Feature request: support for PDBQT

[lucifer1004]

Hi @lmiq, thank you for writing this package.

I am wondering whether there will be support for PDBQT files, which are widely used in docking.

See https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/AutoDock4.2.6_UserGuide.pdf (Page 28)

[lmiq]

PDBTools only read the atom data from the file (not the headers), and in that sense it seems very similar. What exactly do you need to read from those fields?

Do you have an example file to share? Does the current readPDB fails when reading it or it just ignores some fields you would need to read?

[lucifer1004]

• It adds two custom fields, which can be easily handled.
• It also adds a tree structure description of rotatable bonds, which conflicts with the current design of PDBTools (parse .pdb files as Vector{Atom}.

[lmiq]

Custom fields is something that could be a nice addition, I can think about adding something like that.

The connectivity (or rotatable bonds) I would rather read in another structure. A reader of this kind of file could return a different data structure containing all the information. Something like:

struct PDBQTData
     atoms::Vector{PDBTools.Atom}
     rotatable_angles::SomethingAdequate
end

We can keep this open, although sincerely I don't have much time now to implement these features.

One thing to have in mind is that, not being a user of that kind of file myself, it is hard for me to come with a design that will be actually useful. If you can provide an example file and some description on how you use these files (pass to the data to other programs? In which format?), it would help thinking about something that would be potentially useful.