adding ability to generate and relax pdb files

[gwirn]

This adds the ability to generate pdb files from protein coordinates that were generated when decoding latent space variables and also relax them.

• generate pdb file based on the selected atoms during training (gets data from PDBdata.frame().data and formats the string for each atom including the new coordinates to be in the pdb format
• optionally relaxes generated structures and stores them in NAME_relaxed.pdb files. This only works with all atom training!!.
• moves data to device if device is GPU in the generate function.
• it also removes to from modeller import * imports to more specific imports
• adds structure generation example file

[degiacom]

Useful update.
Note: in the future, please avoid including in the same pull request systematic code formatting alongside functional code edits. Format edits adds many, many extra lines to the diff, that obfuscate the actual functional edits proposed.