Sponsored Content
Top Forums Programming Question regarding Bash program Post 302860483 by biochemist on Sunday 6th of October 2013 12:29:56 PM
Old 10-06-2013
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 Smilie
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

BASH: how to launch a program with parameters

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)
Discussion started by: TinCanFury
5 Replies

2. Shell Programming and Scripting

[bash] Run a program many times

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)
Discussion started by: Dedalus
2 Replies

3. Shell Programming and Scripting

PROGRAM BASH

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)
Discussion started by: danihj
1 Replies

4. Shell Programming and Scripting

Program Bash VERY URGENT

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)
Discussion started by: danihj
1 Replies

5. Shell Programming and Scripting

Display output bash program

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)
Discussion started by: dutchspiders
6 Replies

6. Shell Programming and Scripting

Creating Printing Program in bash

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)
Discussion started by: bganse
12 Replies

7. Programming

Putting bash script in C program

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)
Discussion started by: SkySmart
15 Replies

8. UNIX for Dummies Questions & Answers

Kill a program from bash

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)
Discussion started by: arpagon
7 Replies

9. Shell Programming and Scripting

Question regarding whence program

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)
Discussion started by: ramkumar15
1 Replies

10. Homework & Coursework Questions

Bash Scripting program

#! /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)
Discussion started by: rami-ali
2 Replies
RBASH(1)						      General Commands Manual							  RBASH(1)

NAME
rbash - restricted bash, see bash(1) RESTRICTED SHELL
If bash is started with the name rbash, or the -r option is supplied at invocation, the shell becomes restricted. A restricted shell is used to set up an environment more controlled than the standard shell. It behaves identically to bash with the exception that the follow- ing are disallowed or not performed: o changing directories with cd o setting or unsetting the values of SHELL, PATH, ENV, or BASH_ENV o specifying command names containing / o specifying a file name containing a / as an argument to the . builtin command o specifying a filename containing a slash as an argument to the -p option to the hash builtin command o importing function definitions from the shell environment at startup o parsing the value of SHELLOPTS from the shell environment at startup o redirecting output using the >, >|, <>, >&, &>, and >> redirection operators o using the exec builtin command to replace the shell with another command o adding or deleting builtin commands with the -f and -d options to the enable builtin command o using the enable builtin command to enable disabled shell builtins o specifying the -p option to the command builtin command o turning off restricted mode with set +r or set +o restricted. These restrictions are enforced after any startup files are read. When a command that is found to be a shell script is executed, rbash turns off any restrictions in the shell spawned to execute the script. SEE ALSO
bash(1) GNU Bash-4.0 2004 Apr 20 RBASH(1)
All times are GMT -4. The time now is 03:07 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy