Open outihaa opened 2 years ago
Hello hello! We did consider this (at least for resid numbers), but decided against it for 2 reasons: 1) the file format specification uses base 10 numbers; and 2) if we misinterpret base-10 numbers as hexadecimal the difference between them (i.e. resid_1 - resid_2
) goes wrong. The latter is a problem, since we use the difference in resid numbers for applying links (specifically the BB +BB type).
There are 2 solutions: 1) stop using resid differences for links, and use graph distance instead; 2) implement a mmcif parser (which is the successor of the pdb format).
I'm not sure we use atomid's anywhere, so I'm not sure duplicate atom ids are a problem.
In pbd format hexadecimal numbering kicks in after 99999 for atom numbering but martinize2 doesn't support that. I'm not sure if the hexadecimal system is used for residues as well :')