Dear All,
I have executed >1000 drug molecules in a Vina docking study. Now I have >1000 log files that contain the top ten binding scores for every compound in a log file for each. I want to extract only the lowest binding energy from each log file and get it as an output.txt file. Can anybody show me the python script for this kind of workflow?
A sample log file is attached here. It is a default Vina output file. I have over 2000 of these files in a single folder. Please see the attachment.
Thank you,
Amal.
Can you also post an example file here?
It can be easily solved by sort and head/tail functions..you don't need a script!
Dear Rajesh Pal,
As you requested, I have attached one of the many log files generated by Vina software. I want to extract the lowest affinity (kcal/mol) value, which is the topmost value in the table in the log file. I want to extract all 2000 of them and make it into a txt or CSV file that contains the file name and the affinity energy values in two columns. So I can use it for further classification. Actually, I do not a script yet.
Thank you, So much.
Amal.
Hi Amal,
Assuming that the affinity scores always begin from the 23rd row, and are always in the second column.
here it goes
1. First remove the first 23 rows and write it to new files
for x in *.txt; do
awk 'NR >23 { print }' "${x%.txt}.data"
done
2. keep only 2nd column from the ".data" files
for x in *pdbqt_log.data; do
awk '{ print $2 }' "${x%.txt}.2data"
done
3. merge them together in text or csv file with file name
combine() {
local IFS=$'\t' f
local -a header
for f in "$@"; do
header+=("$(basename "$f" .txt)")
done
printf "%s\n" "${header[*]}"
paste "$@"
}
after running the above command, run
combine *pdbqt_log.data.2data > merge.txt
***You can run these on terminal
*not the elegant solution,
it was quick and dirty.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology