Bash script for making complexes of ligands and receptor
I am working with autodock vina for virtual screening and docking with cygwin. Autodock vina generates conformers for multiple ligands. I want to make the complex of these conformers with receptor. e.g. I have 100 .pdbqt files form vina output and one receptor pdbqt file. By running command-
Code:
cut -c-66 inh*.pdbqt > inh*.pdb
I can convert inh*.pdbqt to pdb, but I have to do this individually for all ligands (* here are random numbers from pubchem database).
With this command the pdb of complex of receptor and ligand is generated, but again this I have to do for each ligand, receptor file is fixed in this case.
I want a bash script for above to commands to run in cygwin. Aim is to use multiple ligand files - convert them to pdb - merge with receptor.pdbqt - generate multiple complexes as per ligand names.
This may need a simple script. Though I have worked with many scripts I don't know how to write such bash scripts. Naively, I have given a try and wrote one script-
Code:
#!/bin/bash
for f in inh*.pdbqt; do b=`basename $f .pdbqt`;
$b; mkdir -p data02; cut -c-66 inh*.pdbqt > inh*.pdb;
cat 3V3VN.pdbqt inh*.pdb | grep -v '^END' | grep -v '^END$' > complex*.pdb;
$f --out data02/$f.pdbqt --log data02/$f.txt; done
It generates the complex but only one complex with all ligands in it !!!
Last edited by Scrutinizer; 01-18-2015 at 04:05 AM..
Reason: code tags
I'm using Mac OSX.
And i want to make an visual application based on bash command.
But, apple script doesn't support Terminal command.
So please tell me how to turn my dream into a reality. :o
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LEARN ABOUT DEBIAN
git-sh-setup
GIT-SH-SETUP(1) Git Manual GIT-SH-SETUP(1)NAME
git-sh-setup - Common git shell script setup code
SYNOPSIS
. "$(git --exec-path)/git-sh-setup"
DESCRIPTION
This is not a command the end user would want to run. Ever. This documentation is meant for people who are studying the Porcelain-ish
scripts and/or are writing new ones.
The git sh-setup scriptlet is designed to be sourced (using .) by other shell scripts to set up some variables pointing at the normal git
directories and a few helper shell functions.
Before sourcing it, your script should set up a few variables; USAGE (and LONG_USAGE, if any) is used to define message given by usage()
shell function. SUBDIRECTORY_OK can be set if the script can run from a subdirectory of the working tree (some commands do not).
The scriptlet sets GIT_DIR and GIT_OBJECT_DIRECTORY shell variables, but does not export them to the environment.
FUNCTIONS
die
exit after emitting the supplied error message to the standard error stream.
usage
die with the usage message.
set_reflog_action
set the message that will be recorded to describe the end-user action in the reflog, when the script updates a ref.
git_editor
runs an editor of user's choice (GIT_EDITOR, core.editor, VISUAL or EDITOR) on a given file, but error out if no editor is specified
and the terminal is dumb.
is_bare_repository
outputs true or false to the standard output stream to indicate if the repository is a bare repository (i.e. without an associated
working tree).
cd_to_toplevel
runs chdir to the toplevel of the working tree.
require_work_tree
checks if the current directory is within the working tree of the repository, and otherwise dies.
require_work_tree_exists
checks if the working tree associated with the repository exists, and otherwise dies. Often done before calling cd_to_toplevel, which
is impossible to do if there is no working tree.
require_clean_work_tree <action> [<hint>]
checks that the working tree and index associated with the repository have no uncommitted changes to tracked files. Otherwise it emits
an error message of the form Cannot <action>: <reason>. <hint>, and dies. Example:
require_clean_work_tree rebase "Please commit or stash them."
get_author_ident_from_commit
outputs code for use with eval to set the GIT_AUTHOR_NAME, GIT_AUTHOR_EMAIL and GIT_AUTHOR_DATE variables for a given commit.
GIT
Part of the git(1) suite
Git 1.7.10.4 11/24/2012 GIT-SH-SETUP(1)
01-18-2015
