Firecode

- Expanded debug functionality (DEBUG keyword): printouts of RunEmbedding status (dump_status)
- Added a xtb_pre_opt wrapper for xtb_opt that retains every bond present in the initial set of graphs, in addition to provided constraints. This will greatly increase the quality of structures coming from embeds into force_field_refining. Added before force_field_opt for embed runs (>1 self.objects) that use XTB as FF calculator.
- Introduced orbital subtypes (atom.subtype) to offer more flexibility for embed types. These do not alter default pairing_dists but allow for specific orbital arrangements around the reactive atom.
- New Ketone atom subtype: 'trilobe' - three lobes at the opposite end of alkoxide/sulfonamide substituents relative to oxygen.
- Added the DRYRUN keyword. Skips lengthy operations (operators, embedding, refining) but retains other functions and printouts. Useful for debugging and checking purposes.
- Compacted output information: individual candidate details only printed with DEBUG keyword, average time per structure and estimate of completion given instead every 20 iterations when saving checkpoints

- Added energy table at the end of runs that generate energetic data
- Fixed bug in force_field_refining that runs with no pairings
- Fixed lack of output in optimization_refining when less than 20 structures were optimized
- Brought back MOI-based pruning, when the ensemble is <200 structures, as it proves fast and beneficial for locally symmetric (dummy) rotations not yet identified by rmsd_rot_corr. Threshold is statically set at 1% (10E-2). In the future, it could be possible to uniform to CREST's approach of adjusting it from 1 to 2.5 % dynamically based on the anisotropy of moments of inertia.
- Adjusted default threshold for RMSD similarity from 0.5 to 0.25 A (benchmarked to retain all methylcyclohexane conformers)
- Cleaned residuals of the ENANTIOMERS keyword and related prune_enantiomers (now prune_by_moment_of_inertia)
- Renamed every "indexes" to "indices", as I should have done a long time ago...
- The function distance_refinement is now just incorporated in force_field_refinement and optimization_refinement as an option (only_fixed_constraints). First, an optimization is done with all specified constraints (fixed and interactions, at loose convergence for force field) and then the interaction constraints are released (tight convergence for FF). This process should be more robust than the one before, as it minimizes scrambling/separation of multimolecular arrangements and avoids the limitations of xtb-python when using XTB as calculator (since everything is now dealt with without ASE). Moreover, energy pruning is only performed after the interaction constraints have been released, so that random fluctuations in interaction distances constraints do not bias conformer selection (imperfect embedding geometries in mind).
- Rotationally corrected RMSD-based pruning in similarity_refining is now only done for molecules with at least one locally symmetric torsion (saves time)

- Implemented nested operators call ('refine> rsearch> opt> mol.xyz 2a 7a'), executed in reversed order (opt>, then rsearch>, then refine>)
- Removed checkpoint automatic restart, as it was not compatible with the new nested operator routine
- To remedy the last point, the last 'checkpoint' ensemble is now not deleted after optimization_refinement
- The opt> operator is now aware of internal constraints and performs constrained optimizations (moved letter/pairing/dist functions from RunEmbedder to Embedder)
- Updated README and ReadTheDocs documentation

- 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.