Scrambler: blind structure prediction

A package of the classes for scrambling and blind structure prediction in cgexplore.

The graphing aspect and the graphs available in cgexplore.scram for performing blind structure prediction is now part of agx, which can be found in the agx documentation.

There are also agx recipes that highlight how to explore graphs before construction.

• Available graphs

The iterators

This class now handles graph and building block configuration exploration.

• TopologyIterator

Containers

These are likely to be updated, but when performing structure prediction, you will use these classes to access the new graphs/configurations.

• TopologyCode

• Configuration

Performing target optimisation

Using cgexplore.scram.target_optimisation(), it is now possible to optimise a forcefield or a produced structure to minimise the structure energy (energy per building block).

Note

Examples of this function can be found in recipe 6.

• target_optimisation

Construction with arbitrary graphs

• get_vertexset_molecule

• get_regraphed_molecule

• get_stk_topology_code

• optimise_cage

• optimise_from_files

• graph_optimise_cage

• points_on_sphere

• try_except_construction