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        "author": "Felipe S. S. Schneider",
        "author_email": "schneider.felipe@posgrad.ufsc.br",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Education",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3",
            "Topic :: Education",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Software Development :: Libraries :: Python Modules"
        ],
        "description": ".. |build-badge| image:: https://travis-ci.org/schneiderfelipe/pnictogen.svg?branch=master\n   :target: https://travis-ci.org/schneiderfelipe/pnictogen\n   :alt: Travis CI Status\n\n.. |pypi-badge| image:: https://badge.fury.io/py/pnictogen.svg\n   :target: https://badge.fury.io/py/pnictogen\n   :alt: PyPI Version\n\n|build-badge| |pypi-badge|\n\nWelcome to pnictogen\n====================\n\npnictogen_ is both a library and a command-line tool that helps composing input\nfiles for computational chemistry packages.\nIt is based on Jinja2_, a modern and friendly templating language for Python:\n\n.. code:: bash\n\n    $ cat new_template.ORCA.inp\n    # {{ molecule.name }}\n    ! Opt\n\n    * xyz {{ molecule.charge }} {{ molecule.mult }}\n    {{ molecule.to_string(\"xyz\") }}\n    *\n    $ pnictogen new_template.ORCA.inp data/water.xyz\n    data/water.inp written\n    $ cat data/water.inp\n    # A water molecule\n    ! Opt\n\n    * xyz 0 1\n    O          0.05840        0.05840        0.00000\n    H          1.00961       -0.06802        0.00000\n    H         -0.06802        1.00961        0.00000\n    *\n\n.. _pnictogen: https://github.com/schneiderfelipe/pnictogen\n.. _Jinja2: http://jinja.pocoo.org/docs/latest/\n\nInstallation\n------------\n\nYou can get pnictogen directly from PyPI:\n\n.. code:: bash\n\n    $ pip install -U pnictogen\n\nThe above will install the the version from PyPI, which is recommended.\n\nFor the development version, clone this repository and run:\n\n.. code:: bash\n\n    $ pip install -U -e .\n\nTutorial\n--------\n\npnictogen can currently create boilerplates for\n`ADF <https://www.scm.com/product/adf/>`_,\n`DALTON <http://daltonprogram.org/>`_,\n`GAMESS (US) <http://www.msg.ameslab.gov/GAMESS/GAMESS.html>`_,\n`GAMESS-UK <http://www.cfs.dl.ac.uk/>`_,\n`Gaussian <http://www.gaussian.com/>`_,\n`Jaguar <https://www.schrodinger.com/jaguar>`_,\n`Molpro <http://www.molpro.net/>`_,\n`MOPAC <http://openmopac.net/>`_,\n`MPQC <http://www.mpqc.org/>`_,\n`NWChem <http://www.nwchem-sw.org/index.php/Main_Page>`_,\n`ORCA <https://orcaforum.cec.mpg.de/>`_,\n`Psi <http://psicode.org/>`_,\n`Q-Chem <http://q-chem.com/>`_\nand\n`ZINDO <https://comp.chem.umn.edu/zindo-mn/>`_:\n\n.. code:: bash\n\n    $ pnictogen -g new_template.MOPAC.mop\n    new_template.MOPAC.mop written\n    $ cat new_template.MOPAC.mop\n    CHARGE={{ molecule.charge }} MS={{ (molecule.mult - 1)/2 }}\n    {{ molecule.name }}\n\n    {{ molecule.to_string(\"mop\") }}\n\n(``pnictogen -g new_template.inp`` creates a blank file.)\n\nYou can either create and edit a boilerplate template or start fresh.\nOnce you have a template, generating inputs is easy:\n\n.. code:: bash\n\n    $ pnictogen new_template.ORCA.inp data/co.xyz data/water.xyz\n    data/co.inp written\n    data/water.inp written\n\n(Wildcards are allowed, e.g., ``pnictogen new_template.ORCA.inp *.xyz`` works.)\n\nSince\npnictogen is built on top of `Pybel <https://open-babel.readthedocs.io/en/latest/UseTheLibrary/Python_PybelAPI.html>`_, so it is able to read anything `Open Babel <http://openbabel.org/wiki/Main_Page>`_ reads.\nCheck the list of all available file formats `here <https://open-babel.readthedocs.io/en/latest/FileFormats/Overview.html>`_.\n\nTemplates\n---------\n\nYou can use the full Jinja2 syntax within templates (`check here <http://jinja.pocoo.org/docs/2.10/templates/>`_ its documentation for details).