Dear member, Could someone please give me some advices about this problem? Thanks.
Shang From: shanghq...@hotmail.com Date: 2013-01-05 09:45 To: Craig James; openbabel-discuss CC: yuecaili Subject: Re: [Open Babel] substructure search problem Hi All, Thanks for Craig's quick response. I want to build a compound registration system with openbabel and Chemdraw (used as molecule edtior) . The problem I encountered was that when I draw the following two molecules as substructure query, the system returned the same result. Although these two molecules are the same actually, I think their substructure search result should be different. I have tried the following three kinds of command lines: 1) babel chem.fs -Squery.mol result.smi 2) babel chem.fs -s'[H]N([H])C1=CC=CC=C1' result.smi 3) babel chem.fs -s'[H]N([H])c1ccccc1' result.smi Command 1 could work but returned the same result. I have examined this command and found that both molecule 1 and 2 are converted to the same aromatic form:Nc1ccccc1. I think this is the reason of the same search result. Command 2 could not work (The reason should be what you said in the last email) Command 3 could work and give the right result, but another problem is that Chemdraw can only generate the Kekule SMILES like "[H]N([H])C1=CC=CC=C1" . If I convert it to aromatic form, the form will be "Nc1ccccc1", the "H" will be lost. It is strange that when I use molecule 3 as a query, openbabel can convert it to aromatic form: c1cccc(c1)[NH]. and give the correct search result. So It is seems that something wrong happened in the process of convertion. I would like to know what the problem is and how I could convert the mol format or Kekule SMILES to aromatic form correctly. Thanks & Best regards, Shang shanghq...@hotmail.com From: Craig James Date: 2013-01-04 03:13 To: shanghq...@hotmail.com; OpenBabel-discuss Subject: Re: [Open Babel] substructure search problem On Fri, Jan 4, 2013 at 4:25 AM, shanghq...@hotmail.com <shanghq...@hotmail.com> wrote: Dear All, I am using Openbabel to search substructure in my database. I found that when I converted the following two Kekule SMILES (1,2) generated by Chemdraw to aromatic form with Openbabel, I got the same result:Nc1ccccc1 1) NC1=CC=CC=C1 2) [H]N([H])C2=CC=CC=C2 but I think their aromatic form should be Nc1ccccc1 and [H]N([H])c1ccccc1, only then the substructure search result is right. Could anyone tell me what the problem is? how can I solve this problem. Thanks, You haven't given enough details. What does "search substructure in my database" mean? Are you using a babel command, or some other commercial or open-source database? If it's a babel command, what is the exact command you are using? I suspect the problem is that you're confusing SMARTS and SMILES. As SMILES, the Kekule and aromatic forms are equivalent. But as SMARTS (which is how substructure searches are interpreted), they are not the same. A Kekule form of the molecule generally won't find anything in a substructure search. Craig Best regards, Shang shanghq...@hotmail.com ------------------------------------------------------------------------------ Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnmore_122712 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
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