Re: [Rdkit-discuss] Unhashed info in hashed fingerprint
I've never tried it. What would be the motivation for doing so? This would, in general, increase similarity values for molecules, but it will also likely leads to more bit collisions in the fingerprints. Academic interest mainly. I wonder whether the distribution of similarities would just shift so everything was more similar or whether you'd find a more interesting change in the similarity distribution. I highly doubt however that it would improve retrieval rate in a virtual screen. Best, Nick Nicholas C. Firth | PhD Student | Cancer Therapeutics The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey | SM2 5NG T 020 8722 4033 | E nicholas.fi...@icr.ac.ukmailto:nicholas.fi...@icr.ac.uk | W www.icr.ac.ukhttp://www.icr.ac.uk/ | Twitter @ICRnewshttps://twitter.com/ICRnews Facebook www.facebook.com/theinstituteofcancerresearchhttp://www.facebook.com/theinstituteofcancerresearch Making the discoveries that defeat cancer [cid:image001.gif@01CE053D.51D3C4E0] On 21 Jul 2014, at 04:28, Greg Landrum greg.land...@gmail.commailto:greg.land...@gmail.com wrote: On Thu, Jul 17, 2014 at 10:04 AM, Nicholas Firth nicholas.fi...@icr.ac.ukmailto:nicholas.fi...@icr.ac.uk wrote: Thanks Greg, That's exactly what I needed. Excellent. I now have a question though, using modulo arithmetic means each environment only sets one bit in the FP (checking the code this looks true). Is there a reason why we only set a single bit with each environment? I mean we in the greater sense, has anyone ever looked at denser Morgan FP's (with a fixed radius)? I've never tried it. What would be the motivation for doing so? This would, in general, increase similarity values for molecules, but it will also likely leads to more bit collisions in the fingerprints. -greg The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.-- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] A case of the jaggies
Hi, Why are the structure images in the RDKit documentation nice and smooth but mine have the jaggies? What do I have to do to my PIL (or something?) for such smoothness? Thanks, Paul. -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] A case of the jaggies
Hi Paul, On Mon, Jul 21, 2014 at 3:36 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk wrote: Why are the structure images in the RDKit documentation nice and smooth but mine have the jaggies? The jagged lines are because the RDKit is using its fall-back mechanism for generating PNGs. To get the higher quality drawings, you need either the python cairo bindings (py2cairo) or the python aggdraw bindings installed. If you can, I'd suggest the cairo bindings; the aggdraw wrapper is no longer supported by its author. -greg -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] A case of the jaggies
On 21/07/14 17:22, Greg Landrum wrote: Hi Paul, On Mon, Jul 21, 2014 at 3:36 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk mailto:pems...@mrc-lmb.cam.ac.uk wrote: Why are the structure images in the RDKit documentation nice and smooth but mine have the jaggies? The jagged lines are because the RDKit is using its fall-back mechanism for generating PNGs. To get the higher quality drawings, you need either the python cairo bindings (py2cairo) or the python aggdraw bindings installed. If you can, I'd suggest the cairo bindings; the aggdraw wrapper is no longer supported by its author. py2cairo was just the ticket! (my sketcher uses cairo from C++) Thanks, Paul. -- Want fast and easy access to all the code in your enterprise? Index and search up to 200,000 lines of code with a free copy of Black Duck Code Sight - the same software that powers the world's largest code search on Ohloh, the Black Duck Open Hub! Try it now. http://p.sf.net/sfu/bds ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