\n\nBesides this, pnictogen also understands a special delimiter (``--@``) that allows one to generate many inputs from a single file:\n\n.. code:: bash\n\n    $ cat repo/MOPAC.mop\n    {% for molecule in molecule %}\n    --@{{ loop.index }}\n    CHARGE={{ molecule.charge }} MS={{ (molecule.mult - 1)/2 }}\n    {{ molecule.name }}\n\n    {{ molecule.to_string(\"mop\") }}\n\n    {% endfor %}\n    $ pnictogen repo/MOPAC.mop data/pentane_conformers.xyz\n    data/pentane_conformers_1.mop written\n    data/pentane_conformers_2.mop written\n    data/pentane_conformers_3.mop written\n    data/pentane_conformers_4.mop written\n    data/pentane_conformers_5.mop written\n    data/pentane_conformers_6.mop written\n    data/pentane_conformers_7.mop written\n\nThe rest of the line after ``--@`` is aways added to the name of the inputs after an underscore (``_``).\n\nIn the example above, ``data/pentane_conformers.xyz`` contains seven conformers of pentane, so seven inputs were generated (the counting is provided by ``loop.index``):\n\n.. code:: bash\n\n    $ cat data/pentane_conformers_5.mop\n    CHARGE=0 MS=0.0\n    C5H12\n\n    C   1.23923 1  1.46892 1 -1.23930 1\n    C   1.24920 1  0.57161 1  0.00000 1\n    C  -0.00000 1 -0.31179 1 -0.00000 1\n    C  -1.24920 1  0.57161 1 -0.00000 1\n    C  -2.49842 1 -0.31168 1  0.01981 1\n    H   1.23217 1  0.84960 1 -2.13625 1\n    H   0.34926 1  2.09811 1 -1.22516 1\n    H   2.12917 1  2.09831 1 -1.23936 1\n    H   2.13917 1 -0.05758 1 -0.01415 1\n    H   1.25625 1  1.19094 1  0.89694 1\n    H  -0.00000 1 -0.94109 1 -0.89000 1\n    H  -0.00000 1 -0.94109 1  0.89000 1\n    H  -1.24217 1  1.21085 1  0.88286 1\n    H  -1.25629 1  1.19089 1 -0.89697 1\n    H  -2.50545 1 -0.95092 1 -0.86305 1\n    H  -2.49134 1 -0.93096 1  0.91678 1\n    H  -3.38842 1  0.31762 1  0.01981 1\n\nExample: energy decomposition analysis (EDA) with ADF\n--------------------------------------------------------------\n\nImagine we want to do `energy decomposition analysis <https://doi.org/10.1002/wcms.71>`_ on the following water dimer:\n\n.. code:: bash\n\n        $ cat water-dimer.xyz\n        6\n\n        O          0.12908       -0.26336        0.64798\n        H          0.89795        0.28805        0.85518\n        H          0.10833       -0.20468       -0.33302\n        O          0.31020        0.07569       -2.07524\n        H          0.64083       -0.57862       -2.71449\n        H         -0.26065        0.64232       -2.62218\n\nThe following template uses both ``molecule.split()`` and ``molecule.to_string(\"xyz\")`` functions to generate ADF inputs in bulk:\n\n.. code:: bash\n\n    $ cat split.ADF.in\n    {% set frags = molecule.split([range(3), range(3, 6)]) %}\n    --@eda\n    ATOMS Cartesian\n    {% for frag in frags %}\n    {{ frag.to_string(\"xyz\", dialect=\"adf\", fragment_id=\"f{}\".format(loop.index)) }}\n    {% endfor %}\n    End\n\n    Fragments\n    {% for frag in frags %}\n     f{{ loop.index }} {{ input_prefix }}_f{{ loop.index }}.t21\n    {% endfor %}\n    End\n\n    {% for frag in frags %}\n    --@f{{ loop.index }}\n    ATOMS Cartesian\n    {{ frag.to_string(\"xyz\") }}\n    End\n\n    {% endfor %}\n    $ pnictogen split.ADF.in data/water-dimer.xyz\n    data/water-dimer_eda.in written\n    data/water-dimer_f1.in written\n    data/water-dimer_f2.in written\n\nThe above creates inputs like the following:\n\n.. code:: bash\n\n    $ cat water-dimer_eda.in\n    ATOMS Cartesian\n    O          0.12908       -0.26336        0.64798       f=f1\n    H          0.89795        0.28805        0.85518       f=f1\n    H          0.10833       -0.20468       -0.33302       f=f1\n    O          0.31020        0.07569       -2.07524       f=f2\n    H          0.64083       -0.57862       -2.71449       f=f2\n    H         -0.26065        0.64232       -2.62218       f=f2\n    End\n\n    Fragments\n    f1 data/water-dimer_f1.t21\n    f2 data/water-dimer_f2.t21\n    End\n\n    $ cat water-dimer_f1.in\n    ATOMS Cartesian\n    O          0.12908       -0.26336        0.64798\n    H          0.89795        0.28805        0.85518\n    H          0.10833       -0.20468       -0.33302\n    End\n\n\n",
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