R/384-extractDrugDescOB.R
extractDrugDescOB.Rd
Calculate Molecular Descriptors Provided by OpenBabel
extractDrugDescOB(molecules, type = c("smile", "sdf"))
molecules | R character string object containing the molecules. See the example section for details. |
---|---|
type |
|
A data frame, each row represents one of the molecules,
each column represents one descriptor.
This function returns 14 columns named
abonds
, atoms
, bonds
, dbonds
,
HBA1
, HBA2
, HBD
, logP
,
MR
, MW
, nF
, sbonds
, tbonds
, TPSA
:
abonds
- Number of aromatic bonds
atoms
- Number of atoms
bonds
- Number of bonds
dbonds
- Number of double bonds
HBA1
- Number of Hydrogen Bond Acceptors 1
HBA2
- Number of Hydrogen Bond Acceptors 2
HBD
- Number of Hydrogen Bond Donors
logP
- Octanol/Water Partition Coefficient
MR
- Molar Refractivity
MW
- Molecular Weight Filter
nF
- Number of Fluorine Atoms
sbonds
- Number of single bonds
tbonds
- Number of triple bonds
TPSA
- Topological Polar Surface Area
This function calculates 14 types of the numerical molecular descriptors provided in OpenBabel.
# NOT RUN { mol1 = 'CC(=O)NCCC1=CNc2c1cc(OC)cc2' # one molecule SMILE in a vector mol2 = c('OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2', 'CCc(c1)ccc2[n+]1ccc3c2Nc4c3cccc4', '[Cu+2].[O-]S(=O)(=O)[O-]') # 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 { # Problem (core dump) under Ubuntu 16.04 smidesc0 = extractDrugDescOB(mol1, type = 'smile') smidesc1 = extractDrugDescOB(mol2, type = 'smile') sdfdesc0 = extractDrugDescOB(mol3, type = 'sdf') sdfdesc1 = extractDrugDescOB(mol4, type = 'sdf') # }