From chemistry-request@ccl.net Mon Jul 4 04:04:18 2005 Received: from ppsw-9.csi.cam.ac.uk (ppsw-9.csi.cam.ac.uk [131.111.8.139]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6484C6d018381 for ; Mon, 4 Jul 2005 04:04:13 -0400 X-Cam-SpamDetails: Not scanned X-Cam-AntiVirus: No virus found X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ Received: from sandwi.ch.cam.ac.uk ([131.111.121.130]:47550) by ppsw-9.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.159]:25) with esmtp id 1DpLvz-0005u3-Un (Exim 4.51) (return-path ); Mon, 04 Jul 2005 09:04:07 +0100 Subject: Re: CCL:Two Questions about finding code From: "Noel O'Boyle" To: chemistry-.at.-ccl.net Cc: "Andrew D. Fant" In-Reply-To: <42C55A9D.2040604-.at.-pobox.com> References: <42C55A9D.2040604-.at.-pobox.com> Content-Type: text/plain Date: Mon, 04 Jul 2005 09:04:06 +0100 Message-Id: <1120464246.23142.203.camel-.at.-sandwi.ch.cam.ac.uk> Mime-Version: 1.0 X-Mailer: Evolution 2.0.4 Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net I have used JOELib [1] and the CDK [2] (the Chemistry Development Kit) to calculate molecular descriptors. Both of these programs are open-source, and written in Java. They are intended to be used as libraries for programmers. If you don't want to use Java, you can access these programs through Python (either with Jython or JPype) - for a brief tutorial see my article in the CDK News [3]. [1] JOELib: http://www-ra.informatik.uni-tuebingen.de/software/joelib/ [2] CDK: http://almost.cubic.uni-koeln.de/cdk/cdk_top [3] "Accessing the CDK using Python", CDK News, 2(2), 40, 2005 : http://almost.cubic.uni-koeln.de/cdk/cdk_top/cdk_news/ Regards, Noel. On Fri, 2005-07-01 at 11:00 -0400, Andrew D. Fant wrote: > Good Morning all, > > I have two questions about source code I am looking for and would > appreciate any help that anyone can offer. > > 1) Can anyone recommend a good source for code that can calculate > various molecular descriptors (a la QSAR/QSPR use)? Open Source would > be really nice, though I would settle for anything that I don't actually > have to pay for. Fortran or Python would be easiest for me to read, but > I am not fussy. This is just for a personal project of mine where I > would rather borrow code for the descriptors that has already been > tested to some degree than roll my own from scratch > > 2) Has anyone got any knowledge of the python bindings for openbabel? > I keep hearing rumors of their existence but confirmed sightings are > rare. Any pointers to actual code and download sites would be really > spiffy if possible. > > Thanks for your time and help. > > Andy Fant > > > -= 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-.at.-ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-.at.-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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Mon Jul 4 00:59:43 2005 Received: from mx1.ustc.edu.cn (ns.ustc.edu.cn [202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j644xbEW005481 for ; Mon, 4 Jul 2005 00:59:38 -0400 Received: from dxl ([210.45.66.65]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j644tef21765 for ; Mon, 4 Jul 2005 12:55:40 +0800 Message-Id: <200507040455.j644tef21765|at|mx1.ustc.edu.cn> Date: Mon, 4 Jul 2005 12:57:35 +0800 From: "Ding Xunlei" Reply-To: dxl|at|ustc.edu.cn To: "chemistry" Subject: how to read orbitals in molpro Organization: University of Science and Technology of China X-mailer: Foxmail 5.0 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="gb2312" X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_WHOIS,MIME_BASE64_BLANKS,MIME_BASE64_TEXT autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id