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From: Vicky M. <deb...@ca...> - 2006-11-02 12:36:27
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Great volume in the last couple days has sent our feature way up, and the big announcement isn't even out yet! The inside scoop is that we are looking at record earnings! Tomorrow, November 2nd is going to be the last chance to take profit of this incredible information. Current: O.69 (+13%) Insiders accumulating? Projected: 1.3O Rating: 5/5 Ever Glory International (EGLY) is involved in one of the most lucrative areas of business these days, manufacture in China. Quarter after quarter they show themselves as one of the top businesses in their sector. Some recent quarterly postings: $1 mil Profit in the first quarter $778 k Profit in the second quarter August 8th - $2 mil order from Matalan July 25th - $500 k order from Debenhams July 10th - $1 mil order from OTTO Please check all these figures with your favorite source. EGLY is the good deal! We are expecting third quarter numbers to be out soon and are telling all of our members to take a position in EGLY before the data hits the street. These fortuitous figures are going to shock the market and send this one way up! Give yourself the chance to come out WAY ahead here. Fortune favors the bold! also news is PALM BEACH, Florida (AP) -- Donald Trump's display of patriotism is apparently too flamboyant for this chic oceanside town. RICHMOND, Virginia (AP) -- A heckler who confronted Sen. George Allen at a campaign appearance Tuesday was put in a chokehold and slammed to the floor by three of the Republican's supporters in an incident captured on video. ATHENS, Greece (Reuters) -- China's control of the Internet stirred controversy at the first global Internet governance forum on Tuesday when a rights group accused western firms of providing Chinese police with technology to limit Web freedom. WASHINGTON (CNN) -- Sen. John Kerry apologized Wednesday for a "poorly stated joke," which the Massachusetts senator says was aimed at the president but was widely perceived as a slam on U.S. troops. EL SEGUNDO, California (AP) -- Roseanne Barr sings! And it's not the national anthem! |
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From: Beulah L. <erx...@ba...> - 2006-10-31 13:16:23
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The Good PR blitz has start! A-U-N-I is up 33% in the last week leading up to todays information. NEW YORK--(MARKET WIRE)--Oct 30, 2006 Mr. Christian Lillieroos, AUNI's newly-appointed President and CEO, who addressed the audience and announced the new vision statement of the group: American Unity Investments - a business portal that unites the capital flow between the US and China. "In the future, AUNI will focus more of its attention on creating capital opportunities for US investors in the China market and giving Chinese companies opportunities to get access to the US capital market," The Chinese dragon is wide awake and the region is awash in opportunities. With AUNI strong management team and proven track record we expect some very positive news reports throughout this week to push the share price through the roof! Sym: AUNI Price: O.85 Projected: 2.3O Rating: 5/5 This is the break you've been waiting for! Spice up your holdings with A-U-N-I ! Buy on 31 Oct. ----- STATESBORO, Georgia (AP) -- President Bush, faced with polls that show his party's hold on Congress slipping, said Monday that Democrats haven't won anything yet. NEW YORK (Reuters) -- News Corp.'s MySpace.com said Monday it had licensed a new technology to stop users from posting unauthorized copyrighted music on the social networking Web site and oust frequent violators of its policy. |
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From: Matilda d. <con...@ro...> - 2006-10-18 01:14:10
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML><HEAD> <META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> <META content="MSHTML 6.00.2900.2963" name=GENERATOR> <STYLE></STYLE> </HEAD> <BODY bgColor=#ffffff> <div align="left"> <p><font face=Arial = >There is little or no mystique left, and the globalisation of football shows no sign of slowing down.</font><BR><font face=Arial = >last minute of extra-time, after going all-out for a win to avoid the risk of facing theIf the world's richest club in the transfer market, Chelsea, was looking for the player</font><BR><IMG alt="" hspace=0 src="cid:X4FICQVSPYH48MXL8RFC" align=baseline border=0><BR><font face=Arial = >of humour and sarcasm by journey's end.Very good games, but were either of them classics? Are they the games that peopleArgentina lit up Group C with some great efforts, most notably Esteban Cambiasso's</font><BR><font face=Arial = >This goalless draw was the first time Portugal had failed to win inside 90 minutes atdeliver, with negative coaches cancelling each other out and the goals drying up as a</font><BR><BR><font face=Arial = >A deep Luis Figo free-kick was not dealt with by Gary Neville or Lampard and there</font></p> </div> </BODY></HTML> |
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From: demitting <cov...@ro...> - 2006-10-11 12:29:52
