Guillaume Fraux

Symmetry operations (pdbx_struct_oper_list) in mmCIF

6

It looks like we should use the symmetry operations defined in [pdbx_struct_oper_list](https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/pdbx_struct_oper_list.html) when reading the structure. Otherwise, we would be missing a subset of atoms in the full structure. @sguionni...

Implement PSF file format

10

These files only contain topology information and seem to be widely used in bio-molecules simulations. See here for a description: https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node23.html The format is a simple text-based format that looks...

We try to enforce `A` and `fs` as units, but depending on the format this might not be true all the time. For example, XYZ can contain data in any...

Speed-up bonds detection

2

The idea comes from this github project: https://github.com/PorridgeBear/imvs/blob/master/IMVS/AtomCloud.swift. Creating an octree will allow for faster lookup in bonds detection, replacing the brute-force 2D loop here: https://github.com/chemfiles/chemfiles/blob/3cbd6d78bc99ded786044eee6db7022ed2bf4c75/src/Frame.cpp#L60-L80 Instead of looping over...

We should add a small tutorial for contributors looking to add a new format to chemfiles. It should include the following: - how to add new files to the tests...

Support for 1-based indexing in the C API

6

Fortran and Julia use 1-based indexing, but the current bindings use the standard 0-based indexing (for example `chfl_atom_from_frame(frame, 11)` will return the 12th atom in the frame. For a better...

This would greatly improve the user experience with invalid files, and should not be too hard to implement overall.

This is a follow up to #301. The algorithm used in `Frame::guess_bonds`, while an OK default is not very good and often fails to find bonds or find extraneous bonds....

CIF files

10

| File Type | text | | --- | --- | | Topological information | Yes | | Positions | Yes | | Velocities | Maybe | Reference of the...

See https://www.unidata.ucar.edu/software/netcdf/docs/md__home_wfisher_Desktop_gitprojects_netcdf-c_docs_inmemory.html for the corresponding documentation.