Description Usage Arguments Details Value Author(s) References Examples
View source: R/902-calcDrugMCSSim.R
Calculate Drug Molecule Similarity Derived by Maximum Common Substructure Search
1 2 |
mol1 |
The first molecule. R character string object containing the molecule. See examples. |
mol2 |
The second molecule. R character string object containing the molecule. See examples. |
type |
The input molecule format, 'smile' or 'sdf'. |
plot |
Logical. Should we plot the two molecules and their maximum common substructure? |
al |
Lower bound for the number of atom mismatches. Default is 0. |
au |
Upper bound for the number of atom mismatches. Default is 0. |
bl |
Lower bound for the number of bond mismatches. Default is 0. |
bu |
Upper bound for the number of bond mismatches. Default is 0. |
matching.mode |
Three modes for bond matching are supported:
|
... |
Other graphical parameters |
This function calculate drug molecule similarity derived by
maximum common substructure search. The maximum common substructure search
algorithm is provided by the fmcsR
package.
A list containing the detail MCS information and similarity values. The numeric similarity value includes Tanimoto coefficient and overlap coefficient.
Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>
Wang, Y., Backman, T. W., Horan, K., & Girke, T. (2013). fmcsR: mismatch tolerant maximum common substructure searching in R. Bioinformatics, 29(21), 2792–2794.
1 2 3 4 | mol1 = 'CC(C)CCCCCC(=O)NCC1=CC(=C(C=C1)O)OC'
mol2 = 'O=C(NCc1cc(OC)c(O)cc1)CCCC/C=C/C(C)C'
sim1 = calcDrugMCSSim(mol1, mol2, type = 'smile')
print(sim1[[2]]) # Tanimoto Coefficient
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