j644xhEW005502 Dear chemistry#: I have these definitions in the molpro calculation: -d/var/tmp/$LOGNAME \ -I/var/tmp/$LOGNAME \ -W$HOME/wfu \ But I find that nothing have been saved in these directories. Then how can I read orbitals from files like 2100.2? In a molpro job which has different calculations, I know that the later calculations will use the orbitals before them. But how to read orbitals from other molpro jobs? Thank you for your help! Yours sincerely, Ding Xunlei 2005-07-04 ______________________________________________ From chemistry-request@ccl.net Mon Jul 4 08:45:42 2005 Received: from web33203.mail.mud.yahoo.com (web33203.mail.mud.yahoo.com [68.142.206.101]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j64Cjbs5008476 for ; Mon, 4 Jul 2005 08:45:38 -0400 Received: (qmail 20046 invoked by uid 60001); 4 Jul 2005 12:45:37 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=FBXVoS0XyrR+cNmqYP6uNZDaEZkUmeP5+gOP2Wjuea3P1doekOiSECBvXilJE5/1Sjl0ilXfMrLRIP8iT6nOUpfwyngdzEsHyPGYp2ri7tfcYPpJAlUk/W0XbsBVjzorw1ouiPt9y5/iOL4LvhxC2FYIGCGZNMWrzcJrfOU5tRg= ; Message-ID: <20050704124537.20044.qmail-.at.-web33203.mail.mud.yahoo.com> Received: from [139.184.30.16] by web33203.mail.mud.yahoo.com via HTTP; Mon, 04 Jul 2005 05:45:36 PDT Date: Mon, 4 Jul 2005 05:45:36 -0700 (PDT) From: Ricardo Oliveira Subject: CCL:How to define HOMO-LUMO gap in open shell system ? To: chemistry-.at.-ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear all, I have noticed that some excitation energies , in closed shell systems, have energies similar to the HOMO-LUMO gap. Considering that the term 'HOMO-LUMO gap' is not very appropriate for open shell systems, how can we do a rough estimate of the excitation energies in this case? Shall they be somewhat similar to the homo-somo(singly occupied orbital) gap? Can the gaps mentioned by Ding Xunlei,on his CCL communication, have any meaning at all? Thanks Ricardo O Esplugas Dept of Chemistry Sussex University UK __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Mon Jul 4 19:22:21 2005 Received: from cmsout01.mbox.net (cmsout01.mbox.net [165.212.64.31]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j64NMFEh021230 for ; Mon, 4 Jul 2005 19:22:15 -0400 Received: from cmsout01.mbox.net (cmsout01.mbox.net [165.212.64.31]) by cmsout01.mbox.net (Postfix) with ESMTP id 0134878068 for ; Mon, 4 Jul 2005 22:34:55 +0000 (GMT) Received: from uadvg131.cms.usa.net [165.212.11.131] by cmsout01.mbox.net via smtad (C8.MAIN.3.21U); Mon, 04 Jul 2005 22:34:56 GMT X-USANET-Source: 165.212.11.131 IN david.w.miller * stanfordalumni.org uadvg131.cms.usa.net X-USANET-MsgId: XID727JgDwI57600X01 Received: from cmsweb15.cms.usa.net [165.212.8.1] by uadvg131.cms.usa.net (ASMTP/) via mtad (C8.MAIN.3.21E) with ESMTP id 846JgDwI20468M31; Mon, 04 Jul 2005 22:34:53 GMT X-USANET-Auth: 165.212.8.1 AUTO david.w.miller * stanfordalumni.org cmsweb15.cms.usa.net Received: from 68.35.94.182 [68.35.94.182] by cmsweb15.cms.usa.net (USANET web-mailer CM.0402.7.24); Mon, 04 Jul 2005 22:34:52 -0000 Date: Mon, 04 Jul 2005 15:34:52 -0700 From: David Miller To: Subject: CCL: new ActiveX/DLL product X-Mailer: USANET web-mailer (CM.0402.7.24) Mime-Version: 1.0 Message-ID: <137JgDwI16512S15.1120516492 * cmsweb15.cms.usa.net> Content-Type: text/plain; charset=ISO-8859-1 Z-USANET-MsgId: XID846JgDwI20468X31 X-Spam-Status: No, score=1.6 required=5.0 tests=FORGED_RCVD_HELO, RCVD_NUMERIC_HELO autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j64NMLEh021239 Sage Informatics has just released ChemTKX, an ActiveX and DLL product allowing users to incorporate features of the ChemTK desktop product into their own Windows