molsystem 2023.4.6

molsystem

MolSystem

Molsystem provides a general class for handling molecular and periodic systems

• Free software: GNU Lesser General Public License v3+

• Documentation: https://molsystem.readthedocs.io.

Features

• Complete the initial version!

  • Remove the coordinates from the Atoms class and allow for multiple sets of coordinates – conformers, trajectories, etc.

  • Provide a concept of the ‘current’ system

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award OAC-1547580 and CHE-2136142.

History

2023.4.6 – Enhancements for CIF files

• Handle uncertainties in CIF files expressed as ‘(x)’ at end of value.

2023.3.30 – Enhancements to QCSchema support

• Improved naming of molecule in QCSchema

• Added creation of configurations from QCSchema objects.

2023.2.13 – Fixed issue with valence in RDkit for cations like NH4+

2022.11.20 – Added a method to copy a configuration.

Added a new method to the system class, copy_configuration, that creates a copy of the configuration using the same atomset and bonset, but new coordinates and cell so that any changes to coordinates and cell are not shared between the configurations. By default it copies the current configuration.

2022.11.18 – Fixed bug with handling for Open Babel

The total charge and multiplicity were not correctly set when creating an Open Babel molecule.

2022.11.3 – Add handling of strain and improved handling of properties

Added methods for straining the unit cell, and also straining a configuration, correctly handling the coordinates for an affine transformation. In the future will add e.g. affine transformation of the centers of molecules, which is useful for molecular fluids.

Added the system for properties, in addition to the configuration. This allows system properties that are not associated with a particular configuration, which is often appropriate for experimental results. It also makes it much easier to search for systems where any configuration has a particular property.

2022.10.26 – Improved database write performance.

Switched to write-ahead mode and tweaked memory settings. This gives a large performance improvement (10x or more) for large database (~1 GB).