I have an xyz file upon which after processing in Python, I determine bonds between different atoms. What would be the correct file type that I can write to visualize this bond information in VMD?
In the VMD user guide different file formats natively handled by VMD are specified, including
PARM that can both contain bond connectivity:
PSF and PARM files contain atoms, residues, segment names, residue types, atomic mass and charge, and the bond connectivity.
Depending on how your atoms and bonds are represented in python, you may choose to use the file input/output functions of the ParmEd library which include support for PSF files (or any other library that supports it).