Release 0.12.0

0.12.0 - 2024-12-18

Removed

• 🚨 Python 3.8 support.

Changed

• Dropped black and isort in favor of ruff.

Release 0.11.17

0.11.17 - 2024-12-11

Changed

• structure_to_smiles() (and by extension Structure.to_smiles()) now use the Hueckel method by default for rdkit's DetermineBonds function. This is more robust than the default connect-the-dots method. Parameters for use_hueckel, use_vdw and allow_charged_fragments are now available for more optionality when determining the bonding in a structure (a prerequisite to generating the SMILES string). Default changed to use_hueckel since this should be the most robust.
  • This may result in structures that could formerly use struct.to_smiles() directly needing to update the arguments they pass to get the same result. struct.to_smiles(use_hueckel=False, allow_charged_fragments=True, robust=False) will result in the same behavior as before.
  • Default behavior to .structure_to_smiles() is to use robust=True mode which will try to determine the bonds with the user-supplied (or default) values first and then iterate through other possible methods (Van der Waals, varying whether charged fragments are allowed or not, trying the connect-the-dots method) to see if one method can successfully determine the bonding.
• rmsd function align parameter changed to best.
• rmsd function with best=False now does a naive alignment of structures with no determination of connectivity though it will try to align the structures by making the assumption that the atom indices are are the same between the two structures.

Release 0.11.16

0.11.16 - 2024-11-13

Added

• utils.rmsd() and utils.align() functions for computing rmsd between structures and aligning structures.

Release 0.11.15

0.11.15 - 2024-11-11

Added

• Structure.swap_indices() method for changing the indices of a structure's symbols and geometry. Helpful for setting up structures for an NEB run or RMSD calculation in which index labels are important.

Release 0.11.14

0.11.14 - 2024-10-16

Fixed

• view.view(...) displays an empty string if .model is None on DualProgramInput rather than raising an exception.

Release 0.11.13

0.11.13 - 2024-10-01

• interval to view animations. Sets the interval between frames in milliseconds. Defaults to 100.

Release 0.11.12

0.11.12 - 2024-10-01

Added

• Added charge and multiplicity to the Structure column of the output table view.

Release 0.11.11

0.11.11 - 2024-09-30

Changed

• Attributes on models that are not explicitly set (i.e., values set to their default value) will not be serialized and saved. This behavior can be modified by passing exclude_unset=True to .save(...).
• Model in the table view is now a mini table to better visualize method and basis.

Release 0.11.10

0.11.10 - 2024-09-23

Added

• Structure.distance(i, j, units='bohr' | 'angstrom') returns the distance between atoms i, j.
• view.view(... distances=[(0, 1), (4,27), ...]) will display the distances between atoms at these indices.

Release 0.11.9

0.11.9 - 2024-08-16

Changed

• Structure views now use GridViewer when laying out multiple structures with py3Dmol so as to use only one WebGL context for all images. This dramatically improves performance and reduces lag.

Added

• View for ConformerSearchResults.
• view_2d option for viewing a 2D image of a molecule rather than the 3D viewer.