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How to prepare a text summary of a directory of AutoDock4 docking results

This How-to applies to: AutoDock 4
This How-to is intended for: User

This How-to explains how to use the python script "summarize_results4.py" to create a text file which summarizes the results of all the AutoDock4 log files in a single directory. The output from this script is in CSV (comma separated value) format. Optional arguments can be used to set the rmsd tolerance used for clustering and to specify which results to report. The clustering is based on the input ligand coordinates unless a reference file is specified. (NOTE: You must have installed MGLTools).

Overview

Each AutoDock 4 calculation results in a docking log file which contains information about the best docked ligand conformation found in each of the docking 'runs' specified in the input parameter file (dpf). If several processors are available, they can be used for multiple AutoDock calculations using the same input. The results of these calculations can clustered interactively using AutoDockTools (ADT) or with summarize_results4.py, a Python script which can be found in MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24. Typing just the name of the script at a shell prompt and pressing <Enter> causes the script to print the usage documentation, which gives an overview of the flags it understands and how to use the script.

Usage

Usage: summarize_results4.py -d directory
Description of command...
-d directory
Optional parameters:
[-t] rmsd tolerance (default is 1.0)
[-f] rmsd reference filename
(default is to use input ligand coordinates)
[-b] print best docking info only
(default is print all)
[-L] print largest cluster info only
(default is print all)
[-B] print best docking and largest cluster info only
(default is print all)
[-o] output filename
(default is 'summary_of_results_1.0')
[-a] append to output filename
(default is to open output filename 'w')
[-k] build hydrogen bonds
[-r] receptor filename
[-u] report unbound energy
[-v] verbose output

Procedure

1. Install MGLTools if you have not already done so. This will install the graphical user interface and the Python shell scripts for ADT (AutoDockTools). See also: How to setup ADT scripts.

2. In your working directory either copy 'summarize_results4.py' from "MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24", or make sure your path includes 'yourpath', the directory where MGLTools is installed locally.

yourpath = local_install/MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24

On Linux, "local_install" is either "/usr/local" or "$HOME", on Mac OS X it is "/Library". For Windows, see 1. above.

3. Run the script at the command prompt using the "pythonsh" script with the desired flags and arguments:
    pythonsh [yourpath or .]/summarize_results4.py -d directory [options]

Input

The input directory should contain docking log files resulting from the same input. That is, docking the same ligand against the same receptor using the same parameters.

Output

The default output filename is 'summary_of_results' . The default is to open this file for writing.

Options

1. -t rms tolerance
The results will be clustered using this rms tolerance. The default is 1.0
2. -f rms reference filename.
Use the ligand coordinates from this file for rms calculations instead of the input coordinates from the docking log. This file must be in the directory specified with the -d flag.
3. -b
Only report information about the 'best' cluster, that is the one containing the overall lowest energy conformation. The default is to print information about the lowest energy conformation in each of the clusters.
4. -L
Only report information about the lowest energy conformation in the 'largest' cluster ie the cluster with the largest number of conformations. The default is to print information about the lowest energy conformation in each of the clusters.
5. -B Report information about the lowest energy conformation in both 'largest' cluster ie the cluster with the largest number of conformations and in the 'best' ie cluster containing the conformation with the overall lowest energy . The default is to print information about the lowest energy conformation in each of the clusters.
6. -o output filename (default is 'summary_of_results')
7. -a append to output filename (default is to open output filename for writing which overwrites an existing file with the same name.)
8. -u report unbound energy from docking log.
9. -r receptor filename. This must be specified in order to report the number of hydrogen bonds between docked conformations and the receptor and/or to report the energy breakdown by term. The receptor file must be in the specified directory.
10. -k build hydrogen bonds between docked ligand and receptor. (default is not to do this)
11. -v verbose output option.


Known problems



by Ruth Huey last modified 2007-12-07 18:23
Contributors: Garrett Morris

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