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
Code:
#!/bin/bash
for f in Frog-mol-ryan_*; do
if [ -d "${f}" ]; then
echo Loading structures in Pymol: $f
cat <<EOF >log.pml
load /server/John/Docking-Studies/docking-FC996-analog/MR1004/test/Frog-mol-ryan_*/out_Frog-ryan-mol_ligand_*.pdbqt
reset
load /server/John/Docking-Studies/Insilico-mod-FC996/docking-FC996-analog/PDBs/Holo-with-Bpore.pdb
cmd.hide("everything","holo-with-Bpore")
cmd.show("cartoon" ,"holo-with-Bpore")
cmd.show("sticks", "out_Frog-mol-ryan_ligand_*.pdbqt")
EOF
/usr/bin/pymol log.pml
fi
done
Hi, I'm a pretty big fan of BASH scripting. I've got a bunch I use for random things and lately a couple issues have been plaguing me.
Both are somewhat related, in that they deal with filenames with spaces and "escaped" characters and with launching a program with command line arguements... (5 Replies)
Hi
I'm running a program many times with differents input.
I mean that i run my_prog with some parameters and i wait till the end, then i start again another simulations with some others differents parameters.
Is possible to make it automatic with a script bash.
Maybe i need some... (2 Replies)
Hola tengo que hacer un programa en Bash, necesito ayuda porque no me sale y llevo bastante tiempo con esto!!
Los cinco directorios que más ocupan, ordenados según tamaño. Para medir el tamaño de cada directorio no debe incluirse el tamaño de sus subdirectorios.
Los diez archivos normales que más... (1 Reply)
Hello I have to do a program in Bash, need help because it does not go out for me and go enough time with this!!
Five directories(boards of directors) that more occupy, arranged according to size. To measure the size of every directory(board of directors) there must not be included the size... (1 Reply)
Hello, i have a problem with the output from my bash program.
I made this program
#!/bin/bash
BESTANDEN=$* # Plaatst bestanden in de variabele BESTANDEN
TMPFILE=xmlprog.sh.$$.$RANDOM # basisnaam voor tijdelijke bestanden
# controller of het programma correct is aangeroepen
if
then
... (6 Replies)
HI
I am trying to create a bash script to print whatever i type in
It has to have these below to define the size of the label and what size to print the text
N
q609
A100,10,0,5,2,2,N," "
P1
It has to be sent to below
> /dev/usblp0
So what it has to be is
Written... (12 Replies)
suppose i have a bash script:
#!/bin/bash
echo "hello"
echo "how are you"
echo "today"
how can i put the entire script above into a basic c program?
i do not want to translate the bash code to a c code. i want C to run the bash code. is this possible?
i found this on the... (15 Replies)
to kill a program in bash, for instance 'mousepad' I use
kill $(pidof mousepad);
or
pkill mousepad
But it only works if we use another bash window;
If it is started from the same bash, that does not work:
#mousepad;kill $(pidof mousepad);
In this case, it looks like mousepad hangs... (7 Replies)
Hi all,
In production code, if using the whence command it picks the production file.if I am using the test code file. by using whence command it not picking the file. do you have any idea on this.
Whence prodcode
it picks the exact path of the prodcode.
whence testcode.
it... (1 Reply)
#! /bin/bash
# program to creat a backup copy for every deleted file or dierctores
mv -t /home/$USER/.local/share/Trash/files $1
rsync -a /home/$USER/.local/share/Trash/files /usr/share/trash
didn't work (2 Replies)
10-05-2013
