#85 Stereochemistry not inserted as defined in SMIRKS

[Martin Gütlein]

The ambit library does only retain existing stereo-info in the compounds, but does not introduce stereo-chemistry as defined in the SMIRKS. It would be great if you could add this feature to your library. Two examples are given below.

Examples are also provided as short, self-contained Java Unit Test:
https://github.com/mguetlein/TestAmbitSmarts/blob/master/src/test/java/org/kramerlab/test/TestAmbit.java

String smirks = "[#8-:11]-[#6:9](=[O:10])-[#6:1]([H])([H])-[c:2]1[c:3]([H])[c:4]([H])[c:5]([H])[c:6]([H])[c:7]([H])1>>[#8-:11]-[#6:9](=[O:10])\\[#6:1]([H])=[#6:2]-1\\[#6:7]([H])([H])-[#6:6]([H])=[#6:5]([H])-[#6:4]([H])=[#6:3]([H])-[#8]-1";
String smi = "C1=CC=C(C=C1)CC(=O)[O-]";
String expectedSmiles = "[O-]C(=O)\\C=C1\\CC=CC=CO1");

String smirks = "[H][C:2]([#6:5]([H])([H])([H]))([#1,#6:4])!@-[#6:1]([H])([H])-[#6:3](-[#8-:8])=[O:6]>>[#6:5]([H])([H])([H])\\[#6:2](-[#1,#6:4])!@=[#6:1]\\[#6:3](-[#8-:8])=[O:6]";
String smi = "CCC(C)CC(=O)[O-]";
String expectedSmiles = "CC\\C(C)=C/C([O-])=O";

[Martin Gütlein]

envipath ids:
rule4230
u145861

rule2844
u114856

[Nikolay Kochev]

Already fixed in Ambit-Smarts library.

[Nina Jeliazkova]

Fixed in 3.0.3-SNAPSHOT latest revision 7696