Using the chiralcenter and asymmetricatom calculations in Marvin 4.1.4 I'm getting N atoms identified as chiral that are not usually considered as chiral (due to fast inversion), as well as P centers of phosphates identified as asymmetric that are not chiral in practice due to delocalization. Is there any way to identify only chiral carbon centers?
What molecule did you use? I cannot reproduce it. See the attached screenshot made by Marvin 4.1.4
The definitions of the functions:
asymmetricAtomCount: "Calculates the number of asymmetric atoms. Asymmetric atoms have four different ligands."
I took your first example molecule. The two asymmetric atoms are highlighted in the attached screenshot. The nitrogen is not considered, since has no four different ligands.
chiralCenterCount: "Calculates the number of tetrahedral stereogenic centers. This function identifies two chiral centers in 1,4-dimethylcyclohexane, which does not contain asymmetric atoms."
The 3 chiral centers are highlighted in the attached screenshot. It includes a bridged nitrogen in the ring system. No fast N inversion in that special case!
So, nitrogen is tetrahedral, but has no four different ligands. Do you think, that this approach should be improved?
The above two functions return the "possibilities" only, not the actual number of stereo atoms. Anyway, do you need a function to calculate the number of stereo atoms? It is available in the API, but not yet in the TopologyAnalyser plugin. We've just added two new functions to retrieve the stereo configuration of given atoms and given double bonds. However no counter is added yet.
Regarding your second example molecule with the phosphates, I think, that you are right. The phosphorous atoms should not be considered in the asymmetric atom count calculation. Do you think, that in that case both the asymmetricAtomCount and the chiralCenterCount functions should return 4? Should we skip all phosphorous atoms or just the phosphate ones?