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<HTML><HEAD> <STYLE></STYLE> </HEAD> <BODY bgColor=#ffffff> <div align="left"> <p><font face=Arial = size=2>Michael Owen can be forgotten for most of next season, so McClaren will surely put<BR><BR></font></p> <p><IMG alt="" hspace=0 src="cid:XUMLHK7OMTFCH00LLNKU" align=baseline border=0><BR><BR><BR><BR></p> </div> <div align="left"><FONT face=Arial size=2></FONT><FONT face=Arial = size=2>Will he go for what appears to be the tabloid choice of John Terry - a superb</FONT><FONT face=Arial = size=2>Crouch almost got on the end of a Gerrard cross but at the other end it needed some</FONT><BR><BR> <FONT face=Arial = size=2>Of those 10, three are over 30 and the average age is 29.3. Going into the World Cup</FONT><BR><FONT face=Arial = size=2>treatment was performed on his ankle, although he did later bear the pain long enough</FONT><FONT face=Arial = size=2>Rooney saw red after 62 minutes for stamping on Carvalho</FONT><BR><FONT face=Arial = size=2>Very good games, but were either of them classics? Are they the games that people</FONT><FONT face=Arial = size=2>Take the Swiss. Rarely has a team ever played with less inclination to attack than</FONT><BR><FONT face=Arial = size=2>shoot-out history to save three penalties.</FONT><FONT face=Arial = size=2>they all had major tournament experience.</FONT><BR><FONT face=Arial = size=2>stretching reality to breaking point.</FONT><FONT face=Arial = size=2>solve the issue of who plays with him when he returns from a two-match ban.</FONT><BR><BR><FONT face=Arial = size=2>same to France in 2002.</FONT><FONT face=Arial = size=2>Only four men have scored three goals in World Cup final matches - Geoff Hurst</FONT><BR><FONT face=Arial = size=2>nations to have lost all three World Cup shoot-outs they have been involved in.</FONT><FONT face=Arial = size=2>desperate last-ditch defending and some solid keeping from Robinson.</FONT><BR><FONT face=Arial = size=2>But he may not be around for the 2008 European Championship finals and is a non-</FONT><FONT face=Arial = size=2>Beckham almost won a penalty with his last contribution of the game - and probably</FONT><BR><FONT face=Arial = size=2>Most embarrassing moment? Giving my know-it-all theories on England's midfield</FONT><FONT face=Arial = size=2>was very much on the body of England's World Cup ambitions.</FONT><BR><BR><FONT face=Arial = size=2>Chelsea's Michael Essien, and in captain Stephen Appiah they had a player who</FONT></div> </BODY></HTML> |
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From: Geoff H. <ge...@ge...> - 2005-06-02 01:29:47
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I'm happy to announce the release of the first public snapshot of the Open Babel test file repository 2005-06-01. This repository is an open resource for the purposes of test molecules, scripts and results in various chemical file formats. Releases are expected several times a year. The test set includes 39 "canonical" files (including 20 formats) and 47 additional files. Many file formats have formal specifications (e.g., CML or PDB) but realistically, such specifications evolve, many files are passed around which do not adhere to these specifications, and without example reference files, the details of file format specifications are not always clear. Importantly these files can be used for testing import/export routines in many chemical programs, not just Open Babel. By providing such a resource, we hope that developers of chemical software will minimize bugs when translating chemical and molecular data between different file formats and different representations. Additionally, we hope to encourage the community of chemical software developers to support open, well-defined file formats to facilitate interconversion and collaboration in the chemical sciences. * For more information, check: <http://openbabel.sourceforge.net/ repository/> * To download the release: <http://sourceforge.net/project/ showfiles.php?group_id=40728&package_id=152710> * To discuss the release (ope...@li...): <http://sourceforge.net/mailarchive/forum.php?forum_id=45088> Please consider contributing files: http://sourceforge.net/tracker/? atid=740158&group_id=40728&func=browse Cheers, -Geoff (Please distribute this announcement as you see fit to chemistry/ cheminformtics software developers, etc.) |
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From: rich a. <che...@ya...> - 2005-03-03 09:44:29
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Hi All, I administer a couple of open source molecular informatics projects, one of which is called "Octet". I found myself asking how we could keep existing users updated, get new users up to speed quickly, and do all of this in a collaborative environment where the software can change weekly. It would be great if this could be done, but who has time for all of that? To address this problem I have been looking at several Content Management Systems (CMS's). For those that may not be familiar with them, a CMS makes dynamic websites practical by automating the drudgery of website design and maintenance and by enabling users to become content providers. I have a working prototype for a website that I hope will become a hub for Octet development, and possibly useful to a broader audience. The URL is here: http://octetsource.com This site is part user/developer forum, part documentation repository, part project update, and part slashdot-style general molecular informatics news. It does what it needs to do with minimal intervention, and makes it easy for users to submit their own content. The site runs with an open source LAMP-based CMS called "Mambo" (http://mamboserver.com). I looked at many of these CMS's and Mambo greatly surpassed its closest competition in terms of ease of use, stability, functionality, and development activity. If you have some time, I would be grateful if you could have a look at the site and provide any comments you think could improve it. Everything should work, including new user registration and forums. There are almost certainly snags that I don't know about, so please report any you find. One note, if you use "http://octetsource.net", you will be directed to another website altogether (a failed experiment with a web-host), So please use the .com domain instead for now. One final note: to keep down mailing list traffic, I would prefer feedback via the octetsource.com online feedback form or directly to me, rather than to one of the lists I posted this message to. many thanks, rich __________________________________ Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web http://birthday.yahoo.com/netrospective/ |
