Hi Greg, > On Sat, Dec 18, 2010 at 6:27 AM, Greg Landrum > <[email protected]> wrote: > > I just checked in a set of changes that should get this > (mostly) working correctly. Here's a demonstration with Geldanamycin: > > In [7]: > smi=r'NC(=O)o...@h]1c(/C)=C/[...@h](C)[C@@H](O)[C@@H](OC)c...@h](C > )C\C2=C(/OC)C(=O)\C=C(\NC(=O)C(\C)=C\C=C/[C@@H]1OC)C2=O' > > In [8]: print Chem.CanonSmiles(smi) > COC1=C2C[C@@H](C)c...@h](OC)[...@h](O)[C@@H](C)/C=C(\C)[...@h](OC(N > )=O)[C@@H](OC)/C=C\C=C(/C)C(=O)NC(=CC1=O)C2=O
Thanks for looking into this so quickly! > It would be *really* useful to have some more real-world > cases like this one to use as tests. So if you happen to have > others you can send I would be quite happy to have them. On that note, I have added a comment to the bug tracker (https://sourceforge.net/tracker/?func=detail&aid=3139534&group_id=16013 9&atid=814650) - but was not sure how to attach a file (eg sdf) there, so apologies for it ending up on more lines than I intended... Also, I logged in with my google account, but it looks like it may not be clear who it is! The first two examples are two marine natural products that only differ in the geometry of the double bond in the medium ring. The final example is a cis- analogue that I synthesised during my PhD for which a crystal structure was also obtained. The stereochemistry in these systems is 'challenging' to say the least, so I thought they would make reasonable test cases. I should say that even for the cis- double bond cases, RDKit does a rather ugly job of the 2D depiction - but I am not sure if other depictors will perform much better... On a related note, I was keen to manually double-check the stereochemistry that had been assigned to each of the chiral centres (particularly the ones involving the 9-5 ring connections - as these are potentially troublesome), and found myself wishing there was a way to easily label a 2D depiction of the molecules with the atom ID. What I ended-up doing was the following: 1. Getting the R/S info + atomIdx back from RDKit (example output): >>> Chem.FindMolChiralCenters(mol) [(3, 'R'), (7, 'R'), (8, 'S'), (9, 'R'), (11, 'R'), (18, 'R'), (24, 'R')] 2. Opening the molfile in a program where I know how to label with atom IDs (pymol) 3. Check which atom is which manually (had to add 1 to the RDKit atomIdx values as they start at 0) then double-check with reference values. RDKit performed admirably - but I presume this is dependant on the quality of the wedge info coming in from the SDF(?) Kind regards James ______________________________________________________________________ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or [email protected]. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies Oakdene Court 613 Reading Road Winnersh, Berkshire RG41 5UA. Tel: +44 118 977 3133 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the "Company address and registration details" link at the bottom of the page.. ______________________________________________________________________ ------------------------------------------------------------------------------ Learn how Oracle Real Application Clusters (RAC) One Node allows customers to consolidate database storage, standardize their database environment, and, should the need arise, upgrade to a full multi-node Oracle RAC database without downtime or disruption http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
