Molecularnodes

Added

- Panel for adding multiple selection strings, which will become boolean attributes on the imported model when importing via MDAnalysis.

Fixed

- Ball and stick node sphers now support field input for scaling the radius
- Error with initial node setup breaking when in non-english Blender UI ([139](https://github.com/BradyAJohnston/MolecularNodes/pull/139)) contributed by YaoYinYing
- Problems with biological assemblies failling on larger structures. ([143](https://github.com/BradyAJohnston/MolecularNodes/pull/145))
- Problem with Animate Frames node defaulting to wrong from range on start

Added

Fixed

- Issue on linux and with newer versions of Numpy where `np.bool` is deprecated and was erroring on import.

Added

- multi-model `b_factor` is added when importing from `.pdb` files via biotite [133](https://github.com/BradyAJohnston/MolecularNodes/pull/133)
- 'Invert' field option to atom_properties and other selection nodes to optionally invert the selection
- Added better detection of ligands and modifcations (such as sugars) and a separate selection node for them. Currently ligands are stored on the `res_name` attribute, starting at 100 and incrementing one for each unique ligand.

Fixed

- `include_bonds` option was not being utilised on MD import [132](https://github.com/BradyAJohnston/MolecularNodes/pull/132)
- `MOL_animate_res_wiggle` was wiggling the `OXT` (`res_name == 38`) oxygen when a peptide chain ended. Added additional selection to not wiggle this atom, which should only ever appear when a peptide chain terminates.
- fixed import of `vdw_radii` for elements not supported by biotite (such as Fe) by moving vdw_radii to the data dictionary rather than relying on a function from biotite which had a limited dictionary for vdw_radii lookup

Added

- `atom_name` attribute, which is a numerical representation of the atom name (C, CA, C5 etc)
- Dicussed in [118](https://github.com/BradyAJohnston/MolecularNodes/issues/118)
- Allows for more precise selections for new styling and animation nodes
- Reimplemented amino acid 'wiggle' node: using the `atom_name` attribute
- 3x faster with the improved `atom_name` attribute and refactor of the underlying nodes
- Reimplemented the amino acid to curve node
- Ribbon Style Nucleic: A ribbon representation for nucleic acids to complement the ribbon represenation of the proteins from alpha carbons. Enabled now thanks to the `atom_name` attribute.
- Capturing the `Index` field in the selection node before the selection occurs, and added an `Index` field input to the `MOL_animate_frames` node to enable selection to occur before animating between frames, if the `Pre-Sel Index` field is used in the `Index` field of the `MOL_animate_frames` node
- Added cutoff field for limiting the interpolation of atoms between frames based on a distance cutoff
- Added bonds through MDAnalysis import when a trajectory supports it [129](https://github.com/BradyAJohnston/MolecularNodes/issues/129)
- Added `is_solvent`, `is_nucleic` and `is_peptide` boolean attributes when importing via MDAnalysis
- Added frame-specific attribute `occupancy` which is added to each frame of the trajectory when imported via MDAnalysis. [128](https://github.com/BradyAJohnston/MolecularNodes/issues/128)

Fixed

- Changed naming of `MOL_style_atoms` to `MOL_style_atoms_cycles` and `MOL_style_ribbon` to `MOL_style_ribbon_protein`

Added

- `CHANGELOG.md` for tracking changes to the project
- Issue templates for GitHub issues
- Proper support for Fields for ribbon width, enabling 'licorice' representation amoung others
- Tooltips documentation for each of the custom node groups that can be added in Geometry Nodes
- More selection nodes for distance, XYZ slice and whole residues.
- Custom selections using a string when importing via MDAnalysis [123](https://github.com/BradyAJohnston/MolecularNodes/pull/123)
- Added option to disable interpolation of atom positions between frames
- Added node for animating any field between frames of a trajectory (no fields currently added on import, but used in the new Aniamte Frames backend)
- UVs are now available for the ribbon mesh style, idea from [ErikMarklund](https://github.com/BradyAJohnston/MolecularNodes/issues/77#issuecomment-1273598042) and implemented by [quellenform](https://github.com/quellenform/blender-CurveToMeshUV)

Fixed

- Error when defaulting to `connect_via_distance()` when importing with 'Find Bonds' enabled
- Adding of a color node which was mis-labelled and couldn't be added
- Non-`.gro` topology files were failling to add `vdw_radii` attribute [124](https://github.com/BradyAJohnston/MolecularNodes/issues/124)
- Remove use of `np.int` which is now deprecated and was causing errors when [linking python on M1 Mac](https://github.com/BradyAJohnston/MolecularNodes/issues/108#issuecomment-1365540371)
- Attributes now available on ribbon mesh which are [sampled from backbone](https://github.com/BradyAJohnston/MolecularNodes/issues/77)
- Changed starting material to be appended instead of created, which should avoid duplication of material.

Fixed

- Error on reporting the success of improting a molecule