Issue #41 new

Rewrite alpha/beta stereochemistry assignment handling code

Daniel Lowe
repo owner created an issue

Currently alpha/beta stereo are treated like other stereochemistry terms and applied to the stereoparent after it has been constructed. Alpha/beta stereochemistry indicates the position of a group relative to the plane of the unsubstituted parent, hence to do this in general the term must be associated with the atom through which the group that was added attached. [The current implementation makes the assumption that the non-hydrogen is the atom added and hence fails when a position is double substituted] Proposal: Keep alpha/beta stereochemistry in much the way it is originally parsed. In bridge assignment, suffix assignment and substitutent attachment add consider being preceded either by a locant or a stereochemistry element of this type. Once the group is attached, the stereochemistry term should be moved in front of the stereoparent and associanted with the atomid of the atom that attached to the stereoparent.

Bracketed alpha/beta stereochemistry can be handled as it is currently. Alpha/beta stereo directly in front of a stereoparent should probably be recognized at the point that it is currently applied.

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