Hi Christian, As long as your input SMILES contains stereochemistry, the fragmentation and indexing should keep it (so hopefully, it should just be the case of checking your input SMILES).
The output I get from the SMILES below (default settings): CC[C@H](Cl)Br a CCC[C@H](Cl)Br b is: CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[C@H](Cl)Br>>[*:1]CC[C@H](Cl)Br,[*:1]C CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[*:2]>>[*:1]CC[*:2],[*:1]C.[*:2][C@H](Cl)Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])Cl>>[*:1]C[C@@H]([*:2])Cl,[*:2]Br.[*:1]CC CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]CC>>[*:1]CCC,[*:1][C@H](Cl)Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[C@@H]([*:2])Cl>>[*:1]CC[C@@H]([*:2])Cl,[*:1]C.[*:2]Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])CC>>[*:1]C([*:2])CCC,[*:1]Cl.[*:2]Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C>>[*:1]CC,[*:1]C[C@H](Cl)Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1][C@@H](Cl)CC>>[*:1][C@@H](Cl)CCC,[*:1]Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])Br>>[*:1]C[C@@H]([*:2])Br,[*:2]Cl.[*:1]CC CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1][C@H](Cl)Br>>[*:1]C[C@H](Cl)Br,[*:1]CC CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C([*:2])[*:3]>>[*:1]CC([*:2])[*:3],[*:3]Cl.[*:2]Br.[*:1]CC CCC[C@H](Cl)Br,CC[C@H](Cl)Br,b,a,[*:1]C>>[*:1][H],[*:1]CC[C@H](Cl)Br CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1][C@@H](Br)CC>>[*:1][C@@H](Br)CCC,[*:1]Cl CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]C[C@@H]([*:2])Br>>[*:1]CC[C@@H]([*:2])Br,[*:1]C.[*:2]Cl CC[C@H](Cl)Br,CCC[C@H](Cl)Br,a,b,[*:1]CC([*:2])[*:3]>>[*:1]CCC([*:2])[*:3],[*:1]C.[*:3]Cl.[*:2]Br Thanks Jameed -----Original Message----- From: Christian Kramer [mailto:[email protected]] Sent: 11 November 2013 13:31 To: [email protected] Subject: [Rdkit-discuss] MMP and Stereo Perception Hi RD-Kitters, I have a question to all of you using the great MMP implementation from Jameed: How do you treat stereochemistry? When I run the programs, the output of the fragmentation and the matching does not contain any stereo information any more. Is there a way to keep this during the fragmentation? Do you add the stereo information after the matching and check whether the major parts or scaffolds of the two molecules have the same stereochemistry? Thanks for your ideas, Christian ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ________________________________ This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
