distanceselection, and sub-selections in
is_bondedand friends. The syntax would look like
resname HOH and distance(#1, resname Y Z) < 12.5. The changes should be relatively simple so if you want to dig a bit into C++ and implement it yourself I would be happy to help you! Else I'll open an issue on the repo and try to do it soon-ish.
"[chainname] A"should work, but the issue here is that
chainnameis a residue property, and only atomic properties are checked when evaluating selection. That something I think we should fix, I'll open an issue. And yes, the docs for the selection language are not very good, sorry about that.
chainnameon atoms too and recompile chemfiles. If you want to go this route, I can help.
resid 3 to 17? Similar syntax exists in vmd, pymol, mdtraj, etc., and it is more compact than chemfiles'
resid >=3 and resid <=17. Another option could be
3 <= resid <= 17, but
resid 3-17might be cleaner.
resid >=3 and resid <=17. My favorite alternatives would be
3 <= resid <= 17, or
between(resid, 3, 17). Could you open an issue to discuss what syntax this could use?
resid 3-17would clash with
resid == 3 - 17i.e.
resid == -14
chemfilespackage only contains the shared library,
chemfiles-staticcontains the static library &
chemfiles-dev(Debian & friends) /
chemfiles-devel(CentOS & friends) contains the headers.
file1) with coordinates and another one (
file2) with a topology that you want to modify and then use for reading
file1? The easiest way to do this would be something like
// get topology from the first frame of the file auto topology = Trajectory("file2").read().topology(); // modify topology topology.set("foo", false); // use the modified topology to read the other file auto traj = Trajectory("file1"); traj.set_topology(topology); // read, etc. auto frame = traj.read();
If the failed assertion comes from chemfiles, that's a bug on our side! What is the selection you are using? It sounds like you are checking a residue property/residue name.
so my hunch is there's some limit somewhere?
The limit should be max
size_t, i.e. 4294967295 for 32-bit systems & 18446744073709551615 on 64-bits
dnf downgrade chemfiles-0.9.3and potentially the same for