model.patch_ss() -- guess MODEL disulfides from model structure

Description:

This command defines and patches disulfide bonds in MODEL using MODEL's current structure. A disulfide bridge is declared between all pairs of Cys residues whose SG-SG distances are less than 2.5. The covalent connectivity is patched accordingly.

This command should be run after model.read() and before optimization to ensure that the disulfides are fixed properly and that no SG-SG non-bonded interactions are applied.

topology.submodel is needed to make sure the correct atomic radii are used in CYS-CYS patching.

Example: See model.patch_ss_templates() command.