searchDrug {Rcpi} | R Documentation |
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 |
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.
Named numerical vector. With the decreasing similarity value of the molecules in the database.
Nan Xiao <https://nanx.me>
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 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')