Chemistry::Bond::Find - Detect bonds in a molecule from atomic 3D coordinates and assign formal bond orders River stage one • 4 direct dependents • 8 total dependents

This module provides functions for detecting the bonds in a molecule from its 3D coordinates by using simple cutoffs, and for guessing the formal bond orders. This module is part of the PerlMol project, <http://www.perlmol.org/>....

ITUB/Chemistry-Bond-Find-0.23 - 10 May 2009 20:05:27 UTC

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

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

Chemistry::Ring::Find - Find the rings (cycles) in a molecule River stage one • 4 direct dependents • 6 total dependents

The Chemistry::Ring::Find module implements a breadth-first ring finding algorithm, and it can find all rings that contain a given atom or bond, the Smallest Set of Smallest Rings (SSSR), or the "almost SSSR", which is an unambiguous set of rings for...

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

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

Chemistry::File::SLN - SLN linear notation parser/writer River stage zero No dependents

This module parses a SLN (Sybyl Line Notation) string. This is a File I/O driver for the PerlMol project. <http://www.perlmol.org/>. It registers the 'sln' format with Chemistry::Mol, and recognizes filenames ending in '.sln'. Optional attributes for...

ITUB/Chemistry-File-SLN-0.11 - 29 Mar 2005 16:42:04 UTC

Chemistry::File::VRML - Generate VRML models for molecules River stage zero No dependents

This module generates a VRML (Virtual Reality Modeling Language) representation of a molecule, which can then be visualized with any VRML viewer. This is a PerlMol file I/O plugin, and registers the 'vrml' format with Chemistry::Mol. Note however tha...

ITUB/Chemistry-File-VRML-0.10 - 16 May 2005 21:17:49 UTC

Chemistry::File::SMILES - SMILES linear notation parser/writer River stage one • 3 direct dependents • 4 total dependents

This module parses a SMILES (Simplified Molecular Input Line Entry Specification) string. This is a File I/O driver for the PerlMol project. <http://www.perlmol.org/>. It registers the 'smiles' format with Chemistry::Mol. This parser interprets anyth...

ITUB/Chemistry-File-SMILES-0.47 - 08 Jul 2010 03:16:39 UTC

Chemistry::File::InternalCoords - Internal coordinates (z-matrix) molecule format reader/writer River stage zero No dependents

This is a subclass of Chemistry::File for reading and writing the zmatriz (aka Z-matrix aka InternalCoords) molecule data format. It registers the 'zmat' file extension with Chemistry::Mol. For example, here is hydrogen: H H 1 B1 B1 0.70000000 and wa...

DAVIDRW/Chemistry-File-InternalCoords-0.03 - 07 Apr 2007 23:59:47 UTC

Chemistry::InternalCoords::Builder - Build a Z-matrix from cartesian coordinates River stage one • 2 direct dependents • 3 total dependents

This module builds a Z-matrix from the cartesian coordinates of a molecule, making sure that atoms are defined in a way that allows for efficient structure optimizations and Monte Carlo sampling. By default, the algorithm tries to start at the center...

ITUB/Chemistry-InternalCoords-0.18 - 24 Sep 2004 20:51:39 UTC
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