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@jmohin Could you please share the code you are currently using? Unless the ring you wish to replace benzene with is symmetric (e.g., cyclohexane), you will also need to indicate which bond of the incoming ring you would like to condense with, or alternatively enumerate all possible condensation products. For example, replacing benzene with pyridine could be done in 6 different ways, leading to 6 different condensation products. |
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Here's an example which illustrates the problem: Yields an invalid/unkekulized molecule wherein the thiophene is singly-bonded to a fragment from the indole. I know there's six ways to attach a pyridine to the pyrrole resulting from deleting benzene in indole -- lets assume I know the atom indices I want to bond to on both the pyrrole and incoming pyridine. What functionality would I use? |
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I'm aware of the option to ReplaceSubstructs: |
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@jmohin Does the Chem.ReplaceCore() help? |
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When programmatically building molecules, it's often desirable to replace a fused ring group. For instance, if I want to replace the benzene ring in indole, I can easily identify it's substructure using GetSubstructureMatch() but when I replace it, it's singly-bonded to the remaining pyrrole group. What functionality, if any, allows me to specify HOW I substitute a substructure?
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