RxnSim-package: Functions to compute chemical reaction and molecular...
In RxnSim: Functions to Compute Chemical and Chemical Reaction Similarity
RxnSim-package R Documentation
Functions to compute chemical reaction and molecular similarity
Description
RxnSim provides methods to compute molecular and reaction similarity. It uses rCDK package (R Interface to the CDK Libraries) and fingerprints package for chemoinformatic routines.
Details
RxnSim provides methods to compute chemical similarity between two or more reactions and molecules. Molecular similarity is computed based on structural features. Reaction similarity is a function of similarities of participating molecules. The package provides multiple methods to extract structural features as fingerprints (or feature vectors) and similarity metrics. It additionally provides functionality to mask chemical substructures for weighted similarity computations. It uses rCDK and fingerprint packages for cheminformatics functionality.
User functions:
rs.computecomputes similarity between two reactions.
rs.compute.listcomputes similarity between all pairs of reactions from two lists.
rs.compute.sim.matrixcomputes pairwise similarity between all reactions in a list.
rs.compute.DBcomputes similarity of a reaction to those in a reaction database (DB) object read from a text file.
rs.makeDBreads a text file containing EC Numbers, Reaction Names and Reaction SMILES and converts it into a reaction DB object.
ms.computecomputes similarity between two molecules.
ms.compute.sim.matrixcomputes pairwise similarity between all molecules in a list.
rs.clearCacheclears fingerprint cache.
rs.masksubstitutes given sub-structure in the molecules of a reaction by a user defined mask.
ms.masksubstitutes given sub-structure in a molecule by a user defined mask.
Author(s)
Varun Giri varungiri@gmail.com
Maintainer: Varun Giri
See Also
rs.compute, ms.compute
Examples
# Reaction similarity
rs.compute('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C')
# Metabolite similarity
ms.compute('CCC=O', 'CC(O)C')
RxnSim documentation built on July 26, 2023, 5:41 p.m.
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| RxnSim-package | R Documentation |
Functions to compute chemical reaction and molecular similarity
Description
RxnSim provides methods to compute molecular and reaction similarity. It uses rCDK package (R Interface to the CDK Libraries) and fingerprints package for chemoinformatic routines.
Details
RxnSim provides methods to compute chemical similarity between two or more reactions and molecules. Molecular similarity is computed based on structural features. Reaction similarity is a function of similarities of participating molecules. The package provides multiple methods to extract structural features as fingerprints (or feature vectors) and similarity metrics. It additionally provides functionality to mask chemical substructures for weighted similarity computations. It uses rCDK and fingerprint packages for cheminformatics functionality.
User functions:
rs.computecomputes similarity between two reactions.
rs.compute.listcomputes similarity between all pairs of reactions from two lists.
rs.compute.sim.matrixcomputes pairwise similarity between all reactions in a list.
rs.compute.DBcomputes similarity of a reaction to those in a reaction database (DB) object read from a text file.
rs.makeDBreads a text file containing EC Numbers, Reaction Names and Reaction SMILES and converts it into a reaction DB object.
ms.computecomputes similarity between two molecules.
ms.compute.sim.matrixcomputes pairwise similarity between all molecules in a list.
rs.clearCacheclears fingerprint cache.
rs.masksubstitutes given sub-structure in the molecules of a reaction by a user defined mask.
ms.masksubstitutes given sub-structure in a molecule by a user defined mask.
Author(s)
Varun Giri varungiri@gmail.com
Maintainer: Varun Giri
See Also
rs.compute, ms.compute
Examples
# Reaction similarity
rs.compute('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C')
# Metabolite similarity
ms.compute('CCC=O', 'CC(O)C')
R Package Documentation
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