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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.

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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

‎docs/clients/index.rst

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Command-line interfaces
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=======================
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HADDOCK3 has a series of command-line interfaces (CLIs), from which the most important
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one is ``haddock3``. You can ask help to the CLIs with the ``-h`` flag::
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haddock3 -h
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The available CLIs are the following:
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.. toctree::
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:maxdepth: 1
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clihd3
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clicfg
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clibm
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clidmn
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climpi

‎devtools/docs-conf.py renamed to ‎docs/conf.py

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mock_modules = [
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'Bio',
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'Bio.Align',
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'Bio.Seq',
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'biopython',
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'fccpy',
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'fccpy.contacts',
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'jsonpickle',
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'mpi4py',
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'numpy',
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'pdbtools',
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'pdbtools.pdb_segxchain',
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'pdbtools.pdb_splitchain',
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'pdbtools.pdb_splitmodel',
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'pdbtools.pdb_tidy',
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'pyyaml',
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'Bio',
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'Bio.Align',
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'Bio.Seq',
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'fccpy',
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'fccpy.contacts',
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]
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for modulename in mock_modules:
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napoleon_use_ivar = True
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napoleon_use_rtype = False
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napoleon_use_param = False
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# myst options
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myst_heading_anchors = 3

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.. include:: ../INSTALL.md
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.. include:: ../CONTRIBUTING.md
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:parser: myst_parser.sphinx_

‎docs/examples.md

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corresponding to different types of complexes, scenarios and data.
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1. [docking-antibody-antigen](#docking-antibogy-antigen)
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1. [docking-protein-DNA](#docking-protein-DNA)
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1. [docking-protein-DNA](#docking-protein-dna)
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1. [docking-protein-homotrimer](#docking-protein-homotrimer)
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1. [docking-protein-ligand](#docking-protein-ligand)
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1. [docking-protein-ligand-shape](#docking-protein-ligand-shape)
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The `caprieval` module is called at various stages during the workflow to assess the quality of the models with respect to the known reference structure.
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## docking-protein-DNA
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## docking-protein-dna
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A protein-DNA docking example making use of rather specific protein-DNA distance restraints defined in the `ambig.tbl` file in the `data` directory.
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‎docs/index.rst

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.. toctree::
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:maxdepth: 1
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installation
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usage
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INSTALL
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USAGE
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examples
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tutorials/index
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clients/index
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modules/index
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reference/clients
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testing/index
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contributing
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citing
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reference/index

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‎docs/reference/core/cns_paths.rst

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CNS paths definitions
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=====================
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.. automodule:: haddock.core.cns_paths
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:members:
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:show-inheritance:
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:inherited-members:

‎docs/reference/core/defaults.rst

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Defaults definitions
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=====================
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.. automodule:: haddock.core.defaults
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:members:
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:show-inheritance:
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:inherited-members:

‎docs/reference/core/exceptions.rst

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Exceptions
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==========
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.. automodule:: haddock.core.exceptions
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:members:
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:show-inheritance:
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:inherited-members:

‎docs/reference/core/index.rst

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Core Reference
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==============
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Here, you will find documentation for core haddock3 functionalities.
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.. toctree::
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:maxdepth: 1
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cns_paths
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defaults
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exceptions
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‎docs/reference/gear/config_reader.rst

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Config Reader
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=============
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.. automodule:: haddock.gear.config_reader
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:members:
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:show-inheritance:
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:inherited-members:

‎docs/reference/gear/config_writer.rst

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Config Writer
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=============
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.. automodule:: haddock.gear.config_writer
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:members:
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:show-inheritance:
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:inherited-members:

‎docs/reference/gear/expandable_parameters.rst

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Expandable Parameters
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=====================
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:show-inheritance:
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:inherited-members:

‎docs/reference/gear/greetings.rst

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Greetings messages
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==================
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:show-inheritance:
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:inherited-members:

‎docs/reference/gear/haddockmodel.rst

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HADDOCK Models
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==============
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‎docs/reference/gear/index.rst

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Gear Reference
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==============
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Here, you will find documentation to use HADDOCK3 Gears as a library.
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.. toctree::
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:maxdepth: 1
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config_reader
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config_writer
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expandable_parameters
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greetings
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haddockmodel
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parameters
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prepare_run
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restart_run
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validations
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yaml2cfg
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zerofill

‎docs/reference/gear/parameters.rst

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Parameters helper
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=================
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:members:
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:show-inheritance:
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:inherited-members:

‎docs/reference/gear/prepare_run.rst

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Prepare Run
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===========
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‎docs/reference/gear/restart_run.rst

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Restart Run
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===========
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‎docs/reference/gear/validations.rst

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Validations
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===========
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:inherited-members:

‎docs/reference/gear/yaml2cfg.rst

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Yaml configs
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============
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‎docs/reference/gear/zerofill.rst

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Zero fill prefix
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================
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‎docs/reference/index.rst

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Library Reference
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=================
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Here, you will find documentation to use HADDOCK3 as a library.
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.. toctree::
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:maxdepth: 1
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core/index
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libs/index
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gear/index

‎docs/reference/libs/index.rst

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Libs Reference
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==============
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Here, you will find documentation for general haddock3 functionalities.
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.. toctree::
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:maxdepth: 1
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libcli
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libcns
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libfunc
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libhpc
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libio
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liblog
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libmath
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libmpi
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libontology
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libparallel
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libpdb
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libstructure
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libsubprocess
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libutil
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libworkflow

‎docs/reference/libs/libcli.rst

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libcli: functions helping clients
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=================================
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:inherited-members:

‎docs/reference/libs/libcns.rst

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libcns: creating CNS files
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==========================
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:members:
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:show-inheritance:
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:inherited-members:

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