chemcoord 2.0.5

Website

The project’s website with documentation is: http://chemcoord.readthedocs.org/

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 as a python module ;)

Installation guide

A working python 3 installation is required (>=3.7 are possible).

It is highly recommended to use this module in combination with Ipython and jupyter. They come shipped by default with the anaconda3 installer

conda install -c mcocdawc chemcoord

pip install chemcoord

git clone https://github.com/mcocdawc/chemcoord.git
cd chemcoord
pip install .