Re: [Rdkit-discuss] name generator
Thanks Greg, I agree, it certainly works for molecules, however I am testing whether cactus is able to provide names to molecular fragments as well. Things like methyl phosphinite (COP) are named after that. See: http://cactus.nci.nih.gov/chemical/structure/COP/iupac_name Do you have any hints on systematically naming molecular fragments? On 28 August 2013 05:53, Greg Landrum greg.land...@gmail.com wrote: On Tue, Aug 27, 2013 at 10:32 PM, Sergio Martinez Cuesta sermar...@gmail.com wrote: Oc(:[nH2]):[nH2] does not seem to be in the database http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name molcovert does not generate a name either. That's not actually a stable molecule. it is, at best, a piece of a molecule. OC(N)N works fine with the NCI lookup. What molecule are you trying to name? -greg -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
Hi Sergio,there may be random entries in the Resolver database behindhttp://cactus.nci.nih.gov/chemical/structure but definitelynothing systematic.MarkusOn Wed, 28 Aug 2013 07:54:26 -0400, Sergio Martinez Cuesta sermar...@gmail.com wrote:Thanks Greg,I agree, it certainly works for molecules, however I am testing whether cactus is able to provide names to molecular fragments as well. Things likemethyl phosphinite (COP) are named after that. See:http://cactus.nci.nih.gov/chemical/structure/COP/iupac_nameDo you have any hints on systematically naming molecular fragments? On 28 August 2013 05:53, Greg Landrum greg.land...@gmail.com wrote: On Tue, Aug 27, 2013 at 10:32 PM, Sergio Martinez Cuesta sermar...@gmail.com wrote: Oc(:[nH2]):[nH2] does not seem to be in the databasehttp://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name molcovert does not generate a name either.That's not actually a stable molecule. it is, at best, a piece of a molecule. OC(N)N works fine with the NCI lookup. What molecule are you trying to name?-greg -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] name generator
Hi, is there any IUPAC name generator in RDKit? e.g. for transforming CC(C)O into propan-2-ol ? Many thanks Sergio -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
thanks Greg, indeed, I only found commercial software for it http://www.chemaxon.com/marvin/help/applications/molconvert.html cheers Sergio On 27 August 2013 16:45, Greg Landrum greg.land...@gmail.com wrote: Dear Sergio, On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta sermar...@gmail.com wrote: is there any IUPAC name generator in RDKit? e.g. for transforming CC(C)O into propan-2-ol ? There is not. In fact, I'm not aware of any open source structure-name converters. -greg -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
Hi Sergio, here is a solution that uses a free web service offered by the NIH. It's independent of the rdkit but rather slow. Anyway, if you don't need to process too many molecules at a time or if time is not the critical factor maybe it could serve as an intermediate solution: import urllib2 def smi_to_iupac(smi): try: url = 'http://cactus.nci.nih.gov/chemical/structure/'+smi+'/iupac_name' iupacName = urllib2.urlopen(url).read() #print iupacName return iupacName except urllib2.HTTPError, e: print HTTP error: %d % e.code return None except urllib2.URLError, e: print Network error: %s % e.reason.args[1] return None except: print conversion failed for smiles + smi return None smiles = [CC(O)C,CC(=O)O, O=C2OCC(=C2\c1c1)\c3ccc(cc3)S(=O)(=O)C] for s in smiles: print smi_to_iupac(s) returns Propan-2-ol acetic acid 4-(4-methylsulfonylphenyl)-3-phenyl-5H-furan-2-one By the way, this service offers conversions between many different molecule formats/identifiers. I have used it in the past for CAS number look-up. Best, Markus On 08/27/2013 05:21 PM, Sergio Martinez Cuesta wrote: Hi, is there any IUPAC name generator in RDKit? e.g. for transforming CC(C)O into propan-2-ol ? Many thanks Sergio -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
