Allow user to set size of ghost atom

[matterhorn103]

Is your feature request related to a problem? Please describe.
Sometimes a user might want to show a generic attachment point - coloured spheres in place of R1, R2 etc are all the rage in chemistry talks it seems.

Sometimes a user might want to depict a molecule bound to a nanoparticle or something else "blobby".

Describe the solution you'd like
If the size of a ghost atom was customizable, that would provide a convenient way to create such depictions.

Describe alternatives you've considered
Another option would be an additional atom type that is specifically designed to function as a "blob", but that seems unnecessary.

[ghutchis]

IIRC there are custom elements in there already for coarse-grained MD models. I think the element numbers go up to 255 (i.e. "customElement..." in elements.h / elements.cpp)

[ghutchis]

I guess the first step would be to modify molecule.h to have covalent and VdW radius methods for atom idx, which defaults to the static method in elements.h but could be set for custom elements.

I can provide some pointers to anyone interested in this.

[Tharanishwaran]

can i work on this issue ?

[raunitpatel]

can i work on this issue ?

[Vineet1101]

@matterhorn103 Hi I would like to work on this issue can you tell me how to setup the project and explain a bit more about the issue

[ghutchis]

The build information is here: https://two.avogadro.cc/develop/build.html

For this one, it's actually fairly easy. There's some code in avogadro/core/elements.cpp. At the moment, all custom elements get the same radius (e.g. lines 29, 30).

So this one would require changing these to be std::vector similar to the code for CustomElementSymbols.

There's also some code between lines 233-250 that would need to change, and some methods added to set the radius of the custom elements (again similar to that for symbols).

So far, there isn't a pull request to implement the feature, so no it's not assigned or anything.

[Vineet1101]

@ghutchis alright I understood it thanks for explanation I will start right now working on it and will inform you once its done