Re: [Rdkit-discuss] Canonical smiles for medium and large rings?
Dear James, On Fri, Dec 17, 2010 at 5:35 PM, James Davidson wrote: > > I have been investigating an issue that a colleague of mine identified. > He was working with the RDKit Canon Smiles node in Knime, and found that > for the natural product, Geldanamycin, the double-bond geometry > information was being lost during canonicalisation. I repeated this > result outside of knime: > > from rdkit import Chem > from rdkit.Chem import AllChem > 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' AllChem.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=CC=C(C)C(=O)NC(=CC1=O)C2=O' > > > The simpler example below may be better: > smi1 = r'O1CC/C=C\1' # cyclic ether smi2 = r'OCC/C=C\' # corresponding acyclic alcohol > AllChem.CanonSmiles(smi1) > 'C1C=CCCOCCC1' -> stereochemistry lost AllChem.CanonSmiles(smi2) > '/C=C\\CCO' -> stereochemistry retained >> > So, I am guessing that double-bonds in rings are being 'ignored'(?) by > the canonicaliser? It's actually being done by the molecule cleanup code that is run when a molecule is read. The result is, as far as you're concerned, the same though: there's no stereochemistry on ring double bonds. > For 'classic' aliphatic systems, double-bonds in > 3-7-membered rings can only sensibly exist in the cis orientation, so > 'ignoring' them would be ok. However, for 8-membered and above, cis or > trans are certainly both possible, so it becomes more important to keep > track - particularly if canonical smiles are being used to check for > unique structures, as my colleague was doing with the geldanamycin > example above. yeah, that's clear: for larger ring systems the information should be preserved. That's very easy to do. The more difficult part is going to be making sure the output is actually canonical. I've entered a bug for this (https://sourceforge.net/tracker/?func=detail&aid=3139534&group_id=160139&atid=814650) and I'll take a look to try and get it fixed (and correct). It would be helpful to have some additional test cases; I will generate some, but if you have some examples you could send (or attach to the bug report) it would be quite helpful. Thanks for the report, -greg -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Canonical smiles for medium and large rings?
Dear All, I have been investigating an issue that a colleague of mine identified. He was working with the RDKit Canon Smiles node in Knime, and found that for the natural product, Geldanamycin, the double-bond geometry information was being lost during canonicalisation. I repeated this result outside of knime: from rdkit import Chem from rdkit.Chem import AllChem >>> 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' >>> AllChem.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=CC=C(C)C(=O)NC(=CC1=O)C2=O' The simpler example below may be better: >>> smi1 = r'O1CC/C=C\1' # cyclic ether >>> smi2 = r'OCC/C=C\' # corresponding acyclic alcohol >>> AllChem.CanonSmiles(smi1) 'C1C=CCCOCCC1' -> stereochemistry lost >>> AllChem.CanonSmiles(smi2) '/C=C\\CCO' -> stereochemistry retained So, I am guessing that double-bonds in rings are being 'ignored'(?) by the canonicaliser? For 'classic' aliphatic systems, double-bonds in 3-7-membered rings can only sensibly exist in the cis orientation, so 'ignoring' them would be ok. However, for 8-membered and above, cis or trans are certainly both possible, so it becomes more important to keep track - particularly if canonical smiles are being used to check for unique structures, as my colleague was doing with the geldanamycin example above. Any thoughts / suggestions are much appreciated as always! 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 postmas...@vernalis.com. 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.. __ -- Lotusphere 2011 Register now for Lotusphere 2011 and learn how to connect the dots, take your collaborative environment to the next level, and enter the era of Social Business. http://p.sf.net/sfu/lotusphere-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
