Firecode

- Added rotationally-corrected RMSD pruning, to treat symmetrical rotations and get rid of identical rotamers that only differ from indexing order. The treatment is skipped for ensembles greater than 750 structures, to avoid unnecessarily slowing down the refinement process.
- Renamed clustered_csearch.py as torsion_module.py, since it now contains mostly torsion-based constructs and utilities.
- Resolved a bug for internal constraints preventing paired embeds from being recognized as correct.
- Implemented "multiembed" embeds, able to perform bimolecular cyclical embeds systematically on every arrangement of pairs of multiple atoms (see documentation)
- Fixed dependency requirements (again?)

- Added the ability to recognize interrupted refine> runs and restart from the last checkpoint.
- Moreover, checkpoints now update every 20 optimized structures.
- Layered optimization protocol for optimization_refinement when using ORCA - first round with 3 iterations, then 5 extra, then to convergence.
- XTB calculations that do not reach convergence do not crash the program anymore unless specified with assert_convergence=True.
- XTB force field ensemble optimizations are carried out in two steps, first with loose convergence and then with tight convergence.
- Various small bugfixes and printout beautifications.

- Added "autoneb>" operator, that automatically builds a MEP guess based on input structure. Currently only supporting 7-membered rings inversions.
- The Hypermolecule class can now also accept SMILES strings instead of molecular files. Only embeds with no index to be specified, as "autoneb>"
- Changed run> operator back to refine> (and RUN keyword bask to REFINE).
- Fixed bug with scan> termination called when not required.
- Changed default for conformational search during embeds to false, and NOCSEARCH keyword to CSEARCH.
- Clustered csearch module: added flexibility in some functions to allow external use of them.

- Removed Walrus operators from the code for Python 3.7 compatibility

- Fixed TFD pruning bug for embeds with no rotable bonds.
- approach> operator is now called scan> and automatically infers the scan direction (approaching or separating the atoms based on their distance).
- Fixed bug in specifying indices without letters (in _remove_internal_constraints)
- Minor bug fixes
- Added flexibility in NEB keyword, allowing optimization of start/end points and specifying the number of images (NEB keyword)
- NEB calculations now support two, three or a greater odd number of structures as input, to facilitate computational refinement of MEPs

- Fixed run> operator bug (leftover refine> references)
- Implemented a fast, preliminary torsion fingerprint deviation-based similarity pruning (prune_confs_tfd, faster than prune_confs_rmsd) for similarity_refining
- Added this TFD pruning in the most_diverse_conformers function (this is fast enough, RMSD-based was not) and at the end of clustered_csearch and csearch_aug as well
- Refined distance constraining for XTB optimizations as well, guided by the target length. More accurate distances, so more accurate energies for constrained structures. Also less work for the final refinement step.
- Implemented wider compatibility for internal constraints - intramolecular distances that have to be respected (so that csearch is aware of them) and even enforced to a specific distance (with DIST)