Thanks Greg, Greg wrote: > Ah yes, the depictions that you get look rather silly, no?
Yes they do! > You're doing it correctly; no worries there. The problem is > that most pieces of chemical drawing software generate 2D > coordinates for molecules such that a C-C single bond is 1.0A > long. The RDKit, on the other hand, sets the C-C single bond > to be 1.5A long. The consequence is a depiction with a core > that's smaller than it should be. I was using ISISDraw for sketching the core motif. It seems that the single-bond length (from the Origdraw settings) is ~ 0.825 A (!) So I modified the scalar to 1.818 (1.5/0.825) in your code and it works beautifully! > It should be possible to specify the scale used in the RDKit > depictions so that these contortions are not necessary. I > will put a feature request in for this and get it in the next version. Thanks for this - I certainly think this would be a worthwhile feature. What I may implement in the meantime is running through all the bonds of type SINGLE in the core molecule, taking the average, then using 1.5/(average) as the scalar to protect against differing user settings! 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.. ______________________________________________________________________ ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