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From: Joerg K. W. <we...@in...> - 2005-01-26 13:37:07
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From: Joerg K. W. <we...@in...> - 2005-01-18 10:00:42
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Hi all, the SF maintenance is finished and i've succeded to upload the new relase, i've announced yesterday: https://sourceforge.net/project/showfiles.php?group_id=39708&package_id=137589 And again, i've updated the object oriented statistic metrics page: http://www-ra.informatik.uni-tuebingen.de/software/joelib/statistics.html DESIGN: BTW, 'stability metric' has nothing to do with the stability of the functionality, it means the object oriented stability for the future, which means does interface changes and further redesign affect your application... so, its only a metric ... FUNCTIONALITY: The stability of the functionality is another question ... so, i've started to add JUnit tests (its not a disadvantage to have them), but i'm still really confident about the functionality code quality, because there are some industrial users and i've had only a small number of bugs in the tracking system over the last three years. Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2005-01-17 17:47:34
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Hi all, two important news: 1. JOELib2 switches from pre-alpha to alpha, so the most serious and critical refactorings are done (at least from my PhD driven perspective). All further recommended heavy weight refactorings are possible but out of the focus of JOELib2, so any complaints can be discussed and be part of a hypothetical JOELib3 release :-) 2. The results were published at http://www-ra.informatik.uni-tuebingen.de/software/joelib/statistics.html and i used the new and excellent CAP project (thanks guys), a plugin for eclipse to get a more or less objective measure for the redesign: http://sourceforge.net/projects/cap4e/ I will publish the new release as soon as possible, but not before the SF team has fixed the FTP problems :-) Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-12-29 15:16:20
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Hi all, So if you are thinking about possible speed-ups and optimization tasks, here are the most frequent dependencies. They are cached anyway, at least until you do not call molecule.endModify(nukeData=true). Being really exact this means, that the largest runtime for each algorithm bounds the whole dependency tree runtime ... see also Cormen, Leiserson,Rivest: Introduction to Algorithms for O-Notation and runtime-complexity definition: 283 joelib2.feature.types.atomlabel.AtomInRing 196 joelib2.feature.types.atomlabel.AtomIsHydrogen 166 joelib2.feature.types.atomlabel.AtomImplicitValence 162 joelib2.feature.types.atomlabel.AtomHybridisation 162 joelib2.feature.types.atomlabel.AtomHeavyValence 155 joelib2.feature.types.bondlabel.BondInRing 151 joelib2.feature.types.atomlabel.AtomInRing 137 joelib2.feature.types.bondlabel.BondInAromaticSystem 137 joelib2.feature.types.atomlabel.AtomInAromaticSystem 136 joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount 136 joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount 132 joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum 132 joelib2.feature.types.atomlabel.AtomIsElectronegative 132 joelib2.feature.types.atomlabel.AtomInRingsCount 132 joelib2.feature.types.atomlabel.AtomBondOrderSum 131 joelib2.smarts.SMARTSParser 130 joelib2.smarts.SMARTSPattern 99 joelib2.data.AtomTyper 45 joelib2.ring.RingDetector 26 joelib2.feature.types.atomlabel.AtomIsOxygen 24 joelib2.smarts.ProgrammableAtomTyper 22 joelib2.data.ElementHolder 20 joelib2.feature.types.atomlabel.AtomInRing 18 joelib2.feature.types.bondlabel.BondIsClosure 15 joelib2.feature.types.atomlabel.AtomIsNitrogen 13 joelib2.feature.types.atomlabel.AtomIsSulfur 13 joelib2.data.AromaticityTyper 12 joelib2.feature.types.atomlabel.AtomIsCarbon 11 joelib2.algo.BFS 10 joelib2.feature.types.DistanceMatrix Kind regads, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: Joerg K. W. <we...@in...> - 2004-12-29 11:17:28
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Hi all, Cross-Posting -> please reply ONLY TO the following lists, if your reply affects not your library and software package: joe...@li... and qsa...@li... As you all know the 'in silico' chemistry is pretty complex and i've now implemented a trace back routine to identify how complex. This routine was implemented for JOELib2 (not JOELib1, so use: cvs co joelib2). The complexity is more or less analogue to OpenBabel, since both libraries uses the same SMARTS-matching and text definition files. As already discussed several times, we had serious problems to trace back algorithms (chemical expert systems) and feature calculation algorithms, because the complex dependencies trees hidden to the users. The only way to get a feeling for those dependencies was to read the source code. This is even more serious for using algorithms depending on the underlying expert systems, like file conversion (force fields), QSAR descriptor (feature) calculation, SMARTS substructure search, and so on ... Until now we were unable to formalize and assign a unique version number to the applied algorithms. Hence this may be critical for QSAR, because one single change in the aromaticity typer (source code or text definition file) forwards those changes to all depending algorithms. But which one depends on the aromaticity, and affects this the algorithm of interest? Yes, definitely yes! Now, for JOELib2 we can calculate a hashed dependency tree identifier for each expert system, feature calculation algorithm and this version identifier is calculated automatically using the source code CVS tags, which are unique! And i'm pretty proud to present this hack, because even with Java reflection this was tricky. Here is an admonitory remark for the new year 2005 to all users: 'Never mess around with chemical expert systems, and never believe anyone telling you that a fingerprint is a simple 1D descriptor for screening.' Why not? 1. '1D': As you can see the calculation requires the full chemical expert system and this is at least a 2D dependency, 1D is only valid for primitive elemental counts, without any neighborhood. 