I'm looking for console tool (preferably pythonic) tool to parse PDB file to Stockholm format. The goal is to gain a sequence with information of missing residues. Tool should be insensitive to errors in PDB numberings or insertion codes or alternate locations.

DSSP doesn't provide such information.

I know that Chimera can do it, but it is quite slow in script usage and need a lot of tricks with GUI, that I would like to avoid.

Thanks in advance.