Firecode

- Added pretty error traceback with rich.
<!-- SMARTS Constraint class -->

- Implemented planar angle and dihedral constraints in ensemble optimization (only intra-file, but also available in embedding runs). These are propagated to xtb, ASE-mediated calculators and PyTorch models, as well as to operators like mtd> (CREST). These constraints can be specified in new input lines that start with a blank space under the reference molecule line, with the syntax "i1 i2 i3 \[i4\] target(float)" (i.e. "0 1 2 3 90.0" for dihedrals or "0 1 2 0.0" for planar angles). For now, these constraints are enforced at every step (as capital letter constraints, but not associated to any letter).
- Improved comments parsing: possible to comment in any input line (with "", following a Pyhton-style syntax).
- Tweaked similarity_refining maximum ensemble size thresholds to carry different pruning steps.
- Turned off interactive ASE GUI specification of Sp3 atoms leaving groups for orbital building.

- Minor bugfixes and printout clean-ups.

- Renamed project to better reflect the expanded functionality of the toolbox! 🔥
- New Pruner class: simpler, more homogenized implementation of iterative subset pruning, sharing the same basic architecture across different similarity evaluation functions, with cached calls to the eval similarity function.
- Added new debug dedicated log, that collects all debug messages if the DEBUG keyword is specified.
- Fixed bug with some parts of torsion_module for segmented graphs, mainly for rotationally corrected RMSD calculation.
- General code debug and PEP 8 cleanup (thanks Ruff).
- Informative suggestions: keywords that are not understood can generate suggestion of known keywords to use instead.
- Removed rmsd library dependency for local numba numpy implementation.
- Increased similarity_refining thresholds for the maximum number of structures to be compared: 1E5 for RMSD and MOI, 1E4 for rotationally corrected RMSD. Added printouts in log if we skip a pruning stage because the ensemble is too large.
- Fixed a bug in _get_rotation_mask that would rotate the wrong part of the molecule (spotted because prune_by_rmsd_rot_corr would not reject some molecules that it should have)
- Added a debug messages printout function for the Pruner class, which by default is set to embedder.debuglog
- Added support for AIMNET2 Pytorch models, including GPU support, with the package aimnet2-firecode. If a solvent is specified, the ALPB ΔGsolv (XTB) is added to the vacuum SP EE.
- Removed support for the THREADS keyword and command line setting, as the number of workers in every multithreaded parallelism is now automated.

TSCoDe Changelog (old)

- Solved bugfix in check_objects_compenetration.
- Updated compenetration_check warning printouts, specifying the number of compenetrations found.

- Reinstated the only_refined option at the end of optimization_refining.
- Solved bugfix in operators.