2. 'simple': even if you apply a 'simple' Query (e.g. SMARTS) matching task, the underlying complexity is far away from being simple (requires 47 algorithms and feature calculation methods for 'SSKey3DS'). Here are two small examples and the full dependency tree can be calculated with JOELib2, 'sh joelibKernel.sh' (requires Java 1.5) and is available online: http://www-ra.informatik.uni-tuebingen.de/software/joelib/KernelLog.txt Now, the examples: 1. chemical expert system identifier: jk:k-1566956551:softDependencies:joelib2.data.AtomTyper (992650183) joelib2.data.AtomTyper http://joelib.sf.net joelib2/data/plain/atomtype.txt 1.1.1.1 2004-12-06_15-33-18 2. dependency for simple a 'simple' paharmacophore fingerprint: dependency class is: joelib2.feature.types.SSKey3DS dependency version hash code is: 1113779298 (including chemistry kernel hash: -1566956551) dependency algorithm complexity is at least: 47 (+ basic user input graph, + recursive dependencies, + data structure dependencies, + forgotten dependencies) class joelib2.feature.types.SSKey3DS(version 1.4) depends on class joelib2.feature.types.count.AromaticBonds(version 1.2) depends on class joelib2.feature.types.atomlabel.AtomIsHydrogen(version 1.2) class joelib2.feature.types.bondlabel.BondInAromaticSystem(version 1.3) depends on class joelib2.data.AromaticityTyper(version 1.4) depends on class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing class joelib2.feature.types.atomlabel.AtomHybridisation(version 1.3) depends on class joelib2.data.AtomTyper(version 1.4) depends on class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing class joelib2.feature.types.atomlabel.AtomImplicitValence(version 1.3) depends on class joelib2.data.AtomTyper(version 1.4) depends on class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing class joelib2.feature.types.atomlabel.AtomInRing(version 1.3) depends on class joelib2.ring.RingDetector(version 1.3) class joelib2.feature.types.atomlabel.AtomIsHydrogen(version 1.2) class joelib2.feature.types.bondlabel.BondInRing(version 1.2) depends on class joelib2.ring.RingDetector(version 1.3) class joelib2.feature.types.bondlabel.BondIsClosure(version 1.2) class joelib2.feature.types.atomlabel.AtomIsHeteroatom(version 1.2) depends on class joelib2.feature.types.atomlabel.AtomIsHalogen(version 1.3) class joelib2.ring.RingFinderSSSR(version 1.2) depends on class joelib2.feature.types.atomlabel.AtomInRing(version 1.3) depends on class joelib2.ring.RingDetector(version 1.3) class joelib2.feature.types.bondlabel.BondInRing(version 1.2) depends on class joelib2.ring.RingDetector(version 1.3) class joelib2.feature.types.bondlabel.BondIsClosure(version 1.2) class joelib2.feature.types.FractionRotatableBonds(version 1.3) depends on class joelib2.feature.types.atomlabel.AtomIsHydrogen(version 1.2) class joelib2.feature.types.bondlabel.BondIsRotor(version 1.3) depends on class joelib2.feature.types.atomlabel.AtomHeavyValence(version 1.3) depends on class joelib2.feature.types.atomlabel.AtomIsHydrogen(version 1.2) class joelib2.feature.types.atomlabel.AtomHybridisation(version 1.3) depends on class joelib2.data.AtomTyper(version 1.4) depends on class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing class joelib2.feature.types.count.HBA1(version 1.2) depends on class joelib2.smarts.ProgrammableAtomTyper(version 1.4) depends on class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing class joelib2.feature.types.count.HBA2(version 1.2) depends on class joelib2.smarts.ProgrammableAtomTyper(version 1.4) depends on class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing class joelib2.smarts.SMARTSPattern(version 1.3) depends on class joelib2.smarts.SMARTSParser(version 1.4) depends on (WARNING: recursively defined dependencies) class joelib2.feature.types.atomlabel.AtomBondOrderSum class joelib2.feature.types.atomlabel.AtomExplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomHeavyValence class joelib2.feature.types.atomlabel.AtomHybridisation class joelib2.feature.types.atomlabel.AtomImplicitHydrogenCount class joelib2.feature.types.atomlabel.AtomImplicitValence class joelib2.feature.types.atomlabel.AtomInAromaticSystem class joelib2.feature.types.atomlabel.AtomInRing class joelib2.feature.types.atomlabel.AtomInRingsCount class joelib2.feature.types.atomlabel.AtomIsElectronegative class joelib2.feature.types.atomlabel.AtomIsHydrogen class joelib2.feature.types.atomlabel.AtomKekuleBondOrderSum class joelib2.feature.types.bondlabel.BondInAromaticSystem class joelib2.feature.types.bondlabel.BondInRing And a Happy New Year to all ! Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: rich a. <che...@ya...> - 2004-12-23 03:45:12
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I would like to propose a name change for the interfaces containing the "Handle" suffix: AtomHandle BondingSystemHandle GammaSequenceHandle to the corresponding name with the "Proxy" suffix: AtomProxy BondingSystemProxy GammaSequenceProxy This name change will more clearly reflect the intent of these interfaces, which is to provide a Proxy for the objects they are named after. If there are no objections in the next few days, I will go ahead and make the changes. HAPPY HOLIDAYS, rich __________________________________ Do you Yahoo!? All your favorites on one personal page Try My Yahoo! http://my.yahoo.com |
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From: rich a. <che...@ya...> - 2004-12-22 03:57:17
