R/705-searchDrug.R
searchDrug.Rd
Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search
searchDrug(mol, moldb, cores = 2, method = c("fp", "mcs"), fptype = c("standard", "extended", "graph", "hybrid", "maccs", "estate", "pubchem", "kr", "shortestpath", "fp2", "fp3", "fp4", "obmaccs"), fpsim = c("tanimoto", "euclidean", "cosine", "dice", "hamming"), mcssim = c("tanimoto", "overlap"), ...)
mol | The query molecule. The location of a |
---|---|
moldb | The molecule database. The location of a |
cores | Integer. The number of CPU cores to use for parallel search,
default is |
method |
|
fptype | The fingerprint type, only available when |
fpsim | Similarity measure type for fingerprint,
only available when |
mcssim | Similarity measure type for maximum common substructure search,
only available when |
... | Other possible parameter for maximum common substructure search,
see |
Named numerical vector. With the decreasing similarity value of the molecules in the database.
This function does compound similarity search derived by various molecular fingerprints with various similarity measures or derived by maximum common substructure search. This function runs for a query compound against a set of molecules.
# NOT RUN { mol = system.file('compseq/DB00530.sdf', package = 'Rcpi') # DrugBank ID DB00530: Erlotinib moldb = system.file('compseq/tyrphostin.sdf', package = 'Rcpi') # Database composed by searching 'tyrphostin' in PubChem and filtered by Lipinski's Rule of Five # }# NOT RUN { searchDrug(mol, moldb, cores = 4, method = 'fp', fptype = 'maccs', fpsim = 'hamming') searchDrug(mol, moldb, cores = 4, method = 'fp', fptype = 'fp2', fpsim = 'tanimoto') searchDrug(mol, moldb, cores = 4, method = 'mcs', mcssim = 'tanimoto') # }