Currently, rendering the ligand coordinates in the intermediate windows tends to result in a lot of mangled bond orders and difficult to visualize trajectories. This PR adds a utility function SingleTopology::mol() to emit an RDKit mol with a basic attempt at guessing whether or not a bond is present. For tracing replica trajectories in HREX, the SDF format is recommended (over PDB/mmCIF) since the bond orders are read explicitly by common viewers.
Currently, rendering the ligand coordinates in the intermediate windows tends to result in a lot of mangled bond orders and difficult to visualize trajectories. This PR adds a utility function
SingleTopology::mol()to emit an RDKit mol with a basic attempt at guessing whether or not a bond is present. For tracing replica trajectories in HREX, the SDF format is recommended (over PDB/mmCIF) since the bond orders are read explicitly by common viewers.