Small-molecule toolboxLuc Bourhis Durham University, UK
The Small Molecule Toolbox (smtbx) is a sister library of the Computational Crystallography Toolbox (cctbx). Whereas the latter deals with the foundation of crystallography, the former addresses the specific needs of small molecule crystallographers, as the Macro Molecular Toolbox (mmtbx) does for the macro molecular problems.
In my talk, I will focus on the subject of constraints. It is a very popular ingredient of small molecule refinement whereas it is rather challenging from the programming point of view due to the issue of "chained reparameterization". I will first present that mathematical formalism where a crystallographic parameter is expressed as a function of other parameters that in turn can also be expressed as function of yet another parameters and so on. Some of those secondary parameters may be non-crystallographic, which adds to the difficulty of devising a software design if one wishes to retain flexibility, extensibility and generality. We will present our design and implementation in the smtbx and discuss what trade-offs we needed to make.
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