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I have just committed changes to the Octet CVS that address the issue of modular AtomQuery and MoleculeQuery support (http://octet.sourceforge.net). Most of the changes can be found in the net.sourceforge.octet.query package (http://cvs.sourceforge.net/viewcvs.py/octet/octet/src/net/sourceforge/octet/query/) Examples of AtomQueries now available include: MoleculeFeatureAtomQuery - Atom membership in features perceived by a MoleculeQuery (aromaticity, ring membership, etc.) AtomicNumberAtomQuery - atomic number ImplicitHydrogenAtomQuery - implicit H count NegatingAtomQuery - negates the result of another AtomQuery NeighborCountAtomQuery - neighbor count (excludes implicit hydrogens) TemplateAtomQuery - matches atoms corresponding to an Atom template WildcardAtomQuery - matches all Atoms More are on the way. The construction of composite AtomQueries that can contain nested boolean logic is now supported. These AtomQueries can either be used to directly match individual Atoms in a Molecule, or as part of a larger MoleculeQuery created, for example, with a MoleculeQueryBuilder. Examples of MoleculeQueries now available include: AllCyclesMoleculeQuery - perceives cyclic features AromaticityQuery - perceives aromatic features CycleSystemQuery - perceives cycle systems (i.e. fused ring systems useful in SDG, aromaticity perception, and structure->name schemes). To improve MoleculeQuery performance, a CachedMoleculeQuery is now available that will cache the results of a query and automatically use the cached result when appropriate. Only one cached result is now supported, but this could easily be extended to enable any number of results to be cached by a MoleculeQuery - without the need to rewrite any existing MoleculeQueries (Decorator Pattern). To make it easier to use this new capability, work to create a SmartsQueryFactory is underway. The idea is to allow clients to supply the factory with a SMARTS atom primitive as a String and get a pre-configured AtomQuery in return. Currently "a", "A", and "*" are supported. Extension to other query ontologies is, of course, also possible. Many of these changes are intended to move toward an object-oriented Atom typing system. SMARTS is one apporoach, but I believe that the object-oriented approach is much more flexible because clients can use a language that is infinitely more expressive than SMARTS - Java. Atom typing is used extensively in QSAR/QSPR to calculate Molecular properties (TPSA, etc.) JUnit tests for this functionality are available (net.sourceforge.octet.junit). This code will still need some debugging and refactoring, but I believe the overall design may be a useful starting point. best, rich __________________________________ Do you Yahoo!? Jazz up your holiday email with celebrity designs. Learn more. http://celebrity.mail.yahoo.com |
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From: Peter Murray-R. <pm...@ca...> - 2004-12-16 13:42:29
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At 16:12 15/12/2004 +0100, E.L. Willighagen wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA1 > >On Monday 13 December 2004 13:36, Matteo Floris wrote: > > > What services would people like? > > > Our own list includes but is not limited to: > > > - calculate 2D coords for connection table > > > - calculate 3D coords for molecule > > > - MM, MD, MO calculations > > > - calculate descriptors for molecule > > > - calculate properties for molecules > > > - legacy conversions > > > - search databases > > > - create SVG diagrams for molecules and reactions > > > - create PNGs > >Peter, the system you describe, is that using SOAP? I shall let YY answer definitively, but I am sure it does. > So that it could integrate >with SciTegic's PipeLine Pilot, which can use SOAP services as nodes in the >pipeline? I you have PLP and want to integrate, then fine. I have worked with PLP and it is a good product. However I do not know its data architecture but I strongly suspect it is not compatible with what we are developing here. >At the CIC Workshop I met Asutosh Yagnik of SciTegic and talked with him a >bit >on their software, and talked about integrating CDK functionality with >PipeLine pilot... And it was reasonably straightforward to integrate SOAP >services... My concern is primarily about the data objects, particularly the XML serialisation. If PLP does not support them then it may not be easy to do it. What I am suggesting here is that we look at systems like Taverna (or Kepler). We have built a very successful workflow with Taverna that works well. There is quite a large development team and they are very responsive. They already have Jmol as a viewer. They have a model where (say) other renderers such as JCP could be integrated. The system can run as standalone, web services grid-enabled, etc. The first task is for us to agree on the object we pass. These are safest if they are serialized (e.g. in CML) but it appears that for non-persistent objects Java will work (works fine for me). It could be that octet has a role here. YY is currently setting up pages where you can develop your own simple WS aggregation. A typical example is "find the molecular mass for a SMILES".* We can do this in two steps: - convert SMILES to CML (OB) - calculate MWt (JUMBO: MoleculeTool.getMolecularMass()); The idea will be to create (very simple) workflow on-the-fly. It is likely that we shall be able to save these as Taverna XML objects P. * - I expect that some systems may be able to do this directly, but this is just an example. Moreover it could be that other components could be substituted for each step >Egon > >- -- >e.w...@sc... >PhD-student on Molecular Representation in Chemometrics >Radboud University Nijmegen >http://www.cac.science.ru.nl/people/egonw/ >GPG: 1024D/D6336BA6 >-----BEGIN PGP SIGNATURE----- >Version: GnuPG v1.0.7 (SunOS) > >iD8DBQFBwFRbd9R8I9Yza6YRApFvAKCcOzK+9n5xiT2cPCAtvB9WqrEzZQCfYI73 >D1dZx7wtYnfNiMfRltni0us= >=XDrF >-----END PGP SIGNATURE----- Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |
