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https://github.com/nlesc-nano/cat

A collection of tools designed for the automatic construction, and subsequent analysis, of chemical compounds.
https://github.com/nlesc-nano/cat

automation chemistry molecular-mechanics python quantum-mechanics science scientific-workflows

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A collection of tools designed for the automatic construction, and subsequent analysis, of chemical compounds.

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README 

        
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########################

Compound Attachment Tool

########################



**CAT** is a collection of tools designed for the construction of various chemical compounds.

Further information is provided in the documentation_.



Package installation

--------------------

**CAT** can be installed via pip as following:



- **CAT**: ``pip install nlesc-CAT --upgrade``



Note that, while not strictly necessary, it is recommended to first create a conda environment:



- Download and install miniconda for python3: miniconda_ (also you can install the complete anaconda_ version).



- Create a new virtual environment:  ``conda create --name CAT python``



- Activate the environment:: ``conda activate CAT``



Input files

============



Running **CAT** and can be done with the following command:

``init_cat my_settings.yaml``. The user merely has to provide a yaml_ file

with the job settings, settings which can be tweaked and altered to suit ones

purposes (see example1_). Alternatively, **CAT** can be run like a regular

python script, bypassing the command-line interface

(*i.e.* ``python input.py``, see example2_).



An extensive description of the various available settings is available in

the documentation_.



References

==========

* Belić, J.; van Beek, B.; Menzel, J. P.; Buda, F.; Visscher, L. `Systematic Computational Design and Optimization of Light Absorbing Dyes `__. *J. Phys. Chem. A* **2020**, *124* (31), 6380–6388.

* van Beek, B.; Zito, J.; Visscher, L.; Infante, I. CAT: A Compound Attachment Tool for the construction of composite chemical compounds. *J. Chem. Inf. Model.* (submitted).



.. _yaml: https://yaml.org/

.. _documentation: https://cat.readthedocs.io/en/latest/

.. _miniconda: http://conda.pydata.org/miniconda.html

.. _anaconda: https://www.continuum.io/downloads

.. _installConda: https://docs.anaconda.com/anaconda/install/

.. _HDF5: http://www.h5py.org/

.. _here: https://www.python.org/downloads/

.. _rdkit: http://www.rdkit.org

.. _PLAMS: https://github.com/SCM-NV/PLAMS

.. _QMFlows: https://github.com/SCM-NV/qmflows

.. _example1: https://github.com/BvB93/CAT/blob/master/examples/input_settings.yaml

.. _example2: https://github.com/BvB93/CAT/blob/master/examples/input.py