Metadata-Version: 2.1
Name: tscode
Version: 0.2.0
Summary: Computational chemistry general purpose transition state builder
Home-page: https://www.github.com/ntampellini/tscode
Author: Nicolò Tampellini
Author-email: nicolo.tampellini@yale.edu
License: UNKNOWN
Description: ## TSCoDe: Transition State Conformational Docker.
        Systematically generate poses for bimolecular and trimolecular transition states. Support for open and cyclical transition states, exploring all regiosomeric and stereoisomeric poses.
        
        ## TSCoDe Changelog
        
        ### 0.0.1 (Aug 10 2021)
        - First release
        
        ### 0.0.2 (Aug 10 2021)
        - If pivots decrease during a bend, an exception is raised. Future versions might have a different behavior in this scenario.
        
        ### 0.0.3 (Aug 10 2021)
        - setup.py bugfixes.
        
        ### 0.0.5 (Sep 1 2021)
        - SADDLE keyword implementation.
        - Added keywords print at top of log
        - Pairings are now of two types: reactive atoms (a, b, c) or NCIs (x, y, z). The latter are adjusted when specifying distances with DIST but are left free to reach their equilibrium distance (HalfSpring constraint + additional relax).
        - Major code cleaning, refactoring and reordering
        - Added solvent support for calculators (SOLVENT keyword)
        - Dihedral embeds now support both the SADDLE and NEB keywords
        - Similar structures are now pruned in a rational way: the best looking is kept (fast_score)
        
        ### 0.0.6 (Oct 19 2021)
        - 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)
        
        ### 0.0.7 (Oct 20 2021)
        - Import bugfix
        
        ## 0.0.8 (Oct 21 2021)
        - 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)
        
        ## 0.0.9 (Dec 2021)
        - 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
        
        ## 0.1.0 (May 14 2022)
        - 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 indexes 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>
        
        ## 0.2.0 (Jun 26 2022)
        - 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)
        
        ## 0.2.1 (2022)
        - 
Keywords: computational chemistry,ASE,transition state,xtb
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
