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biotite-dev / hydride

Adding hydrogens to molecular models
https://hydride.biotite-python.org/
BSD 3-Clause "New" or "Revised" License
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Functionality for relaxation of rotatable hydrogen positions #3

Closed JacobAnter closed 3 years ago

JacobAnter commented 3 years ago

This PR provides the functionality for the energy-based relaxation of the position of rotatable hydrogen atoms. For this purpose, the heuristic optimisation technique of simulated annealing is applied. The computation of the energy of a certain configuration is based on electrostatic / Coulomb interaction on the one hand and steric repulsion on the other hand. Computation of electrostatic interaction is performed according to the PEOE algorithm developed by Gasteiger and Marsili. The algorithm is sophisticated as it differentiates between freely rotatable terminal groups and terminal groups with restricted rotatability (double bonds) and changes the orientation of the latter only if one hydrogen atom is bound to this terminal double bond.

padix-key commented 3 years ago

Closed due to being outdated.