I have set of files in a folder as follows :
nlb_1.pdb
nlb_2.pdb
nlb1_1.pdb
nlb1_2.pdb
How to access all the files in the folder in rscript and execute following commands for each of the files :
library(bio3d)
nlb_1 <- read.pdb('nlb_1.pdb',multi = TRUE)
ca.inds_nlb_1 <- atom.select(nlb_1,elety = 'CA')
First, you need to make a temp vector of the files in your folder:
temp = list.files(path = "path/to/your/folder", pattern="*.pdb")
Then, lapply the read.pdb function to read them in a list that here we call datasets
datasets = lapply(temp, read.pdb, multi = TRUE)
Then you can loop through your datasets applying the function you like.
just use the list.files command.
files=list.files(desired_folder,full=TRUE,pattern='pdb$')
library(bio3d)
processed_files=lapply(files,function(x){
temp=read.pdb(x,multi=TRUE)
atom.select(temp,elety='CA')
})
the elements in the list will be result of the process from your files.
