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Welcome to ChemCoord's documentation!

The code can be found here.

Features

  • Molecules are reliably transformed between cartesian space and non redundant internal coordinates (Zmatrices). Dummy atoms are inserted and removed automatically on the fly if necessary.
  • The created Zmatrix is not only a structure expressed in internal coordinates, it is a "chemical" Zmatrix. "Chemical" Zmatrix means, that e.g. distances are along bonds or dihedrals are defined as they are drawn in chemical textbooks (Newman projections).
  • Analytical gradients for the transformations between the different coordinate systems are implemented.
  • Performance intensive functions/methods are implemented with Fortran/C like speed using numba.
  • Geometries may be defined with symbolic expressions using sympy
  • Built on top of pandas with very similar syntax. This allows for example distinct label or row based indexing.
  • It derived from my own work and I heavily use it during the day. So all functions are tested and tailored around the work flow in theoretical chemistry.
  • The classes are safe to inherit from and can easily be customized.
  • It is a python module ;)

Contents

.. toctree::
    :maxdepth: 2

    installation.rst
    tutorial.rst
    documentation.rst
    references.rst
    bugs_and_contributors.rst
    license.rst

The changelog can be found here.

Citation and mathematical background

The theory behind chemcoord is described in this paper. If this package is used in a project that leads to a scientific publication, please acknowledge it by citing.

@article{https://doi.org/10.1002/jcc.27029,
    author = {Weser, Oskar and Hein-Janke, Björn and Mata, Ricardo A.},
    title = {Automated handling of complex chemical structures in Z-matrix coordinates—The chemcoord library},
    journal = {Journal of Computational Chemistry},
    volume = {44},
    number = {5},
    pages = {710-726},
    keywords = {analytical gradients, geometry optimization, non-linear constraints, transition state search, Z-matrix},
    doi = {10.1002/jcc.27029},
    year = {2023}
}

My (Oskar Weser) master thesis including a more detailed derivation of implemented equations and the mathematical background can be found here. It also has a ready-made BibTeX entry:

@mastersthesis{OWeser2017,
    author = {Oskar Weser},
    title = {An efficient and general library for the definition and use of internal coordinates in large molecular systems},
    school = {Georg August Universität Göttingen},
    year = {2017},
    month = {November},
}