I was wondering if there were any reliable algorithms out there that could allocate bond orders and formal charges of a given molecular structure if just the atomic coordinates (x,y,z) and atom type were present in a file (C, N, O, H, etc...). The atoms are most likely ones found in organic molecules so complicated heavy metals with multiple charged states are unlikely.
In a step within a molecular modelling workflow, I only have a set of atomic coordinates but no explicit bond or charge information is kept so I need re-derive them as the coordinates have changed (within reasonable extents like bond lengths) relative to the ones from the input structure which has the bond and charge information. So taking the bond and charge information from the input structure probably won't be feasible.
Any references to papers with code would be really helpful for this.