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From: Peter Murray-R. <pm...@ca...> - 2004-12-16 00:05:02
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At 13:13 15/12/2004 +0100, Stefan Kuhn wrote: >Hi everybody, I have answered this on the QSAR list - a brief additional comment >I just wanted to mention that NMRShiftDB offers certain web services, like >searches etc. These are mainly used by the stand-alone client, similar to >RPC, but can be used by every client. They are actually restricted to= access >from Java programs, since some input is cdk objects, but this could be >changed. We do also currently not have WSDL descriptions, since I did not >find a good description/example of it. But I would try to do this, so we >could do something like a chemoinformatics web services directory. >Generally speaking I got the impression that the interoperability of web >servies has its limitions. Apart from the obvious problem with data types,= I >would not bet on being able to use any service with any client indepently= of >langage, server etc. used. This need not be a problem. Web services does not necessarily need a human-operated client emitting=20 photons. They can be called from a program. So it would be perfectly=20 possible to create a WS chain with contributions like - read journal TOC (JUMBO) - substructure search of known data (OB) - extract supplemental 3D data and spectra (JUMBO) - calculate NMR spectrum GAMESS - calculate NMR spectrum (NMRShiftDB) - calculate descriptors (CDK, JOELib) etc. - this is just an example to show that different groups contribute=20 different services If the data are agreed types and all serialized in agreed format then it's= =20 trivial to call them from programs. That is what we are all working on... If there are objects (e.g. spectra) we need agreed representations=20 (CMLSpect, JCAMP) and GUIs for humans. But we need this anyway. P. >Stefan Kuhn > >Am Sunday 12 December 2004 17:17 schrieb Peter Murray-Rust: > > [Crossposted to several OpenSource lists - please reply thoughtfully. I > > will collate significant replies] > > > > We have been investigating Web Services as a means of distributing Open > > molecular functionality. YY has set up a range of services on our site: > > http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere > > I believe that web services provide a valuable approach for some of what= we > > want to do. Rather than linking a library or executable into the code, a > > call is made to a WS. Thus, for example, we have set up an InChI server: > >= http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=3Dgenerateinchi&JavaScri= pt > >=3Denabled where the input is supplied as CML or legacy ASCII and the= output > > returned as ASCII. > > > > Note that WS do not require graphical i/o or a human to click for the > > service - they can be called programmatically from a wide range of= bindings > > (probably not FORTRAN) > > > > WS have several advantages: > > - the user doesn't have to install the code > > - the user doesn't have to maintain the code > > - complex architectures can be hidden behind the surface > > - it leads to cleaner component design > > - the developer may not have to worry about porting > > - it avoids the "jar explosion and version" problem that we have when= using > > other systems > > - assuming the WS is open it can be cloned and installed elsewhere, thus > > adding redundancy > > - several generic systems (e.g. http://taverna.sf.net) are being= developed > > to support component-based approaches including WS. > > - attractive when the operation is a relatively infrequent requirement > > - good for teaching > > > > There may be some disadvantages: > > - the user may not always be connected or the service is not available. > > Solution: install the service on your local machine and/or create= mirrors > > - there may be a performance hit - is this is actually a problem? > > - the application requires the state to be maintained (WS are easier for > > stateless protocols). All our protocols are stateless. > > > > I think WS has a lot to offer our community. For example I'd like to use > > JOELib or CDK to calculate molecular properties. It's an effort to link > > these into a single bloated app as every time some library changes the > > whole lot has to be recompiled. With WS I can calculate the properties I > > want independently of the implementation. > > > > Are others in this community interested? What services would people= like? > > Our own list includes but is not limited to: > > - calculate 2D coords for connection table > > - calculate 3D coords for molecule > > - MM, MD, MO calculations > > - calculate descriptors for molecule > > - calculate properties for molecules > > - legacy conversions > > - search databases > > - create SVG diagrams for molecules and reactions > > - create PNGs > > > > If you have a working application it's relatively easy to create a WS.= YY > > has created pages: > > http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage > > http://wwmm.ch.cam.ac.uk/moin/WebServiceDev > > > > P. > > > > > > Peter Murray-Rust > > Unilever Centre for Molecular Informatics > > Chemistry Department, Cambridge University > > Lensfield Road, CAMBRIDGE, CB2 1EW, UK > > Tel: +44-1223-763069 > > > > > > > > ------------------------------------------------------- > > SF email is sponsored by - The IT Product Guide > > Read honest & candid reviews on hundreds of IT Products from real users. > > Discover which products truly live up to the hype. Start reading now. > > http://productguide.itmanagersjournal.com/ > > _______________________________________________ > > Qsar-devel mailing list > > Qsa...@li... > > https://lists.sourceforge.net/lists/listinfo/qsar-devel > >-- >Stefan Kuhn M. A. >Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) >Z=FClpicher Str. 47, 50674 Cologne >Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 >My public PGP key is available at http://pgp.mit.edu Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |
