Calculate the FP3 Molecular Fingerprints
extractDrugOBFP3(molecules, type = c("smile", "sdf"))
molecules | R character string object containing the molecules. See the example section for details. |
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type |
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A matrix. Each row represents one molecule, the columns represent the fingerprints.
Calculate the 64 bit FP3 fingerprints provided by OpenBabel.
# NOT RUN { mol1 = 'C1CCC1CC(CN(C)(C))CC(=O)CC' # one molecule SMILE in a vector mol2 = c('CCC', 'CCN', 'CCN(C)(C)', 'c1ccccc1Cc1ccccc1', 'C1CCC1CC(CN(C)(C))CC(=O)CC') # multiple SMILEs in a vector mol3 = readChar(system.file('compseq/DB00860.sdf', package = 'Rcpi'), nchars = 1e+6) # single molecule in a sdf file mol4 = readChar(system.file('sysdata/OptAA3d.sdf', package = 'Rcpi'), nchars = 1e+6) # multiple molecules in a sdf file # }# NOT RUN { smifp0 = extractDrugOBFP3(mol1, type = 'smile') smifp1 = extractDrugOBFP3(mol2, type = 'smile') sdffp0 = extractDrugOBFP3(mol3, type = 'sdf') sdffp1 = extractDrugOBFP3(mol4, type = 'sdf') # }