes of vibration
Many common molecules, for example, water, ammonia, methane,etc., possess some symmetry. In calculating the normal modes and frequencies of vibration, symmetry considerations can reduce enormously the labor of the calculations. The symmetry and geome...
MANFREDI/Chemistry-PointGroup-0.01 - 20 Feb 2006 07:50:33 UTC