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Add install to README.rst
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I think this is needed because so many people are running into problems with this these days.
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jamesmkrieger authored Feb 24, 2025
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Expand Up @@ -34,6 +34,24 @@ Further details are described in the ProDy papers:
| *ProDy* 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python.
| *Bioinformatics* **2021** 37(20):3657-3659.
INSTALLING PRODY
________
ProDy is under active development, so we recommend installing it from source from GitHub to ensure everything works properly.

We recommend downloading and installing the Anaconda package manager to handle dependencies in controlled environments.

Then you should download the ProDy code either as a zipped folder to extract or using git as directed at the big green button says code. For example, if you have git installed then you can do the following.

git clone https://github.com/prody/ProDy.git

Then change directory into the ProDy directory tree and install it by running the following commands.

cd ProDy
python setup.py build_ext --inplace --force
pip install -Ue .

More instructions can be found at http://bahargroup.org/prody/downloads/ and http://bahargroup.org/prody/manual/devel/develop.html

MODULES
--------

Expand Down Expand Up @@ -141,4 +159,4 @@ C++ code of hpb.so was developed by Xin Cao and Fortran code by Xin Cao,
Michelle H. Hummel, Bihua Yu, and Evangelos A. Coutsias (License in
prody/proteins/hpbmodule folder). Details of the method can be found
in the Supplementary Material of InSty manuscript
(soon will be submitted for publication).
(soon will be submitted for publication).

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