Search results for "module:Chemistry::Atom"
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::Pattern::Atom - An atom that knows how to match
Objects of this class represent atoms in a pattern. This is a subclass of Chemistry::Atom. In addition to the properties of regular atoms, pattern atoms have a method for testing if they match an atom in a molecule. By default, a pattern atom matches...
ITUB/Chemistry-Pattern-0.27 - 10 May 2009 21:00:10 UTC
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::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::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::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::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::Isotope - Table of the isotopes exact mass data
This module contains the exact mass data from the table of the isotopes. It has an exportable function, isotope_mass, which returns the mass of an atom in mass units given its mass number (A) and atomic number (Z); and a function isotope_abundance wh...
ITUB/Chemistry-Isotope-0.11 - 18 May 2005 23:16:55 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::InternalCoords - Represent the position of an atom using internal coordinates and convert it to Cartesian coordinates.
This module implements an object class for representing internal coordinates and provides methods for converting them to Cartesian coordinates. For generating an internal coordinate representation (aka a Z-matrix) of a molecule from its Cartesian coo...
ITUB/Chemistry-InternalCoords-0.18 - 24 Sep 2004 20:51:39 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::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::Harmonia - Decision of simple and difficult chemical puzzles.
The module provides the necessary subroutines to solve some puzzles of the general inorganic and physical chemistry. The methods implemented in this module, are all oriented to known rules and laws of general and physical chemistry....
DONANGEL/Chemistry-Harmonia-0.118 - 18 May 2013 20:01:04 UTC
Chemistry::OpenSMILES - OpenSMILES format reader and writer
Chemistry::OpenSMILES provides support for SMILES chemical identifiers conforming to OpenSMILES v1.0 specification (<http://opensmiles.org/opensmiles.html>). Chemistry::OpenSMILES::Parser reads in SMILES strings and returns them parsed to arrays of G...
MERKYS/Chemistry-OpenSMILES-0.9.0 - 25 Oct 2023 13:13:29 UTC
Chemistry::Canonicalize - Number the atoms in a molecule in a unique way
This module provides functions for "canonicalizing" a molecular structure; that is, to number the atoms in a unique way regardless of the input order. The canonicalization algorithm is based on: Weininger, et. al., J. Chem. Inf. Comp. Sci. 29[2], 97-...
ITUB/Chemistry-Canonicalize-0.11 - 10 May 2009 20:17:04 UTC
Chemistry::MidasPattern - Select atoms in macromolecules
This module partially implements a pattern matching engine for selecting atoms in macromolecules by using Midas/Chimera patterns. See <http://www.cmpharm.ucsf.edu/~troyer/troff2html/midas/Midas-uh-3.html#sh -2.1> for a detailed description of this la...
ITUB/Chemistry-MidasPattern-0.11 - 16 May 2005 23:06:55 UTC
Chemistry::File::PDB - Protein Data Bank file format reader/writer
This module reads and writes PDB files. The PDB file format is commonly used to describe proteins, particularly those stored in the Protein Data Bank (<http://www.rcsb.org/pdb/>). The current version of this module only reads the following record typ...
ITUB/Chemistry-File-PDB-0.23 - 10 May 2009 21:58:55 UTC