ms.compute: Computes Similarity of Molecules

In RxnSim: Functions to Compute Chemical and Chemical Reaction Similarity

Computes Similarity of Molecules

Description

Computes chemical similarity between two (or more) input molecules.

Usage

ms.compute (molA, molB, format = 'smiles', standardize = TRUE, explicitH = FALSE,
            sim.method = 'tanimoto', fp.type = 'extended', fp.mode = 'bit', fp.depth = 6,
            fp.size = 1024, fpCached = FALSE)
ms.compute.sim.matrix (molA, format = 'smiles', standardize = TRUE, explicitH = FALSE,
            sim.method = 'tanimoto', fp.type = 'extended', fp.mode = 'bit', fp.depth = 6,
            fp.size = 1024, clearCache = TRUE)
ms.compute.PCA(molA, format = 'smiles', standardize = TRUE, explicitH = FALSE, 
            fp.type = 'extended', fp.mode = 'bit', fp.depth = 6, fp.size = 1024,
            clearCache = TRUE)

Arguments

molA	input molecule in SMILES format or name (with path) of MDL MOL file. ms.compute.sim.matrix accepts list of molecules as input.
molB	input molecule in SMILES format or name (with path) of MDL MOL file.
format	specifies format of input molecule(s). Molecule(s) can be provided in one of following formats: 'SMILES' (default) or 'MOL'.
standardize	suppresses all explicit hydrogen if set as TRUE (default).
explicitH	converts all implicit hydrogen to explicit if set as TRUE. It is set as FALSE by default.
sim.method	similarity metric to be used to evaluate molecule similarity. Allowed types include: 'simple', 'jaccard', 'tanimoto' (default), 'russelrao', 'dice', 'rodgerstanimoto', 'achiai', 'cosine', 'kulczynski2', 'mt', 'baroniurbanibuser', 'tversky', 'robust', 'hamann', 'pearson', 'yule', 'mcconnaughey', 'simpson', 'jaccard-count' and 'tanimoto-count'.
fp.type	fingerprint type to use. Allowed types include: 'standard', 'extended' (default), 'graph', 'estate', 'hybridization', 'maccs', 'pubchem', 'kr', 'shortestpath', 'signature' and 'circular'.
fp.mode	fingerprint mode to be used. It can either be set to 'bit' (default) or 'count'.
fp.depth	search depth for fingerprint construction. This argument is ignored for 'pubchem', 'maccs', 'kr' and 'estate' fingerprints.
fp.size	length of the fingerprint bit string. This argument is ignored for 'pubchem', 'maccs', 'kr', 'estate', 'circular' (count mode) and 'signature' fingerprints.
fpCached	boolean that enables fingerprint caching. It is set to FALSE by default.
clearCache	boolean that resets the cache before (and after) processing molecule lists. It is set to TRUE by default. Cache can also be explicitly cleared by using rs.clearCache.

Details

See rs.compute functions, for details for fingerprints and similarity matrices. ms.compute can use fingerprint caching by enabling fpCached option. ms.compute and ms.compute.sim.matrix use same cache as rs.compute and other functions in the package. ms.compute.PCA computes PCA based on the fingerprints using prcomp funtion.

Value

Returns similarity value(s).

ms.compute	returns a similarity value.
ms.compute.sim.matrix	returns a m \times m symmetric matrix of similarity values. m is the length of the input list.
ms.compute.PCA	returns prcomp object.

Note

Fingerprint cache stores fingerprints generated for a molecule index based on its SMILES. When caching is enabled, the fingerprint for a molecule, if present, is retrieved from the cache. The parameters pertaining to fingerprint generation are thus ignored. If the fingerprint for the molecule is not already cached, fingerprint based on the input parameters is generated and stored in the cache.

Author(s)

Varun Giri [e-mail]

See Also

rs.compute, rs.clearCache

Examples

ms.compute('N', '[H]N([H])[H]', standardize = FALSE)

RxnSim documentation built on July 26, 2023, 5:41 p.m.