A library for computational chemistry in python.
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chmpy supports handling molecules, crystals, Hirshfeld & promolecule density isosurfaces, spherical harmonic shape descriptors and much more...
Basic installation can be done through the python package manager pip:
pip install chmpy
# or to install directly from GitHub:
pip install git+https://github.com/peterspackman/chmpy.gitFor development or modifications, install locally using pip:
pip install -e .While the library is intended to be flexible and make it easy to build complex pipelines or properties, the following is a brief summary of intended features:
- Load crystal structures from
.cif,.res,POSCARfiles. - Evaluate promolecule and procrystal electron densities.
- Easily generate Hirshfeld or promolecule isosurfaces and associated properties.
- Easily generate spherical harmonic shape descriptors for atoms, molecules, or molecular fragments.
- Efficiently calculate crystal slabs, periodic connectivity and more...
- Automatic parallelization of some calculations using OpenMP (set the
OMP_NUM_THREADSenvironment variable)
It should also serve as a simple, easy to read library for learning how to represent crystal structures, molecules etc. and evaluate scientifically relevant information quickly and efficiently using python.
Loading a crystal structure from a CIF (.cif) or SHELX (.res)
file, or a molecule from an XMOL (.xyz) file is straightforward:
from chmpy import Crystal, Molecule
c = Crystal.load("tests/acetic_acid.cif")
print(c)
# <Crystal C2H4O2 Pna2_1>
# Calculate the unique molecules in this crystal
c.symmetry_unique_molecules()
# [<Molecule: C2H4O2(2.12,1.15,0.97)>]
m = Molecule.load("tests/water.xyz")
print(m)
# <Molecule: H2O(-0.67,-0.00,0.01)>Hirshfeld and promolecule density isosurfaces
Generation of surfaces with the default settings can be done with minimal hassle, simply by using the corresponding members of the Crystal class:
c = Crystal.load("tests/test_files/acetic_acid.cif")
# This will generate a high resolution surface
# for each symmetry unique molecule in the crystal
surfaces = c.hirshfeld_surfaces()
print(surfaces)
# [<trimesh.Trimesh(vertices.shape=(3598, 3), faces.shape=(7192, 3))>]
# We can generate lower resolution surfaces with the separation parameter
surfaces = c.hirshfeld_surfaces(separation=0.5)
print(surfaces)
# [<trimesh.Trimesh(vertices.shape=(584, 3), faces.shape=(1164, 3))>]
# Surfaces can be saved via trimesh, or a utility function provided in chmpy
from chmpy.util.mesh import save_mesh
save_mesh(surfaces[0], "acetic_acid.ply")The resulting surface should look something like this when visualized:
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