extrDrugOBFP3: Calculate the FP3 Molecular Fingerprints
In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Calculate the FP3 Molecular Fingerprints
Usage
1
extrDrugOBFP3(molecules, type = c("smile", "sdf"))
Arguments
molecules
R character string object containing the molecules.
See the example section for details.
type
'smile' or 'sdf'.
Details
Calculate the 64 bit FP3 fingerprints provided by OpenBabel.
Value
A matrix. Each row represents one molecule,
the columns represent the fingerprints.
Author(s)
Min-feng Zhu <wind2zhu@163.com>,
Nan Xiao <http://r2s.name>
Examples
1
2
3
4
5
6
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
smifp0 = extrDrugOBFP3(mol1, type = 'smile')
smifp1 = extrDrugOBFP3(mol2, type = 'smile')
wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
Calculate the FP3 Molecular Fingerprints
Usage
1 | extrDrugOBFP3(molecules, type = c("smile", "sdf"))
|
Arguments
molecules |
R character string object containing the molecules. See the example section for details. |
type |
|
Details
Calculate the 64 bit FP3 fingerprints provided by OpenBabel.
Value
A matrix. Each row represents one molecule, the columns represent the fingerprints.
Author(s)
Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>
Examples
1 2 3 4 5 6 | 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
smifp0 = extrDrugOBFP3(mol1, type = 'smile')
smifp1 = extrDrugOBFP3(mol2, type = 'smile')
|
R Package Documentation
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