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From: E.L. W. <e.w...@sc...> - 2004-12-15 15:13:03
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Monday 13 December 2004 13:36, Matteo Floris wrote: > > What services would people like? > > Our own list includes but is not limited to: > > - calculate 2D coords for connection table > > - calculate 3D coords for molecule > > - MM, MD, MO calculations > > - calculate descriptors for molecule > > - calculate properties for molecules > > - legacy conversions > > - search databases > > - create SVG diagrams for molecules and reactions > > - create PNGs Peter, the system you describe, is that using SOAP? So that it could integr= ate=20 with SciTegic's PipeLine Pilot, which can use SOAP services as nodes in the= =20 pipeline? At the CIC Workshop I met Asutosh Yagnik of SciTegic and talked with him a = bit=20 on their software, and talked about integrating CDK functionality with=20 PipeLine pilot... And it was reasonably straightforward to integrate SOAP=20 services... Egon =2D --=20 e.w...@sc... PhD-student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBwFRbd9R8I9Yza6YRApFvAKCcOzK+9n5xiT2cPCAtvB9WqrEzZQCfYI73 D1dZx7wtYnfNiMfRltni0us=3D =3DXDrF =2D----END PGP SIGNATURE----- |
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From: Stefan K. <ste...@un...> - 2004-12-15 12:17:29
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Hi everybody, I just wanted to mention that NMRShiftDB offers certain web services, lik= e=20 searches etc. These are mainly used by the stand-alone client, similar to= =20 RPC, but can be used by every client. They are actually restricted to acc= ess=20 from Java programs, since some input is cdk objects, but this could be=20 changed. We do also currently not have WSDL descriptions, since I did not= =20 find a good description/example of it. But I would try to do this, so we=20 could do something like a chemoinformatics web services directory. Generally speaking I got the impression that the interoperability of web=20 servies has its limitions. Apart from the obvious problem with data types= , I=20 would not bet on being able to use any service with any client indepently= of=20 langage, server etc. used. Stefan Kuhn Am Sunday 12 December 2004 17:17 schrieb Peter Murray-Rust: > [Crossposted to several OpenSource lists - please reply thoughtfully. I > will collate significant replies] > > We have been investigating Web Services as a means of distributing Open > molecular functionality. YY has set up a range of services on our site: > http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere > I believe that web services provide a valuable approach for some of wha= t we > want to do. Rather than linking a library or executable into the code, = a > call is made to a WS. Thus, for example, we have set up an InChI server= : > http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=3Dgenerateinchi&Java= Script >=3Denabled where the input is supplied as CML or legacy ASCII and the ou= tput > returned as ASCII. > > Note that WS do not require graphical i/o or a human to click for the > service - they can be called programmatically from a wide range of bind= ings > (probably not FORTRAN) > > WS have several advantages: > - the user doesn't have to install the code > - the user doesn't have to maintain the code > - complex architectures can be hidden behind the surface > - it leads to cleaner component design > - the developer may not have to worry about porting > - it avoids the "jar explosion and version" problem that we have when u= sing > other systems > - assuming the WS is open it can be cloned and installed elsewhere, thu= s > adding redundancy > - several generic systems (e.g. http://taverna.sf.net) are being develo= ped > to support component-based approaches including WS. > - attractive when the operation is a relatively infrequent requirement > - good for teaching > > There may be some disadvantages: > - the user may not always be connected or the service is not available. > Solution: install the service on your local machine and/or create mirro= rs > - there may be a performance hit - is this is actually a problem? > - the application requires the state to be maintained (WS are easier fo= r > stateless protocols). All our protocols are stateless. > > I think WS has a lot to offer our community. For example I'd like to us= e > JOELib or CDK to calculate molecular properties. It's an effort to link > these into a single bloated app as every time some library changes the > whole lot has to be recompiled. With WS I can calculate the properties = I > want independently of the implementation. > > Are others in this community interested? What services would people lik= e? > Our own list includes but is not limited to: > - calculate 2D coords for connection table > - calculate 3D coords for molecule > - MM, MD, MO calculations > - calculate descriptors for molecule > - calculate properties for molecules > - legacy conversions > - search databases > - create SVG diagrams for molecules and reactions > - create PNGs > > If you have a working application it's relatively easy to create a WS. = YY > has created pages: > http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage > http://wwmm.ch.cam.ac.uk/moin/WebServiceDev > > P. > > > Peter Murray-Rust > Unilever Centre for Molecular Informatics > Chemistry Department, Cambridge University > Lensfield Road, CAMBRIDGE, CB2 1EW, UK > Tel: +44-1223-763069 > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://productguide.itmanagersjournal.com/ > _______________________________________________ > Qsar-devel mailing list > Qsa...@li... > https://lists.sourceforge.net/lists/listinfo/qsar-devel --=20 Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-7786 My public PGP key is available at http://pgp.mit.edu |
