Hi Greg, Greg wrote: > For what it's worth: the results here are definitely not > correct for the SMILES as provided. Atoms in SMILES that are > in square brackets have no implicit Hs, so [N+] actually has > zero hydrogens. I guess you actually provided the molecules > to MOE in some other form.
Oops - you're quite right - I converted them to MOL format with ChemAxon MolConverter. However, the point about implicit hydrogens for atoms in square brackets had completely passed me by - thanks! > Output with the SVN version of the RDKit: > > #------------------ > Smiles NOCount NHOHCount > CO 1 1 > C(=O)N 2 2 > O 1 2 > CN 1 2 > [OH3+] 1 3 > C[OH2+] 1 2 > [NH4+] 1 4 > C[NH3+] 1 3 > [NH2-] 1 2 > [OH-] 1 1 > C(=O)[NH-] 2 1 > #----------------- Looks great! 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.. ______________________________________________________________________ ------------------------------------------------------------------------------ All of the data generated in your IT infrastructure is seriously valuable. Why? It contains a definitive record of application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-d2dcopy2 _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
