Welcome to ChemCoord’s documentation!¶
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¶
- Installation guide
- Tutorial
- Documentation
- Cartesian coordinates
- Cartesian
- xyz_functions
- chemcoord.xyz_functions.isclose
- chemcoord.xyz_functions.allclose
- chemcoord.xyz_functions.concat
- chemcoord.xyz_functions.write_molden
- chemcoord.xyz_functions.to_molden
- chemcoord.xyz_functions.read_molden
- chemcoord.xyz_functions.view
- chemcoord.xyz_functions.dot
- chemcoord.xyz_functions.apply_grad_zmat_tensor
- Symmetry
- Internal coordinates
- Configuration of settings
- Exceptions
- Cartesian coordinates
- References
- Bugreports and Development
- Previous Contribution
- License
The changelog can be found here.