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Copy file name to clipboardExpand all lines: README.md
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|**Release**|[![Last release tag][badge_release]][url_latest_release]![GitHub commits since latest release (by date) for a branch][badge_commits_since]|
**OpenMMDL** is mainly supported for Linux distribution systems, thus for Windows and MacOS the installation with docker may be preferred,
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due to docker creating an image with ubuntu:22.04
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For this first clone this repository
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cd ~
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git clone https://github.com/wolberlab/OpenMMDL
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change the path to the OpenMMDL folder and build the docker image from there
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cd OpenMMDL
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docker build -t openmmdl_env .
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This will build the OpenMMDL image with docker. Now that it is build you can access it through an interactive terminal
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docker run -it --name openmmdl_test openmmdl_env
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From there you can access all the OpenMMDL entry points. Currently due to OpenMMDL Setup using flask it can be difficult
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to access it through the docker image.
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## Installation via repository
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#### Clone this repository
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#### Visualization
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Most of the analysis outputs are JEPG images and do not need any further preparation to be viewed.
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For the visualization of your trajectory with interaction pointclouds you can use the jupyter notebook prepared in the **OpenMMDL** repository.
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For the visualization of your complex with interaction pointclouds you can use NGLView with the jupyter notebook prepared in the **OpenMMDL** repository or visualize the pointclouds in PyMOL.
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Or use this command:
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### Usage
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```
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openmmdl_visualization
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```
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Then edit the notebook to include the output of your analysis.
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#### Optional:
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--type = Software you wish to visualize openmmdl interactions with. Options: nglview, pymol. Default: nglview
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#### NGLView
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After running the start comand a jupyter notebook will automatically open.
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Edit the notebook to include the output files of your analysis.
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Then run all cells.
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#### PyMOL
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After running the start comand a python skript will apear in your directory.
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Open up PyMOL then run these two comands in the PyMOL console:
If you use OpenMMDL in your research, please cite the following `paper <https://doi.org/10.1021/acs.jcim.4c02158>`_:
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.. code-block:: text
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@article{doi:10.1021/acs.jcim.4c02158,
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author = {Talagayev, Valerij and Chen, Yu and Doering, Niklas Piet and Obendorf, Leon and Denzinger, Katrin and Puls, Kristina and Lam, Kevin and Liu, Sijie and Wolf, Clemens Alexander and Noonan, Theresa and Breznik, Marko and Knaus, Petra and Wolber, Gerhard},
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title = {OpenMMDL - Simplifying the Complex: Building, Simulating, and Analyzing Protein–Ligand Systems in OpenMM},
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journal = {Journal of Chemical Information and Modeling},
Copy file name to clipboardExpand all lines: docs/faq.rst
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**OpenMMDL** is available for Linux and Mac systems. **OpenMMDL Setup** and **OpenMMDL Simulation** are currently incompatible with Windows systems, thus only **OpenMMDL Analysis** of the **OpenMMDL** package can be used on Windows systems.
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How can I install OpenMMDL?
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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**OpenMMDL** is available as a conda package. To install it, you can use the following command:
Copy file name to clipboardExpand all lines: docs/installation.rst
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This page details how to install **OpenMMDL** on your local device.
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Installation via conda-forge
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------------------------------
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**OpenMMDL** is implemented in conda-forge and can be installed for linux-based system with the following command line:
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.. code-block:: text
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conda install -c conda-forge openmmdl
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Installation via repository
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------------------------------
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**OpenMMDL** can be installed through the cloning of the repository and the installation of the required packages listed in *environment.yml* or *requirements.txt*
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The first step of the installation of **OpenMMDL** on your device consists in the cloning of **OpenMMDL** to your home directory.
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This can be achieved by using the following command lines:
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cd ~
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git clone https://github.com/wolberlab/OpenMMDL
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The next step consists of installing all required dependencies in a new separate environment, which will be used to run the **OpenMMDL** package.
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**OpenMMDL** is written in Python 3.10 and uses several packages, which can be easily installed on a separate environment using conda (we recommend using miniconda):
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.. code-block:: text
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cd OpenMMDL
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conda create -n openmmdl c conda-forge --file requirements.txt
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After installation, activate the conda environment and install the **OpenMMDL** package:
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(Be sure, you are still within the OpenMMDL folder)
After installation, activate the conda environment:
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.. code-block:: text
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conda activate openmmdl
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Install the **OpenMMDL** package with the required entry points via pip:
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.. code-block:: text
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pip install .
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This should lead to the environment having now all the required packages and entry points for **OpenMMDL**.
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Installation via Docker
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------------------------------
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**OpenMMDL** is mainly supported for Linux distribution systems, thus for Windows and MacOS the installation with docker may be preferred, due to docker creating an image with *ubuntu:22.04*.
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For this first clone this repository:
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.. code-block:: text
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cd ~
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git clone https://github.com/wolberlab/OpenMMDL
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change the path to the **OpenMMDL** folder and build the docker image from there:
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.. code-block:: text
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cd OpenMMDL
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docker build -t openmmdl_env .
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This will build the **OpenMMDL** image with docker. Now that it is build you can access it through an interactive terminal:
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.. code-block:: text
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docker run -it --name openmmdl_test openmmdl_env
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Now with **OpenMMDL** being installed on the local device, everything is set up to work with **OpenMMDL**.
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From there you can access all the **OpenMMDL** entry points. Currently due to **OpenMMDL Setup** using flask it can be difficult to access it through the docker image.
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