cgexplore.scram.get_regraphed_molecule

cgexplore.scram.get_regraphed_molecule(layout_type, scale, topology_code, iterator, configuration)[source]

Take a graph that considers all atoms, and get atom positions.

The initial graph is generated with stko.Network.init_from_molecule.

Important

Warning: There is no guarantee the graph layout will give identical coordinates in multiple runs.

Parameters:

  • layout_type (str) – Which networkx layout to use (of spring, kamada).

  • scale (float) – Scale factor to apply to eventual constructed molecule.

  • topology_code (TopologyCode) – The code defining the topology graph.

  • iterator (TopologyIterator) – The scram algorithm used to generate the graph and configuration.

  • configuration (Configuration | None) – The configuration of building blocks on the graph.

  • vertex_alignment – The vertex alignment of building blocks on the graph.

Returns:

A constructed molecule at (0, 0, 0).

Return type:

ConstructedMolecule