Firecode

- Implemented pka> operator (xtb calculator only)
- Solved random_csearch bug (when confs < n_out)
- Refined distance constraining for OB optimizations, guided by the target length. More accurate distances, so more accurate UFF energies for constrained structures.
- Reincluded symmetrical aryl ring rotations in clustered_csearch (previously considered dummy and skipped)
- Corrected bug in the approach> operator
- Now multiple molecules are supported for approach> runs and a cumulative output is provided (distance-energy graph)
- Random Csearch now always tries to output n_out conformers (1000 max tries), instead of generating n_out confs and discarding compenetrated ones
- Implemented rsearch> operator
- Added the -cl (command line) argument, to call TSCoDe without writing an inputfile
- Added quote from database at the end of each successful run, courtesy of https://type.fit/api/quotes
- Upgraded startup banner to a benzene-like logo
- Added error logging to file via the logging module
- Solved Profiler bug (adapted to new Embedder architecture)
- Added logging for the exit status on any call to optimize(...) (supporting FF calculations too)
- Added the tscode_procs option for embedder.options, to run python code in parallel (for now just csearch_aug implemented)

- Refined conformational search - better parameters, torsion printout, fixed HB bugs, added secondary amides as rotable, made it faster and more scalable (random sampling overrides KMeans for n>1k)
- Various small bug fixes and print refinements in dihedral embed and ase_neb functions
- Added csearch_hb> operator that allows to keep the current hydrogen bonding situation in conformational sampling
- Added approach> operator that performs automatic linear scans (ideally for locating approach energy maxima)
- Torsional clustering: changed clustering method to DBSCAN over KMeans (better for spatial clusters)
- Added numerous temporary "print" statements to asses code activity at all times
- CSearch now warns when it is fed non-connected complexes of two or more molecules, if no intramolecular HBonds are found
- CSearch now has a random dihedral variant (mode 2) used for faster conformational augmentation
- Implemented conformational augmentation of TS candidates (random dihedral rotations, for three cycles, max 1000 new conformers generated)
- Refined molecule reactive atoms/pairings print statements in log
- Fully implemented the use of constrained indices in prune>/NOEMBED runs (pairing distance can be specified now)
- Maximum number of conformers to use in embed can be specified with the CONFS keyword
- Removed enantiomers pruning for performance reasons
- RIGID keyword is automatically added for cyclical embeds with >100 conformers (override with LET)
- The NOEMBED keyword is now called REFINE, and the prune> operator is called refine>

- Added error message if molecule reading fails
- Operators now support spacing after the > sign
- csearch> operator now works for molecules with more than one conformer
- Improved the speed of the align_vector_pair and rot_mat_from vec functions (numba)
- Periodic table is now in pt.py, removing any cyclical import issue
- Graph manipulations are now organized in their own file, allowing shared use (graph_manipulations.py)
- The old Docker is now called Embedder, leaving the "Docker" name for future docking extension
- If no embed is recognized after applying operators, run is cleanly terminated (embedder.embed attribute in RunEmbedding.run function, run.py)
- NOEMBED keyword still works, but structure pruning now can also be performed calling the prune> operator
- conformational search now discard symmetric rotations involving 6-membered aromatic rings like phenyl, 4-pyridyl, mesityl, ...
- procs == None bugfix
- secondary amides are now considered rotable by the csearch algorithm

- Removed unnecessary for loop in dihedral embed NEB optimizations
- Added pre-optimization before dihedral embed
- Customized text can be inserted in write_structures function
- Dihedral embed structures energies are now relative to equilibrim geometry (direct barrier height)
- Moved "test" folder inside "tscode" (fixes bug)

- Import bugfix

- Updated module call adding __main__.py file to tscode/
- All internal imports are now relative to main module (import 'tscode.module' instead of 'import module')
- Maximum number of conformers per molecule is now 10, since the compenetration/similarity pruning algs are faster and more efficient (still overridden by LET keyword)
- Removed strict versioning for python required libraries
- Removed MMFF keyword
- Added NOEMBED, FFOPT, FFCALC, FFLEVEL and TS keywords
- Added a Clustered Conformational Search implementation
- Old csearch> operator is now called confab>
- New csearch> operator is the TSCoDe conformational search engine
- General code optimizations
- Added profiling command line keyword (-p)