searchDrug {Rcpi} | R Documentation

## Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search

### Description

Parallelized Drug Molecule Similarity Search by Molecular Fingerprints Similarity or Maximum Common Substructure Search

### Usage

    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"), ...)

### Arguments

`mol` | The query molecule. The location of a `sdf` file containing one molecule.
`moldb` | The molecule database. The location of a `sdf` file containing all the molecules to be searched with.
`cores` | Integer. The number of CPU cores to use for parallel search, default is `2`. Users could use the `detectCores()` function in the `parallel` package to see how many cores they could use.
`method` | `'fp'` or `'mcs'`. Search by molecular fingerprints or by maximum common substructure searching.
`fptype` | The fingerprint type, only available when `method = 'fp'`. Rcpi supports 13 types of fingerprints, including `'standard'`, `'extended'`, `'graph'`, `'hybrid'`, `'maccs'`, `'estate'`, `'pubchem'`, `'kr'`, `'shortestpath'`, `'fp2'`, `'fp3'`, `'fp4'`, `'obmaccs'`.
`fpsim` | Similarity measure type for fingerprint, only available when `method = 'fp'`. Including `'tanimoto'`, `'euclidean'`, `'cosine'`, `'dice'` and `'hamming'`. See `calcDrugFPSim` for details.
`mcssim` | Similarity measure type for maximum common substructure search, only available when `method = 'mcs'`. Including `'tanimoto'` and `'overlap'`.
`...` | Other possible parameter for maximum common substructure search, see `calcDrugMCSSim` for available options.

### Details

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.

### Value

Named numerical vector. With the decreasing similarity value of the molecules in the database.

### Author(s)

Nan Xiao <https://nanx.me>

### Examples

    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')

[Package Rcpi version 1.16.2 Index]