DOCK 3.8:How to install pydock3: Difference between revisions

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[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.
[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.


Installation instructions:
Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.
 
== Instructions ==
1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.
 
<code>git clone https://github.com/docking-org/pydock3</code>
 
2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.


Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.  
<code>conda create -n your_env_name python=3.8</code>
 
3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.


== step 1. acquire the DOCK 3.8.5 release ==
<code>conda activate your_env_name</code>
go to the dock.compbio.ucsf.edu license server, request a license, obtain it, and download the software distribution as a tarball.
This documentation describes 3.8.5 and later versions (circa September 2022)


== to install on a new modern computer ==
<code>pip install -e pydock3</code>
If your hardware and OS are modern, you should be able to follow these simple instructions


* tar xzf dock-3.8.tar.gz
4. Check if it is installed by running the following in a folder of your choice. This will create a new folder named 'blastermaster_job' if successful.
* pip install <NAME_OF_WHEEL_FILE>.whl
* you are now ready to go.  


== to install on an AWS instance ==
<code>pydock3 blastermaster - new</code>
* spin up an instance
* same as above?


If the above runs without error, then it's installed. Navigate to [[Blastermaster (pydock3 script)]] for instructions on how to use this software.


'''Note:''' requires Python>=3.8
'''Note:''' requires Python>=3.8


[[Category:DOCK 3.8]]
[[Category:DOCK 3.8]]

Latest revision as of 18:49, 25 August 2026

pydock3 is a Python package wrapping the DOCK Fortran program that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

Instructions

1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

git clone https://github.com/docking-org/pydock3

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

conda create -n your_env_name python=3.8

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.

conda activate your_env_name

pip install -e pydock3

4. Check if it is installed by running the following in a folder of your choice. This will create a new folder named 'blastermaster_job' if successful.

pydock3 blastermaster - new

If the above runs without error, then it's installed. Navigate to Blastermaster (pydock3 script) for instructions on how to use this software.

Note: requires Python>=3.8

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