Release 0.12.3

0.12.3 - 2025-01-29

Added

• qcio.models.utils.to_multi_xyz() function that accepts an array of structures and converts them to a multi-xyz string.

Release 0.12.2

0.12.2 - 2025-01-29

• Updated numpy dependency to support both numpy v1 or v2. qcio does not rely upon any updated numpy 2 API so no changes were made to the code.

Release 0.12.1

0.12.1 - 2025-01-15

Removed

• rdkit-stubs

Added

• eval-type-backport package to dependencies to support the type | type syntax in the package.
• type: ignore statements for rdkit function calls and imports which lack annotations in the rdkit package.

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.