From chemistry-request@ccl.net Sat Apr 23 07:20:44 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3NBKbL5005865 for >ccl.net>; Sat, 23 Apr 2005 07:20:37 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3NBKbuD005864 for chemistry<>ccl.net; Sat, 23 Apr 2005 07:20:37 -0400 Date: Sat, 23 Apr 2005 07:20:37 -0400 Message-Id: <200504231120.j3NBKbuD005864<>server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request<>ccl.net using -f From: "Raji, , Stephen" >chem.iitb.ac.in> To: chemistry<>ccl.net X-Web-Message-Number: 050422011723-27650 Subject: W:Help to obtain orbital diagram using CACAO X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi All, We are using G98 and CACAO softwares for our theoretical studies. But we are unable to get orbital diagram from CACAO as mentioned in its manual. Can anybody help us to get the proper diagram. I am including one sample input, TITL SJ-1-1 PAR 0 d KEYW EL WF RO NC HM CELL ATOM N 0.636435, -0.00061, -0.568066 ATOM O 1.405423, -0.000782, 1.593398 ATOM O 3.183605, -0.000164, -1.383972 ATOM C -1.452972, -1.190218 , -0.082338 ATOM C -2.802214, -1.207024 , 0.239365 ATOM C -3.475148, 0.00134, 0.401081 ATOM C -2.801026, 1.209144, 0.239581 ATOM C -1.4519, 1.190967, -0.082154 ATOM C -0.745107, -0.000011, -0.248471 ATOM C 1.603921, -0.000763, 0.384763 ATOM C 3.031493, -0.000634, -0.173257 ATOM C 4.15263, -0.000774, 0.823333 ATOM H -3.312084, -2.13938, 0.361889 ATOM H -3.309924, 2.141913, 0.362467 ATOM H 4.07862, -0.869045, 1.465203 ATOM H -4.516165, 0.001826, 0.651985 END Hoping help from kind hearts. Thanks in advance. ************************************************* Raji Stephen JRF, Dept. of Chemistry IIT Bombay, India http://www.chem.iitb.ac.in/~pghosh/RS.htm ************************************************* From chemistry-request@ccl.net Fri Apr 22 19:02:09 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3MN28JC024017 for ; Fri, 22 Apr 2005 19:02:08 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3MN28ee024016 for chemistry=at=ccl.net; Fri, 22 Apr 2005 19:02:08 -0400 Date: Fri, 22 Apr 2005 19:02:08 -0400 Message-Id: <200504222302.j3MN28ee024016=at=server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request=at=ccl.net using -f From: "Sean, , OBrien" To: chemistry=at=ccl.net X-Web-Message-Number: 050422190134-23982 Subject: W:Substructure matching X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi All, I am searching for some software that will help me to identify the atoms within a molecule that match a query substructure. For example I wish to find which atoms belong to an imidazole ring. The aim is to extract the matching substructure while keeping the original atomic coordinates. I know that several substructure matching routines exist, and some are even freely available but I haven't found any that return the identity of the matching atoms. Some return the whole molecule or a tally of how many times the substructure is present. They obviously "know" which atoms match but I am having difficulty identifying them. Similarly matching strings in SMILES doesn't return the initial atom ids. I would be very grateful for any routines that do this, or that can be modified for this purpose, Many Thanks, Sean O'Brien From chemistry-request@ccl.net Sat Apr 23 13:49:46 2005 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3NHnd6I026164 for ; Sat, 23 Apr 2005 13:49:40 -0400 Received: from caracas-3738.adsl.interware.hu ([213.178.114.154] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.50 #1 (Debian)) id 1DPNY8-0002YN-I1; Sat, 23 Apr 2005 18:32:08 +0200 Message-ID: <000901c5482a$cf4921f0$6401a8c0@cthulhu> From: "Tamas E. Gunda" To: "Raji, , Stephen" , References: <200504231120.j3NBKbuD005864=at=server.ccl.net> Subject: Re: CCL:W:Help to obtain orbital diagram using CACAO Date: Sat, 23 Apr 2005 18:35:00 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1478 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1478 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j3NHnk6I026176 The molecule contains less hydrogens than necessary. Is it surely correct? Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu ----- Original Message ----- From: "Raji, , Stephen" To: Sent: Saturday, April 23, 2005 12:20 PM Subject: CCL:W:Help to obtain orbital diagram using CACAO > Hi All, > > We are using G98 and CACAO softwares for our theoretical studies. But we are unable to get orbital diagram from CACAO as mentioned in its manual. Can anybody help us to get the proper diagram. I am including one sample input, > > TITL SJ-1-1 > PAR 0 d > KEYW EL WF RO NC HM > CELL > ATOM N 0.636435, -0.00061, -0.568066 > ATOM O 1.405423, -0.000782, 1.593398 > ATOM O 3.183605, -0.000164, -1.383972 > ATOM C -1.452972, -1.190218 , -0.082338 > ATOM C -2.802214, -1.207024 , 0.239365 > ATOM C -3.475148, 0.00134, 0.401081 > ATOM C -2.801026, 1.209144, 0.239581 > ATOM C -1.4519, 1.190967, -0.082154 > ATOM C -0.745107, -0.000011, -0.248471 > ATOM C 1.603921, -0.000763, 0.384763 > ATOM C 3.031493, -0.000634, -0.173257 > ATOM C 4.15263, -0.000774, 0.823333 > ATOM H -3.312084, -2.13938, 0.361889 > ATOM H -3.309924, 2.141913, 0.362467 > ATOM H 4.07862, -0.869045, 1.465203 > ATOM H -4.516165, 0.001826, 0.651985 > END > > Hoping help from kind hearts. > Thanks in advance. > > ************************************************* > Raji Stephen > JRF, Dept. of Chemistry > IIT Bombay, India > http://www.chem.iitb.ac.in/~pghosh/RS.htm > ************************************************* > From chemistry-request@ccl.net Sat Apr 23 13:36:12 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3NHaBUs025486 for ; Sat, 23 Apr 2005 13:36:11 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3NHaBRg025485 for chemistry|at|ccl.net; Sat, 23 Apr 2005 13:36:11 -0400 Date: Sat, 23 Apr 2005 13:36:11 -0400 Message-Id: <200504231736.j3NHaBRg025485|at|server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request|at|ccl.net using -f From: "Hector, , Ismail" To: chemistry|at|ccl.net X-Web-Message-Number: 050423133419-25345 Subject: W:carbon nanotube with cap geometry X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi CCL.net, Would anyone have the cartesian coordinates or z-matrix for any carbon nanotube (of any length or chirality) with an endcap on it? I tried searching the web for one, but I could only find open-ended ones. Thanks, Hector From chemistry-request@ccl.net Sat Apr 23 13:06:54 2005 Received: from moutng.kundenserver.de (moutng.kundenserver.de [212.227.126.187]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3NH6mT4023831 for ; Sat, 23 Apr 2005 13:06:48 -0400 Received: from vpn82-34.vpn.uni-koeln.de[134.95.82.34] (helo=[134.95.82.34]) by mrelayeu.kundenserver.de with ESMTP (Nemesis), id 0ML29c-1DPN591EG0-0007QA; Sat, 23 Apr 2005 18:02:11 +0200 Message-ID: <426A7182.7030409|at|uni-koeln.de> Date: Sat, 23 Apr 2005 18:02:10 +0200 From: Christoph Steinbeck User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "Sean, , OBrien" CC: chemistry|at|ccl.net Subject: Re: CCL:W:Substructure matching References: <200504222302.j3MN28ee024016|at|server.ccl.net> In-Reply-To: <200504222302.j3MN28ee024016|at|server.ccl.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Provags-ID: kundenserver.de abuse|at|kundenserver.de login:a68c2fec921736b0ba6af652eae00843 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi Brian, check out our open source Java library "The Chemistry Development Kit (CDK)" [1]. It lives at http://cdk.sourceforge.net. The class UniversalIsomorphismChecker can do full graph matching, subgraph searches and Maximum Common Subgraph (MCS) matching. On demand, it provides you with a map of matching atoms or bonds in the two graphs under inspection. The CDK comes with an extended set of unit tests which are good examples of how to do certain thing. Below, you also find a small code example > from the tests, showing how to get a subgraph atom map [2]. Cheers, Chris [1] Steinbeck, C.; Han, Y. Q.; Kuhn, S.; Horlacher, O.; Luttmann, E. et al. The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics. Journal of Chemical Information and Computer Sciences 2003, 43, 493-500. http://dx.doi.org/10.1021/ci025584y [2] Example for getting a subgraph atom map. Note that this is a test case. The test makes two molecules, indole and pyrrole, in a predefined way. The arrays result1 and result2 contain the expected (known) mapping of the atom numbers in pyrrole to the atom numbers in indole. The assertions at the end check if the test leads to the expected result. public void testGetSubgraphAtomsMaps() throws java.lang.Exception { int[] result1 = {6, 5, 7, 8, 0}; int[] result2 = {3, 4, 2, 1, 0}; AtomContainer mol = MoleculeFactory.makeIndole(); AtomContainer frag1 = MoleculeFactory.makePyrrole(); HueckelAromaticityDetector.detectAromaticity(mol); HueckelAromaticityDetector.detectAromaticity(frag1); List list = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol, frag1); List first = (List)list.get(0); for (int i = 0; i < first.size(); i++) { RMap rmap = (RMap)first.get(i); assertEquals(rmap.getId1(), result1[i]); assertEquals(rmap.getId2(), result2[i]); } } -- Priv. Doz. Dr. Christoph Steinbeck (c.steinbeck|at|uni-koeln.de) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. Sean, , OBrien wrote: > I am searching for some software that