programs. ChemTKX features include: - Create molecule objects from common text representations such as Daylight Smiles and MDL MOL/SDF, or from scratch using intuitive commands such as CreateAtom and CreateBond - Perform substructure searches using Daylight Smarts syntax or ChemTK Encoded syntax, among others - Convert molecule objects to JPEG or BMP image files, with or without structural highlighting - Generate and display molecule depictions within specified windows, with or without structural highlighting - Generate canonical Smiles representations of molecules - Generate maximum common substructures (MCSs) - Generate 2D atomic coordinates for a molecule - Convert molecules from one representational format to another Visit http://www.sageinformatics.com/chemtkx.html to download the ChemTKX evaluation software and release notes. Best Regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller * sageinformatics.com ____________________________________________________________________ From chemistry-request@ccl.net Mon Jul 4 19:22:51 2005 Received: from cmsout02.mbox.net (cmsout02.mbox.net [165.212.64.32]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j64NMkTZ021272 for ; Mon, 4 Jul 2005 19:22:47 -0400 Received: from cmsout02.mbox.net (cmsout02.mbox.net [165.212.64.32]) by cmsout02.mbox.net (Postfix) with ESMTP id BA1C54C835 for ; Mon, 4 Jul 2005 22:34:54 +0000 (GMT) Received: from cmsapps02.cms.usa.net [165.212.11.138] by cmsout02.mbox.net via smtad (C8.MAIN.3.21U); Mon, 04 Jul 2005 22:34:54 GMT X-USANET-Source: 165.212.11.138 IN david.w.miller ^^^ stanfordalumni.org cmsapps02.cms.usa.net X-USANET-MsgId: XID061JgDwI46383X02 Received: from cmsweb14.cms.usa.net [165.212.8.14] by cmsapps02.cms.usa.net (ASMTP/) via mtad (C8.MAIN.3.21E) with ESMTP id 089JgDwI20446M38; Mon, 04 Jul 2005 22:34:53 GMT X-USANET-Auth: 165.212.8.14 AUTO david.w.miller ^^^ stanfordalumni.org cmsweb14.cms.usa.net Received: from 68.35.94.182 [68.35.94.182] by cmsweb14.cms.usa.net (USANET web-mailer CM.0402.7.24); Mon, 04 Jul 2005 22:34:52 -0000 Date: Mon, 04 Jul 2005 15:34:52 -0700 From: David Miller To: Subject: CCL: new ActiveX/DLL product X-Mailer: USANET web-mailer (CM.0402.7.24) Mime-Version: 1.0 Message-ID: <560JgDwI17776S14.1120516492 ^^^ cmsweb14.cms.usa.net> Content-Type: text/plain; charset=ISO-8859-1 Z-USANET-MsgId: XID089JgDwI20446X38 X-Spam-Status: No, score=1.6 required=5.0 tests=FORGED_RCVD_HELO, RCVD_NUMERIC_HELO autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j64NMpTZ021284 Sage Informatics has just released ChemTKX, an ActiveX and DLL product allowing users to incorporate features of the ChemTK desktop product into their own Windows programs. ChemTKX features include: - Create molecule objects from common text representations such as Daylight Smiles and MDL MOL/SDF, or from scratch using intuitive commands such as CreateAtom and CreateBond - Perform substructure searches using Daylight Smarts syntax or ChemTK Encoded syntax, among others - Convert molecule objects to JPEG or BMP image files, with or without structural highlighting - Generate and display molecule depictions within specified windows, with or without structural highlighting - Generate canonical Smiles representations of molecules - Generate maximum common substructures (MCSs) - Generate 2D atomic coordinates for a molecule - Convert molecules from one representational format to another Visit http://www.sageinformatics.com/chemtkx.html to download the ChemTKX evaluation software and release notes. Best Regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller ^^^ sageinformatics.com ____________________________________________________________________