Merge pull request #423 from ExcitedStates/345-create-environmentyml-…

…file-for-conda-install

install using enviornment.yml

README.md

@@ -7,36 +7,23 @@ qFit is a collection of programs for modeling multi-conformer protein structures
 
 Electron density maps obtained from high-resolution X-ray diffraction data are a spatial and temporal average of all conformations within the crystal. qFit evaluates an extremely large number of combinations of sidechain conformers, backbone fragments and small-molecule ligands to locally explain the electron density.
 
-If you use this software, please cite: 
-- [Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan DW, van den Bedem H, Keedy DA, & Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv. (2023).](https://www.biorxiv.org/content/10.1101/2023.06.28.546963v2.abstract)
-- [Riley BT, Wankowicz SA, et al. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein Sci. 30, 270–285 (2021)](https://dx.doi.org/10.1002/pro.4001)
-- [van Zundert, G. C. P. et al. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. 61, 11183–11198 (2018)](https://dx.doi.org/10.1021/acs.jmedchem.8b01292)
-- [Keedy, D. A., Fraser, J. S. & van den Bedem, H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput. Biol. 11, e1004507 (2015)](https://dx.doi.org/10.1371/journal.pcbi.1004507)
-
-
 ## Installation
 
-You will need the following tools:
+1) Download qFit
+   git clone -b main https://github.com/ExcitedStates/qfit-3.0.git
+   cd qfit-3.0
+
+2) Create the Conda environment using the downloaded file:
 
-* git
-* pip
+   conda env create -f <QFIT-ENV-FILE>
 
-Once these are installed, you can:
+3) After creating the Conda environment, activate it:
 
-1. Install dependencies
-   ```bash
-   pip install -r requirements.txt
-   ```
-
-1. Clone the latest release of the qFit source and install it using pip
-   ```bash
-   git clone https://github.com/ExcitedStates/qfit-3.0.git
-   cd qfit-3.0
-   pip install .
-   ```
+   conda activate qfit
 
-1. You're now ready to run qFit programs! See [usage examples](#sec:usage-examples) below for some examples.
+4) Finally, install qFit:
 
+   pip install .
 
 ### Advanced
 
@@ -49,14 +36,13 @@ If you prefer to manage your environments using other methods, qFit has the foll
 
 Once dependencies are installed, you can clone the qFit source, and install to your env as above.
 
+## Citations
+If you use this software, please cite: 
+- [Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Hogan DW, van den Bedem H, Keedy DA, & Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv. (2023).](https://www.biorxiv.org/content/10.1101/2023.06.28.546963v2.abstract)
+- [Riley BT, Wankowicz SA, et al. qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein Sci. 30, 270–285 (2021)](https://dx.doi.org/10.1002/pro.4001)
+- [van Zundert, G. C. P. et al. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. 61, 11183–11198 (2018)](https://dx.doi.org/10.1021/acs.jmedchem.8b01292)
+- [Keedy, D. A., Fraser, J. S. & van den Bedem, H. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit. PLoS Comput. Biol. 11, e1004507 (2015)](https://dx.doi.org/10.1371/journal.pcbi.1004507)
 
-## Contributing
-
-qFit uses [Black](https://github.com/psf/black) to format its code and provides a git hook to verify that code is properly formatted before allowing you to commit.
-
-Before creating a commit, you will have to perform two actions:
-1. Install Black, either through a package manager or by running `python3 -m pip install --user black`
-2. Run `git config core.hooksPath .githooks/` to use the provided pre-commit hook
 
 ## Usage examples
 
@@ -118,6 +104,13 @@ After *multiconformer_model2.pdb* has been generated, refine this model using:
 
 More advanced features of qFit (modeling single residue, more advanced options, and further explainations) are explained in [TUTORIAL](example/TUTORIAL.md).
 
+## Contributing
+
+qFit uses [Black](https://github.com/psf/black) to format its code and provides a git hook to verify that code is properly formatted before allowing you to commit.
+
+Before creating a commit, you will have to perform two actions:
+1. Install Black, either through a package manager or by running `python3 -m pip install --user black`
+2. Run `git config core.hooksPath .githooks/` to use the provided pre-commit hook
 
 ## License