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. | ||
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. | |||
<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. | |||
<code>conda activate your_env_name</code> | |||
<code>pip install -e pydock3</code> | |||
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. | |||
<code>pydock3 blastermaster - new</code> | |||
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 | |||
[[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