Is your feature request related to a problem? Please describe.
When running a large amount of constrained docking runs with unidock2, the reference molecule has a Pyridine. With the current hard-coded methods in FindMCS for atom comparison results in flipped rings. Ex) the reference has the N of the pyridine in the 2' position, and after constrained docking the N of the pyridine is is the 6' position.
By using rdFMCS.AtomCompare.CompareAnyHeavyAtom, the resulting MCS allows for matches between the Carbon & Nitrogen atoms in the Pyridine ring depending on the order with which the rdkit traverse. This can result in an undesired matching of non-symmetric ring systems as shown below.
If instead, we set the atomCompare=rdFMCS.AtomCompare.CompareElements we get the desired MCS
Describe the solution you'd like
It would be nice if in the configuration YAML we could set the options for the rdFMCS.FindMCS function.
Describe alternatives you've considered
The other solution for this would be to precompute this atom mapping myself and supply it through the core_atom_mapping_dict_list option. But this would require an extra step of external processing. For every ligand I would need to calculate this mapping, and then write out the corresponding YAML configuration. When we are looking at doing this process over many many jobs, that is a lot of extra configurations to output & complexity as compared to letting the user set this option themself.
Is your feature request related to a problem? Please describe.
When running a large amount of constrained docking runs with unidock2, the reference molecule has a Pyridine. With the current hard-coded methods in FindMCS for atom comparison results in flipped rings. Ex) the reference has the N of the pyridine in the 2' position, and after constrained docking the N of the pyridine is is the 6' position.
By using
rdFMCS.AtomCompare.CompareAnyHeavyAtom, the resulting MCS allows for matches between the Carbon & Nitrogen atoms in the Pyridine ring depending on the order with which the rdkit traverse. This can result in an undesired matching of non-symmetric ring systems as shown below.If instead, we set the
atomCompare=rdFMCS.AtomCompare.CompareElementswe get the desired MCSDescribe the solution you'd like
It would be nice if in the configuration YAML we could set the options for the rdFMCS.FindMCS function.
Describe alternatives you've considered
The other solution for this would be to precompute this atom mapping myself and supply it through the
core_atom_mapping_dict_listoption. But this would require an extra step of external processing. For every ligand I would need to calculate this mapping, and then write out the corresponding YAML configuration. When we are looking at doing this process over many many jobs, that is a lot of extra configurations to output & complexity as compared to letting the user set this option themself.