Friday, 21 February 2020

Working around segmentation faults of pyrosetta: threads & processes

Rosetta often does not die gracefully. Pyrosetta is the same. If the starting template is not great segmentation faults will result in the kernel issuing signal 11 to kill the process. The way around it is to spin it up as its own process via the multiprocessing module and not the threading module, because child threads use the same process.

Wednesday, 12 February 2020

Guess bond order in Rdkit by number of bound atoms

Some compChem/Biochem programs do not care about bond order and strip them, which is rather frustrating. Ligands in random PDB files without any name, smiles are a classic example.
There is no single magic mol.CorrectBondOrder() command in Rdkit, but luckily there are some tricks that can be done. Here I will discuss finding out using the number of bound atoms.