DSDHT week 4 Cheminformatics

script for wk 4 quiz on cheminformatics using rcdk package

library(rcdk)

## Loading required package: fingerprint

question `14

dc<-get.desc.categories()
dc

## [1] "protein"        "hybrid"         "constitutional" "topological"   
## [5] "electronic"     "geometrical"

question 13

mol<-parse.smiles("c1([C@@H](C(O)=O)C)ccc(CC(C)C)cc1")[[1]]
get.xlogp(mol)

## [1] 3.641

question 15

mol <- parse.smiles("C1CN(CCC1NC(C2=CN=CC=C2)C3=CN(N=C3)CC(F)(F)F)C4=CC=C(C=C4)C(F)(F)F")[[1]]
atoms<-get.atoms(mol)
cat('No. of atoms =', length(atoms), '\n')

## No. of atoms = 34

q16

mol4 <- parse.smiles("N1(c2c(NC(c3c1nccc3)=O)c(ccn2)C)C1CC1")
descName<-c("org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor") 
desc <- eval.desc(mol4, descName)
desc

##                                             MW
## N1(c2c(NC(c3c1nccc3)=O)c(ccn2)C)C1CC1 266.1168

q 17

mol <- parse.smiles("C1CN(CCC1NC(C2=CN=CC=C2)C3=CN(N=C3)CC(F)(F)F)C4=CC=C(C=C4)C(F)(F)F")[[1]]
bonds <-get.bonds(mol)
cat('No. of bonds =', length(bonds), '\n')

## No. of bonds = 37

q19

fp1 <- new("fingerprint", nbit=10, bits=c(1,2,4,6,9)) 
fp2 <- new("fingerprint", nbit=10, bits=c(2,5,6)) 
distance(fp1,fp2)

## [1] 0.3333333