[Rdkit-discuss] generating scaffold trees
Dear RDKitters, has someone used the RDKit to generate scaffold trees from molecules as described in this paper: Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58 I know that this is possible with ScaffoldHunter and that there is a Pipeline Pilot component for it, but being able to do it in RDKit would fit especially well in my workflow... Kind regards and have a nice weekend, Axel -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Building mol manually
Hello RDKIT users, I have a molecular data structure with the connectivity of all atoms in my molecule. Is there a recommended way to build a mol object by manually specifying each atom and each bond perhaps relaxing the coordinates with a forcefield? Best, Eric -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Notes on building the latest RDKit
Hi Greg, It might be something at this end, but compiling the FMCS target with MSVC 11.0 and Boost 1.49 I have: C:\Boost\include\boost-1_49\boost/property_tree/detail/json_parser_read.hpp(105): error C2664: 'boost::property_tree::basic_ptreeKey,Data::push_back' : cannot convert parameter 1 from 'std::pair_Ty1,_Ty2' to 'const std::pair_Ty1,_Ty2 ' This looks like an MSVC versus Boost issue rather than anything related to RDKit. Regards, - Noel On 21 May 2015 at 03:22, Greg Landrum greg.land...@gmail.com wrote: Hi Noel, On Wed, May 20, 2015 at 10:54 AM, Noel O'Boyle baoille...@gmail.com wrote: This isn't really a bug report, just an FYI that may be helpful. I've been using Boost 1.49 until now to compile RDKit, but this is now too old. Specifically, the FMCS code chokes on it. Though we likely will start requiring a reasonably up-to-date version of boost at some point in the not-too-distant future, that hasn't happened yet. I have built the current release using boost 1.48 and a recent version of the code using v1.42, so the problem isn't boost in general. If you send me the error messages you are seeing, I may be able to help diagnose this. Also, I've been compiling on Windows with mingw-w64 (the fork of MinGW), and I needed to comment out the definition of struct timezone in the FMCS code (DebugTrace.h) as it's already present in mingw-w64's includes. I don't know if it's worth fixing but if so, maybe this link will help: http://quickgit.kde.org/?p=emerge.gita=commitdiffh=cffdf0eb0b8ed8f65c640ba33db03b8f7970a6f0hp=a3f18e16cb9fffa406de70c84b855843e10e98a7 (check_type_size(timezone HAVE_TIMEZONE_DEFINED)) Thanks for pointing that out. I'll take a look. Best, -greg -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building mol manually
Hi Eric, I don't know if there is a recommended way, but there's an easy way for sure! from rdkit import Chem m = Chem.Mol() #creates a blank molecule, can use an existing RDKit molecule though em = Chem.EditableMol(m) idx1 = em.AddAtom(Chem.Atom(6)) #this returns the RDKit index of the atom you're creating, which is atomic number 6 idx2 = em.AddAtom(Chem.Atom(6)) bondIdx = em.AddBond(idx1,idx2, Chem.BondType.SINGLE) #returns the RDKit index of the bond you're creating m = em.GetMol() Chem.SanitizeMol(m) from rdkit.Chem import AllChem AllChem.EmbedMolecule(m) AllChem.MMFFOptimizeMolecule(m) print Chem.MolToMolBlock(m) RDKit 3D 2 1 0 0 0 0 0 0 0 0999 V2000 0.75400.0. C 0 0 0 0 0 0 0 0 0 0 0 0 -0.75400.0. C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 M END 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 22 May 2015, at 15:22, Eric Smoll ericsm...@gmail.commailto:ericsm...@gmail.com wrote: Hello RDKIT users, I have a molecular data structure with the connectivity of all atoms in my molecule. Is there a recommended way to build a mol object by manually specifying each atom and each bond perhaps relaxing the coordinates with a forcefield? Best, Eric -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 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.-- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] generating scaffold trees
Hi all, Coincidentally, we had a chat about this with James the other day. Maybe the good colleagues at the ICR have implemented this already with RDKit? Nick? Cheers, g On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.de wrote: Dear RDKitters, has someone used the RDKit to generate scaffold trees from molecules as described in this paper: Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58 I know that this is possible with ScaffoldHunter and that there is a Pipeline Pilot component for it, but being able to do it in RDKit would fit especially well in my workflow... Kind regards and have a nice weekend, Axel -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] generating scaffold trees
We have an as yet unpublished method which is similar (but performs better) implemented in RDKit. However we use MOE for the scaffold tree. It would be quite easy to implement in RDKit , but I have a thesis to write! My suggestion would be to ask Nathan to write up the paper and then give you guys the code. 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.uk | W www.icr.ac.uk | Twitter @ICRnews From: George Papadatos [gpapada...@gmail.com] Sent: 22 May 2015 16:27 To: Axel Pahl Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] generating scaffold trees Hi all, Coincidentally, we had a chat about this with James the other day. Maybe the good colleagues at the ICR have implemented this already with RDKit? Nick? Cheers, g On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.demailto:axelp...@gmx.de wrote: Dear RDKitters, has someone used the RDKit to generate scaffold trees from molecules as described in this paper: Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58 I know that this is possible with ScaffoldHunter and that there is a Pipeline Pilot component for it, but being able to do it in RDKit would fit especially well in my workflow... Kind regards and have a nice weekend, Axel -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss 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. -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
