EZ isomerism and chirality #39
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| msg = (f"Chiral node {node} has {n} neighbors, which " | ||
| "is different than the four expected for " | ||
| "tetrahedral chirality. If the chiral center " | ||
| "contains hydrogen you need to set explicit_hydrogen " | ||
| "to True.") |
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Why can't there be an implicit hydrogen? That would by definition get the lowest priority, IIRC
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that's not how the open smiles definition works though; the chirality is not according to R/S but a local reference frame that is arbitrary viewed from the first atom which may or may not have lowest priority
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If one of the neighbor atoms is a hydrogen and is represented as an atomic property of the chiral center (rather than explicitly as [H]), then it is considered to be the first atom in the clockwise or anticlockwise accounting.
So if the smiles is: N[C@H](O)Br, then N=0, H=1, O=2, Br=3. i.e., look along N-C bond, and the rotation is H-O-Br
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No it is actually even more crazy:
N[C@H](O)Br --> here it is H0 N1 O2 Br3
N[C][H](O)Br --> here it is N0 H1 O2 Br3
the text reads:
If one of the neighbor atoms is a hydrogen and is represented as an atomic property of the chiral center (rather than explicitly as [H]), then it is considered to be the first atom in the clockwise or anticlockwise accounting. Now the question is how do we figure that out in the workflow?
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Yes, you're right.
Maybe have the central atom with implicit H itself as first "neighbour"?
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I think it is best to tag the node when it has the implicit hydrogen def. This does not change the fact that you cannot have implicit hydrogen here. The entire annotation only makes sense for when you have all hydrogen present.
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I still don't understand the "you cannot have implicit hydrogen". To me "implicit" means that the hydrogen is not an explicit node in the graph, but rather a node attribute
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I guess we should hide this chirality assignment behind a flag, which then requires explicit hydrogen atoms. Basically, the point being that the assignment of node indices makes only sense if these nodes are actually present.
address comments Co-authored-by: Peter C Kroon <[email protected]>
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@pckroon the current state is that I think it correctly interprets the chirality but there is no way I can figure out how to get an absolute assignment from this, which means it is nice but also useless |
Implementation for storing chirality and E/Z isomers across double bonds.
Chirallity is simply annotated onto the chiral center with the ordering of nodes giving the improper dihedral defining that center. Note that in order to get R/S classification one still needs to correctly interpret the chiral center. For building coordinates it should be enough to take the imporper dihedral angle defined by the atoms and give it a positive value.
E/Z isomers are annotated to the outermost atoms, which define the isomerism. The annotation consists of the 4 atoms that would form a proper dihedral angle whose value is either cis=0 degrees or trans=180 degrees.