Patch/canon aam smiles #465
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…mparator to be used.
… By default it produces the exact same ordering as the current bit packing used in Canon. However it is much simpler to add optional invariants (e.g. AtomAtomMaps).
egonw
requested changes
Jun 30, 2018
| @@ -120,7 +123,7 @@ private Canon(int[][] g, long[] partition, boolean[] hydrogens, boolean symOnly) | |||
| /** | |||
| * Compute the canonical labels for the provided structure. The labelling | |||
| * does not consider isomer information or stereochemistry. This method | |||
| * allows provision of a custom array of initial invariants. | |||
| * allows provision of a custom array of initial initial. | |||
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Stupid IDE likes to change all occurrences by default. Should be initial invariants.
|
fixed |
egonw
approved these changes
Jun 30, 2018
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Resolves #274.
Atom Map Index now affects canonical ordering (if and only if output SMILES has atom maps). In this first example the two inputs (left of reaction) are the same except for their atom map numbering. They get different atom-maps.
The more useful
SmiFlavor.AtomAtomMapRenumberflag takes the same input, canonicalises without atom-atom maps and then renumbers them on output:If desired the caller can track the renumbering by parsing the output inspecting the output ordering array.