The ~ProtoCaller.Ensemble.Ligand.Ligand class keeps track of ligand instantiation, minimisation, protonation and parametrisation. It consists of an RDKit object and, when parametrised, a link to the parameter files.
This means that this class has to be provided with complete atom and bond information. This can be done using: SMILES strings, InChI strings, files which keep track of bond connectivity (such as SDF, MOL, MOL2) or an RDKit object. It is also highly advisable to not use SMILES/InChI strings when possible, since these provide no 3D information which is crucial if there are multiple conformational minima. Different conformations will lead to different force field charges and therefore non-reproducible results. Moreover, 1D identifiers are usually not very good at providing protonation state/tautomer information which can be important, depending on the system.
The user can also instantiate the ligand with parameter coordinate and topology files but still needs to provide some bond connectivity information. In this case SMILES/InChI strings are not an issue.
ProtoCaller.Ensemble.Ligand