will help me to identify the atoms within a molecule that match a query substructure. For example I wish to find which atoms belong to an imidazole ring. The aim is to extract the matching substructure while keeping the original atomic coordinates. > > I know that several substructure matching routines exist, and some are even freely available but I haven't found any that return the identity of the matching atoms. Some return the whole molecule or a tally of how many times the substructure is present. They obviously "know" which atoms match but I am having difficulty identifying them. Similarly matching strings in SMILES doesn't return the initial atom ids. > > I would be very grateful for any routines that do this, or that can be modified for this purpose, From chemistry-request@ccl.net Sat Apr 23 16:02:27 2005 Received: from rwcrmhc14.comcast.net (rwcrmhc14.comcast.net [216.148.227.89]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3NK2MHx001114 for ; Sat, 23 Apr 2005 16:02:22 -0400 Received: from xempc (pcp09493545pcs.nrockv01.md.comcast.net[69.140.196.150]) by comcast.net (rwcrmhc14) with SMTP id <20050423185934014009mgd0e>; Sat, 23 Apr 2005 18:59:35 +0000 From: "Wolf-D. Ihlenfeldt" To: "'Sean, , OBrien'" Cc: Subject: RE: W:Substructure matching Date: Sat, 23 Apr 2005 14:59:10 -0400 Organization: Xemistry GmbH Message-ID: <012f01c54836$93fd44d0$6401a8c0@XemPC> Sean, This can easily be done in the academic version of the CACTVS chemoinformatics toolkit (www.xemistry.com/academic) with a very small script, similar to the sample in the attachment. > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request |a| ccl.net] On Behalf Of Sean, , OBrien > Sent: Friday, April 22, 2005 7:02 PM > To: chemistry |a| ccl.net > Subject: CCL:W:Substructure matching > > > Hi All, > > I am searching for some software that will help me to > identify the atoms within a molecule that match a query > substructure. For example I wish to find which atoms belong > to an imidazole ring. The aim is to extract the matching > substructure while keeping the original atomic coordinates. > > I know that several substructure matching routines exist, and > some are even freely available but I haven't found any that > return the identity of the matching atoms. Some return the > whole molecule or a tally of how many times the substructure > is present. They obviously "know" which atoms match but I am > having difficulty identifying them. Similarly matching > strings in SMILES doesn't return the initial atom ids. > > I would be very grateful for any routines that do this, or > that can be modified for this purpose, > > Many Thanks, > > Sean O'Brien > From chemistry-request@ccl.net Sat Apr 23 20:41:22 2005 Received: from fujitsu0.fujitsu.com (fujitsu0.fujitsu.com [192.240.0.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3O0fGI2013338 for ; Sat, 23 Apr 2005 20:41:17 -0400 Received: from fujitsu0.fujitsu.com (localhost [127.0.0.1]) by fujitsu0.fujitsu.com (8.13.1/8.13.1) with ESMTP id j3NNVeiE011143; Sat, 23 Apr 2005 16:31:40 -0700 (PDT) Received: from fujitsui.fna.fujitsu.com ([133.164.253.1]) by fujitsu0.fujitsu.com (8.13.1/8.13.1) with ESMTP id j3NNVdcM011138; Sat, 23 Apr 2005 16:31:39 -0700 (PDT) Received: from cachemail.fnanic.fujitsu.com (localhost [127.0.0.1]) by fujitsui.fna.fujitsu.com (8.13.2/8.13.2) with ESMTP id j3NNVcQ4026179; Sat, 23 Apr 2005 16:31:38 -0700 (PDT) Received: from daveg-lifebook.cachesoftware.com (localhost [127.0.0.1]) by cachemail.fnanic.fujitsu.com (8.13.2/8.13.2) with ESMTP id j3NNXT09024640; Sat, 23 Apr 2005 16:33:34 -0700 (PDT) Message-Id: <6.2.1.2.0.20050423162603.01dd41f0@133.164.253.31> X-Mailer: QUALCOMM Windows Eudora Version 6.2.1.2 Date: Sat, 23 Apr 2005 16:31:09 -0700 To: "Hector, , Ismail" , chemistry () ccl.net From: David Gallagher Subject: Re: CCL:W:carbon nanotube with cap geometry In-Reply-To: <200504231736.j3NHaBRg025485 () server.ccl.net> References: <200504231736.j3NHaBRg025485 () server.ccl.net> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net H56 Hect63r, I have a C460 with both ends closed, as CAChe or pdb format. Let me know which you want and can email it to you. Regards David Gallagher At 10:36 AM 4/23/2005, Hector, , Ismail wrote: >Hi CCL.net, > > Would anyone have the cartesian coordinates or z-matrix for any > carbon nanotube (of any length or chirality) with an endcap on it? I > tried searching the web for one, but I could only find open-ended ones. > >Thanks, >Hector > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY () ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST () ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+