DOCK 3.8:How to install pydock3: Difference between revisions

From DISI
Jump to navigation Jump to search
(updated installation instructions)
Line 1: Line 1:
[[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.  
Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.  


== step 1. acquire this software ==  
== Instructions ==  
go to the dock.compbio.ucsf.edu license server, request a license, obtain it, and download the software distribution as a tarball.
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.
This documentation describes DOCK3.8 v1.0.0 and later versions (circa September 2022)


== to install on a new modern computer ==
```git clone https://github.com/docking-org/pydock3```
If your hardware and OS are modern, you should be able to follow these simple instructions


* pip install dock.3.8-source.tar.gz
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.
* you are now ready to go.


== to install on an AWS instance ==
```conda create -n your_env_name python=3.8```
* spin up an instance
* same as above?


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```


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


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

Revision as of 18:45, 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```

Note: requires Python>=3.8

Retrieved from "http://wiki.docking.org/index.php?title=DOCK_3.8:How_to_install_pydock3&oldid=17468"