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‎CITING.md‎

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# Citing
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Cite HADDOCK3 with the following:
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HADDOCK3, Bonvin's Lab, https://github.com/haddocking/haddock3, 2022.

‎README.md‎

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## 1. Installation
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To install HADDOCK3 follow the instructions in the [INSTALL](INSTALL.md) file.
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To install HADDOCK3 follow the instructions in the [INSTALL](docs/INSTALL.md) file.
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## 2. Examples
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‎INSTALL.md‎ renamed to ‎docs/INSTALL.md‎

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# 1. Installation
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# Installation
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Open a `terminal` window and navigate to the folder where you want to
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install HADDOCK3; for example: `software`. The current installation
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instructions are local and will affect only your user.
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## 1.1 Clone this repository:
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## 1 Clone this repository:
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Mind the `--recursive` flag when cloning!
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By the end of the above commands, you should be back to the `haddock3`
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main folder.
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## 1.2 Create a virtual environment with Python 3.9+ and install dependencies:
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## 2 Create a virtual environment with Python 3.9+ and install dependencies:
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You can use Python's `venv` or Anaconda depending on your choice.
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Commands are provided below:
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conda activate haddock3
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```
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## 1.3 Install the HADDOCK3 package and command line clients
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## 3 Install the HADDOCK3 package and command line clients
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```bash
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python setup.py develop --no-deps
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```
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## 1.4 Make a CNS binary shortcut to the expected path:
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## 4 Make a CNS binary shortcut to the expected path:
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```bash
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mkdir -p bin/
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guidelines](USAGE.md).
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## 1.5 Keep your installation up to date
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## 5 Keep your installation up to date
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Navigate to the `haddock3` installation folder (the one you cloned from
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GitHub). Ensure you have the `haddock3` python environment activated.

‎USAGE.md‎ renamed to ‎docs/USAGE.md‎

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‎docs/usage.rst‎ renamed to ‎docs/citing.rst‎

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.. include:: ../USAGE.md
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.. include:: ../CITING.md
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:parser: myst_parser.sphinx_

‎docs/clients/clibm.rst‎

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Benchmark Client
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================
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.. argparse::
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:module: haddock.clis.cli_bm
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:func: _ap
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:prog: haddock3-bm

‎docs/clients/clicfg.rst‎

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Retrieve config
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===============
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.. argparse::
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:module: haddock.clis.cli_cfg
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:func: _ap
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:prog: haddock3-cfg

‎docs/clients/clidmn.rst‎

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Benchmark Daemon
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================
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.. argparse::
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:module: haddock.clis.cli_dmn
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:func: _ap
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:prog: haddock3-dmn

‎docs/clients/clihd3.rst‎

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Run HADDOCK3
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============
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.. automodule:: haddock.clis.cli
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.. argparse::
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:module: haddock.clis.cli
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:func: _ap
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:prog: haddock3

‎docs/clients/climpi.rst‎

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HADDOCK3 MPI Run
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================
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.. argparse::
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:module: haddock.clis.cli_mpi
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:func: _ap
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:prog: haddock3-mpitask

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