Chemistry::Mok - molecular awk interpreter River stage zero No dependents

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 - Search in distribution
  • mok - an awk for molecules

Chemistry::Obj - Abstract chemistry object River stage two • 19 direct dependents • 19 total dependents

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-0.38 - 09 Apr 2021 12:33:09 UTC - Search in distribution

Chemistry::SQL - Access Database Functions Module River stage zero No dependents

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 - Search in distribution

Chemistry::Ring - Represent a ring as a substructure of a molecule River stage one • 4 direct dependents • 6 total dependents

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...

ITUB/Chemistry-Ring-0.20 - 10 May 2009 21:14:18 UTC - Search in distribution

Chemistry::Domain - Class for domains in macromolecules River stage one • 2 direct dependents • 2 total dependents

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 - Search in distribution

Chemistry::Smiles - SMILES parser (deprecated) River stage zero No dependents

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 - Search in distribution

Chemistry::Isotope - Table of the isotopes exact mass data River stage one • 1 direct dependent • 1 total dependent

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 - Search in distribution

Chemistry::Pattern - Chemical substructure pattern matching River stage one • 6 direct dependents • 6 total dependents

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 - Search in distribution

Chemistry::Elements - Perl extension for working with Chemical Elements River stage one • 1 direct dependent • 1 total dependent

There are two parts to the module: the object stuff and the exportable functions for use outside of the object stuff. The exportable functions are discussed in "Exportable functions". Chemistry::Elements provides an easy, object-oriented way to keep ...

BDFOY/Chemistry-Elements-1.074 - 15 Jan 2021 08:28:11 UTC - Search in distribution

Chemistry::Harmonia - Decision of simple and difficult chemical puzzles. River stage zero No dependents

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 - Search in distribution

Chemistry::Reaction - Explicit chemical reactions River stage zero No dependents

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 - Search in distribution

Chemistry::3DBuilder - Generate 3D coordinates from a connection table River stage one • 1 direct dependent • 1 total dependent

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 - Search in distribution

Chemistry::OpenSMILES - OpenSMILES format reader and writer River stage zero No dependents

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-0.5.1 - 29 Aug 2021 07:01:30 UTC - Search in distribution

Chemistry::PointGroup - Group theory for normal modes of vibration River stage zero No dependents

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 - Search in distribution

Chemistry::Canonicalize - Number the atoms in a molecule in a unique way River stage one • 3 direct dependents • 8 total dependents

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 - Search in distribution

Chemistry::MidasPattern - Select atoms in macromolecules River stage zero No dependents

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 - Search in distribution

Chemistry::MolecularMass - Perl extension for calculating molecular mass of a chemical compound given its chemical formula. River stage zero No dependents

Chemistry::MolecularMass is an Object Oriented Perl module for calculating molcular mass of chemical compounds implemented with Perl and C. Molecular masses of elements stored in the module follow recommendations of IUPAC (1995). The module includes ...

MKHRAPOV/Chemistry-MolecularMass-0.1 - 21 Sep 2000 22:32:47 UTC - Search in distribution

Chemistry::FormulaPattern - Match molecule by formula River stage zero No dependents

This module implements a simple language for describing a range of molecular formulas and allows one to find out whether a molecule matches the formula specification. It can be used for searching for molecules by formula, in a way similar to the NIST...

ITUB/Chemistry-FormulaPattern-0.10 - 11 Aug 2004 23:09:39 UTC - Search in distribution

Chemistry::InternalCoords - Represent the position of an atom using internal coordinates and convert it to Cartesian coordinates. River stage one • 2 direct dependents • 3 total dependents

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 - Search in distribution

Chemistry::File::SDF - MDL Structure Data File reader/writer River stage zero No dependents

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-0.23 - 13 Apr 2021 14:26:30 UTC - Search in distribution
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