Export surface maps to other formats than .dx

[rlavendomme]

Current status

Currently, MoloVol offers the possibility to export surface maps to the OpenDX (.dx) format which defines volumetric data where we can store each voxel type and is conveniently written in ASCII text format. It can be used in various rendering program such as PyMOL and ChimeraX.

Issue

Other formats may be desirable to visualize surfaces in other programs than PyMOL and ChimeraX. A reviewer of the scientific paper asked why we chose OpenDX instead of the more "archaic" and more widespread CCP4 or MRC file formats. One user asked if it was possible to export to .stl format and another asked for .cube format.

Proposed change

Add a dropdown list on the interface to choose the file format to export surface map files. Also add a tag to choose the file format when running MoloVol in command line.
The file types currently considered are:

1. The Gaussian .cube format defines volumetric data and should be easily implemented in the export algorithm as it has a simple and convenient construction, similar to OpenDX. See https://paulbourke.net/dataformats/cube/ for .cube format details.
2. The MRC format defines volumetric data and should be easily implemented, similar to .cube format above. I am not aware yet of any potential restriction that may be problematic. We should read more about the format there: https://www.ccpem.ac.uk/mrc-format/mrc2014/
3. The .stl format defines the surface of a closed object rather than volumetric data where all voxels can be stored to display all kinds of surfaces. So each type of surface (vdw, probe excluded, probe accessible, cavity core, cavity shell) should be exported separately. In stl files, the surface is divided into triangles and their vertices coordinates are stored. More details there: https://en.wikipedia.org/wiki/STL_(file_format)
4. CCP4 maps define volumetric data but are inconvenient since generating them requires mapman as a third-party tool, to my knowledge. Additionally, there are restrictions such as requiring the grid to be aligned on the 0,0,0 cartesian origin. I would prefer not to add it as a choice. If users want a CCP4 map, they can probably convert it themselves from other formats. More details there: https://en.wikipedia.org/wiki/CCP4_(file_format)

Improvement

Propose a more complete set of file format export to match the user needs.