Tsjerk

I don't see where in the code this would be happening. Can you try the latest version (1.2.0) and if it doesn't work send me the input and output?

In an XTC file, the header contains the size of the coordinate section in bytes, and the header itself has a fixed size and starts with the magic number 1993....

Oh, reading through the original issue: 1. Finding the last frame is done by reading the first and saving the header tag (8 bytes: magic number and number of atoms),...

I wouldn't call this an 'arbitrary bond'. That's a different league. Yes, we need to be PBC aware for building systems and converting whole systems (forward or backward), and with...

> > > @Tsjerk how thoroughly did you test this code on pdb files? > > > I tested it with several protein PDB files (single chain and multichain), including...

> * bench marking and profiling; there are several functions that operate on the complete graph. It doesn't look to me like they are very expensive to evaluate, but to...

The problem seems to be that the #meta adds to interactions on the block level. I think splitting this into two dihedral blocks will solve the issue. It does make...

PDB 1KP5 is a cyclic protein. The only solution I see at present is indeed cutting the protein in two different ways, rearranging the residues and present both to DSSP,...

A cyclic protein is one in which the last residue connects (back) to the first. So it's just a matter of checking if last and first in the residue graph...

An SS bridge has no consequences for the secondary structure determination. The only point is that DSSP does not consider the possibility of continuity over the ends of the chain,...