tscode 0.0.6

Computational chemistry general purpose transition state builder

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 (10 Aug 2021)

• First release

0.0.2 (10 Aug 2021)

• If pivots decrease during a bend, an exception is raised. Future versions might have a different behavior in this scenario.

0.0.3 (10 Aug 2021)

• setup.py bugfixes.

0.0.5 (1 Sep 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 (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)