Question regarding Bash program

Hello All,

I am trying to write a small bash script to make my life easier for an analysis. I have multiple folders and inside them are 10 output files with an extension .pdbqt What I am trying to do is to read the folder content and then make a PyMol (.pml) file to load the molecules and then display it. When I close the PyMol, the script should go to the next folder and do the same thing again. Below I am pasting the code, any help is greatly appreciated :o

#!/bin/bash                                                                                                                                                                                   
for f in Frog-mol-ryan_*; do
    if [ -d "${f}" ]; then
        echo Loading structures in Pymol: $f
        
cat <<EOF >log.pml                                                                                                                                                                           
                                                                                                                                                                                              
load /server/John/Docking-Studies/docking-FC996-analog/MR1004/test/Frog-mol-ryan_*/out_Frog-ryan-mol_ligand_*.pdbqt                                                            
                                                                                                                                                                                              
reset                                                                                                                                                                                         
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/PDBs/Holo-with-Bpore.pdb                                                                                
cmd.hide("everything","holo-with-Bpore")                                                                                                                                                 
cmd.show("cartoon"   ,"holo-with-Bpore")                                                                                                                                                 
cmd.show("sticks", "out_Frog-mol-ryan_ligand_*.pdbqt")                                                                                                                                                   
EOF                                                                                                                                                                                           

/usr/bin/pymol log.pml
    fi
done

The output log.pml is:

load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/MR1004/test/Frog-mol-ryan_*/out__ligand_*.pdbqt

reset
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/PDBs/Holo-with-Bpore.pdb
cmd.hide("everything","holo-with-Bpore")
cmd.show("cartoon"   ,"holo-with-Bpore")
cmd.show("sticks", "out__ligand_*.pdbqt")

I am not able to pass the argument in cat EOF section.

Kindly help
Thanks

You've passed hardcoded text, rather than the variable $f ..

load /server/John/Docking-Studies/docking-FC996-analog/MR1004/test/Frog-mol-ryan_*/out_Frog-ryan-mol_ligand_*.pdbqt

becomes

load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/MR1004/test/$f/out_$f*.pdbqt

Assuming the "out_Frog_ryan_mol" was a typo and should have been "out_Frog_mol_ryan"...

Hope this helps

Hello sea,
Thank you for your help. One small problem, the output files are named out_Frog-mol-ryan_ligand_05.pdbqt so if I set as "$f/out_$f*.pdbqt" its not able to find the files.
Kindly suggest.

Thanks

Oh the assumption was wrong

This should do the trick then:
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/MR1004/test/$f/out_Frog-mol-ryan_ligand_*.pdbq

Thanks sea,
Sorry to disturb you so much.
"out_Frog-mol-ryan_ligand_.pdbq" is not getting translated in the log.pml file so the visualizer is not able to understand the "" explicitly.

Let me explain the structure of directories. I have 100 folders named "Frog-mol-ryan_1, Frog-mol-ryan_2, Frog-mol-ryan_3 ... and so on till out_Frog-ryan-mol_ligand_100. Now each folder has 20 output files named "out_Frog-ryan-mol_ligand_1.pdbqt, out_Frog-ryan-mol_ligand_2.pdbqt .... and so on till out_Frog-ryan-mol_ligand_20.pdbqt". What I am trying to do is to make a bash script file which will go inside each folder (Frog-ryan-mol_1), grab all the "out_*.pdbqt" files and write a log.pml file with instructions to load all the molecules in the PyMol. Now after loading the molecules in PyMol, when I close the PyMol window the script will go to the next folder (Frog-ryan-mol_2) and do the same thing as the previous one.

Thank you so much for your time and patience

Can you show us how should a single log.pml look like for a single directory?

cat <<EOF >log.pml

load /server/John/Docking-Studies/docking-FC996-analog/MR1004/test/Frog-mol-ryan_*/out_Frog-ryan-mol_ligand_*.pdbqt

reset
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/PDBs/Holo-with-Bpore.pdb
cmd.hide("everything","holo-with-Bpore")
cmd.show("cartoon" ,"holo-with-Bpore")
cmd.show("sticks", "out_Frog-mol-ryan_ligand_*.pdbqt")
EOF

/usr/bin/pymol log.pml

I mean actual file. Not the code that you are trying to use to generate it. Can you manually prepare one log.pml file that contains all the data for a single directory, that when run with "/usr/bin/pymol log.pml" will produce exepcted output for that directory? Test it by running "/usr/bin/pymol log.pml" and see if it is really working for that single directory.

Hello bartus11,

Thanks for your reply. I am attaching a zip files containing the folders and respective bash script and a dummy Pymol log file.

Thanks once again for the help

Try this:

#!/bin/bash
for dir in Frog-mol-ryan_*; do
  if [ -d "${dir}" ]; then
    echo Loading structures in Pymol: $dir
    cat /dev/null > log.pml
    for file in $dir/*.pdbqt; do
      echo "load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/MR1004/test/$file" >> log.pml
    done
    cat <<EOF>>log.pml
reset
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/PDBs/Holo-with-Bpore.pdb
cmd.hide("everything","holo-with-Bpore")
cmd.show("cartoon"   ,"holo-with-Bpore")
EOF
    for file in $dir/*.pdbqt; do
      echo "cmd.show(\"sticks\", \"`basename $file`\")" >> log.pml
    done
    /usr/bin/pymol log.pml
  fi
done

Hello bartus11,
Thank you so much for the help. The script is working like charm. With so little knowledge about the scripting I would have never figured that out.
I am trying to learn some scripting so that I could use if for my small analysis work, mostly copying, transferring and sorting type works. I have a linux machine at my lab with bash shell.
Could you suggest me some good reference to learn bash scripting (books or online) will be greatly appreciated

Thanks once again for the help

This site is quite comprehensive guide to BASH (with many examples too): Advanced Bash-Scripting Guide