I think this is not an actual structure to name converter but a look-up service based on a a predefined dictionary. If this is true, then it won't return anything for any novel/unseen structures. Give it a try and let us know. George. Sent from my giPhone On 27 Aug 2013, at 18:39, David Hall li...@cowsandmilk.net wrote: Not sure what software is behind it, but the NCI's Chemical Identifier Resolver may suit your needs. For your example, the URL: http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_name returns Propan-2-ol -David On Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta sermar...@gmail.com wrote: thanks Greg, indeed, I only found commercial software for it http://www.chemaxon.com/marvin/help/applications/molconvert.html cheers Sergio On 27 August 2013 16:45, Greg Landrum greg.land...@gmail.com wrote: Dear Sergio, On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta sermar...@gmail.com wrote: is there any IUPAC name generator in RDKit? e.g. for transforming CC(C)O into propan-2-ol ? There is not. In fact, I'm not aware of any open source structure-name converters. -greg -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
Hi, did you tried http://opsin.ch.cam.ac.uk/ ? Vladimir Chupakhin On Tue, Aug 27, 2013 at 6:48 PM, Markus Hartenfeller markus.hartenfel...@molecularhealth.com wrote: Hi Sergio, here is a solution that uses a free web service offered by the NIH. It's independent of the rdkit but rather slow. Anyway, if you don't need to process too many molecules at a time or if time is not the critical factor maybe it could serve as an intermediate solution: import urllib2 def smi_to_iupac(smi): try: url = ' http://cactus.nci.nih.gov/chemical/structure/'+smi+'/iupac_name' iupacName = urllib2.urlopen(url).read() #print iupacName return iupacName except urllib2.HTTPError, e: print HTTP error: %d % e.code return None except urllib2.URLError, e: print Network error: %s % e.reason.args[1] return None except: print conversion failed for smiles + smi return None smiles = [CC(O)C,CC(=O)O, O=C2OCC(=C2\c1c1)\c3ccc(cc3)S(=O)(=O)C] for s in smiles: print smi_to_iupac(s) returns Propan-2-ol acetic acid 4-(4-methylsulfonylphenyl)-3-phenyl-5H-furan-2-one By the way, this service offers conversions between many different molecule formats/identifiers. I have used it in the past for CAS number look-up. Best, Markus On 08/27/2013 05:21 PM, Sergio Martinez Cuesta wrote: Hi, is there any IUPAC name generator in RDKit? e.g. for transforming CC(C)O into propan-2-ol ? Many thanks Sergio -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today!http://pubads.g.doubleclick.net/gampad/clk?id=48897511iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
Yes, in this direction (structure to name) the Resolver is only a database lookup, in the other direction (name to structure), it first uses OPSIN (Daniel Lowe's library)which can resolve correct IUPAC names generically, if OPSIN "fails" it does a database lookup, too.MarkusNot sure what software is behind it, but the NCI's Chemical Identifier Resolver may suit your needs.For your example, the URL:http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_namereturns Propan-2-ol-DavidOn Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta sermar...@gmail.com wrote:thanks Greg,-- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
Oc(:[nH2]):[nH2] does not seem to be in the database http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name molcovert does not generate a name either. On 27 August 2013 18:54, Markus Sitzmann sitzm...@helix.nih.gov wrote: ** Yes, in this direction (structure to name) the Resolver is only a database lookup, in the other direction (name to structure), it first uses OPSIN (Daniel Lowe's library) which can resolve correct IUPAC names generically, if OPSIN fails it does a database lookup, too. Markus Not sure what software is behind it, but the NCI's Chemical Identifier Resolver may suit your needs. For your example, the URL: http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_name returns Propan-2-ol -David On Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta sermar...@gmail.com wrote: thanks Greg, -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] name generator
On Tue, Aug 27, 2013 at 10:32 PM, Sergio Martinez Cuesta sermar...@gmail.com wrote: Oc(:[nH2]):[nH2] does not seem to be in the database http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name molcovert does not generate a name either. That's not actually a stable molecule. it is, at best, a piece of a molecule. OC(N)N works fine with the NCI lookup. What molecule are you trying to name? -greg -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
