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Where can I find the Python scripts for preparing and analysing AutoDock dockings?

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This FAQ applies to: AutoDock 3, AutoDock 4

I've read about the Python prepare scripts like "prepare_dpf4.py" in places like the virtual screening tutorial. This FAQ answers the questions, "Which Python scripts are available?", "Where do I download the Python scripts from?" and "Where are these Python scripts installed?".

Which Python scripts are available?

In version 1.5.0 of MGLTools, these scripts include:
compute_AutoDock41_score.py
compute_consensus_maps_from_dlgs.py
compute_rms_between_methods.py
dpf3_to_dpf4.py
energy_average_maps.py
gpf3_to_gpf4.py
gpf4_to_gpf3.py
pdbq_to_pdbqt.py
pdbqs_to_pdbqt.py
pdbqt_to_pdb.py
pdbqt_to_pdbq.py
pdbqt_to_pdbqs.py
prepare_dpf.py
prepare_dpf4.py
prepare_flexreceptor4.py
prepare_gpf.py
prepare_gpf4.py
prepare_ligand.py
prepare_ligand4.py
prepare_ligand_dict.py
prepare_receptor.py
prepare_receptor4.py
repair_ligand4.py
rotate_molecule.py
summarize_docking_directory.py
summarize_results.py
summarize_results4.py
summarize_time.py
summarize_wcg_docking.py
superimpose_based_on_subset.py
write_all_complexes.py
write_clustering_histogram_postscript.py
write_component_energies.py
write_largest_cluster_ligand.py
write_lowest_energy_ligand.py
write_random_state_ligand.py
Note that the scripts that end in "4.py" are for AutoDock 4.  See the "How to" section to learn more about these scripts.



Where do I download the Python scripts from?

All the AutoDock Python scripts are distributed as part of AutoDockTools, which is distributed as part of the MGLTools bundle.



Where are these Python scripts installed?

They can be found at the following locations, depending on your platform (Linux, Mac OS X or Windows) and on the version of MGLTools you installed (1.5.0):
 

Linux

    <InstallationDirectory>/MGLToolsPckgs/AutoDockTools/Utilities24

    If you install as root, <InstallationDirectory> is:

    /usr/local/MGLTools-1.5.0

    If you install as a regular user, <InstallationDirectory> is:

    $HOME/MGLTools-1.5.0

Mac OS X

    /Library/MGLTools/1.5.0/MGLToolsPckgs/AutoDockTools/Utilities24

Windows

    <InstallationDirectory>\MGLToolsPckgs\AutoDockTools\Utilities24

    Note that by default,  <InstallationDirectory> is:

    C:\Program Files\MGLTools 1.5.0

see also:

Setting up AutoDockTools utility scripts
Describes how to configure Python interpreter so that it can find packages from MGLTools. This How-to is intended for users who use pre-compiled Python interpreter that comes with MGLTools.
by morris last modified 2008-01-30 08:58

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