Rename files from their content

Question

I have thousands of txt files with a .pdbqt extension in a directory named 100000cpds_ligand_00001.pdbqt, 100000cpds_ligand_00002.pdbqt, 100000cpds_ligand_*****.pdbqt and would like to rename them according to a unique identifier from their contents.

The identifier is given as REMARK Name = PV-000009607404 in a single line, where PV-000009607404 can be of variable length, text, and numbers (e.g. ZINC001248485427, etc.). I would like to only keep the identifier part in the file name and not the REMARK Name = part. So, I would e.g. change 100000cpds_ligand_00001.pdbqt to PV-000009607404.pdbqt. I can do it from the command line, but lprefarably I would like to use a small script.

Thank you very much for your help!

Answer 1

I have done an example which should only copy files instead of rename. Comments indicate some of the logic. I'm not a bash expert, but I tested this on a file.

You should create this file in the same directory as your source files, and name it something like pdbqt-mover.sh.

Either call it by typing bash pdbqt-mover.sh or you'll have to set permissions on the file so you can execute it using ./pdbqt-mover.sh.

#!/bin/bash
# process only files starting with 100000cpds_ligand_ and ending in .pdbqt
for infile in 100000cpds_ligand_*.pdbqt; do

  # get the pv-* string from lines beginning with "REMARK  Name = "
  # get the group matching PV-**** up to the end of the line
  pvnum=$(sed -n 's/^REMARK  Name = \(PV-\S*\)/\1/p' "$infile")

  # construct the output filename
  outfile="$pvnum".pdbqt

  # only copy if the output file doesn't exist
  if [ ! -f $outfile ] ; then
    # cp instead of mv
    cp "$infile" "$outfile"
    echo "Copied $infile to $outfile"
  else
    echo "File $outfile exists! Skipping"
  fi
done

Answer 2

This is very easily done using grep and also a terminal file browser called RANGER. First use grep to pull out the lines containing filenames. For example

grep REMARK * > fnlist

edit fnlist and get rid of the redundant string of "REMARK NAME = ". You now have a clean list of new file names.

Launch Ranger, navigate to the directory containing your files and do a bulkrename operation. Paste the contents of nflist when presented and you are done.