Feature request: Java API for retrieving atom references for a tetrahedral stereocentre

[daniel_...@yahoo.co.uk]

Is it possible to add a method to retrieve the atoms that are being used to define stereochemistry.

Essentially the opposite of addStereocenter(type, idx1, idx2, idx3, [idx4])
that would allow retrieval of what atoms were used.

Although I haven't verified this, it looks like this functionality actually is available via the C++ API using the getPyramid function
http://ctr.wikia.com/wiki/Change_stereochemistry_of_certain_atoms_in_SMILES_file

If the stereoconfiguration is not simply a product of the order of the idxs and a parity flag is used that should also be retrievable (cf. CML's implementation of stereochemistry)

[Mikhail Rybalkin]

Hello Daniel,

Sorry for such a long time taken to implement your request. In the Indigo 1.1.10 you can find stereocenterPyramid method that returns 4 integer array with atom indices that first three of them are in a ascending ordering according to clockwise direction if looking from the 4th atom. Also -1 corresponds to an implicit hydrogen (or lone pair in case Nitrogen stereocenter).

Best regards,

Mikhail