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From: rich a. <che...@ya...> - 2004-12-15 07:46:31
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CDKTools-0.4.0 has been released (http://octet.sourceforge.net). This package is a complete rewrite that takes advantage of new features introduced in Octet-0.4.1. Highlights: * Limited support of fractional CDK bond orders/multiatom Octet BondingSystems is now available. For example, if benzene is specified in CDK with bond order = 1.5 for all six Bonds, this will be interpreted as an Octet BondingSystem with six Atoms and six electrons. Similarly, multiatom Octet BondingSystems are interpreted as CDK Bonds with fractional order. * AtomContainerBuilder provides an abstraction layer for the construction of any AtomContainer. For the first time, it is possible to write file parsers (and other molecule representation builders) that use the Octet RepresentationBuilder API and which can be incorporated with minimal effort into both Octet and CDK. * AdapterMolecule inherits the CDK Molecule implementation and the Octet Molecule interface, enabling it to work seamlessly with both Octet and CDK. The Virtual Proxy Pattern is used to defer the full cost of creating an AdapterMolecule until the Octet Molecule interface is actually used. AdapterMolecule can be constructed using either the CDK Molecule API or the Octet RepresentationBuilder API. This release still has features that are not implementented. CDK stereochemistry is not handled, nor are CDK Atom charges. Properly handling the mutablity of CDK's Atoms and Bonds still needs more work. But what is implemented will take care of most of the likely situations. The package includes detailed JavaDoc with code examples: http://octet.sourceforge.net/javadoc/cdktools_0.4.0/index.html The Octet homepage has an updated tutorial section that illustrates the new API: http://octet.sourceforge.net/tutorial.html#cdk best, rich __________________________________ Do you Yahoo!? The all-new My Yahoo! - Get yours free! http://my.yahoo.com |
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From: Christoph S. <c.s...@un...> - 2004-12-14 20:52:51
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Hi everybody, I think, both things would be very beneficial for promoting=20 CDK/JOELib/Jumbo functionality to the public: 1. portal to chemoinformatics functionality and 2. a set of webservices for the tasks stated below. My focus would be the first, but I guess, the second could just easily=20 come with the first as a spin-off. I first thought that a nice wrapper would be a lot of work but then=20 realized that we are already sitting on all the neccessary technology. The Apache JetSpeed portal software is exactly what is needed to display=20 chemoinformatics functionality nicely customisable in a web view. It=20 gives us all the admin stuff for free and all we need to do it wrap the=20 single functionalities in so called "portlets". Portlets can be easily arranged to yield a full portal view using the=20 JetSpeed admin interface and, best of all, every user can create his or=20 her own arrangement and set of portals, depending on whether you want=20 visualisation, conversion of formats, structure generation or QSAR. The principle can be inspected at http://www.nmrshiftdb.org, where, in=20 the start screen, the left, central and right part are different=20 portlets. The layout can be much more sophisticated, though. We might just start with setting up a basic interface, called=20 www.cdkweb.org, or so, and start with a structure input portlet, which=20 can load structures either from file or as SMILES, a central viewer=20 portlet and a portlet to the right which displays some information (ring=20 set, or so) about each molecule. Cheers, Chris --=20 Dr. habil. Christoph Steinbeck (c.s...@un...) Head of the Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=FClpicher 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.. Matteo Floris wrote: >>What >>services would people like?=20 >>Our own list includes but is not limited to: >>- calculate 2D coords for connection table >>- calculate 3D coords for molecule >>- MM, MD, MO calculations >>- calculate descriptors for molecule >>- calculate properties for molecules >>- legacy conversions >>- search databases >>- create SVG diagrams for molecules and reactions >>- create PNGs >=20 >=20 >=20 > Hi all, > as most of you know, Egon has developed a line command > for calculating descriptors with CDK. I think it could > be very easy to develop a WS, with a few minutes work > for a simple web interface.=20 > I see also there is a good request of "web molecular > databases". My modest opinion is that it could be > better to think at an unique WS similar to > not-chemical "web content managers". |
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From: Matteo F. <flo...@ya...> - 2004-12-13 12:37:00
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Hi all, > What > services would people like? > Our own list includes but is not limited to: > - calculate 2D coords for connection table > - calculate 3D coords for molecule > - MM, MD, MO calculations > - calculate descriptors for molecule > - calculate properties for molecules > - legacy conversions > - search databases > - create SVG diagrams for molecules and reactions > - create PNGs Hi all, as most of you know, Egon has developed a line command for calculating descriptors with CDK. I think it could be very easy to develop a WS, with a few minutes work for a simple web interface. I see also there is a good request of "web molecular databases". My modest opinion is that it could be better to think at an unique WS similar to not-chemical "web content managers". Regards, Matteo Floris. > If you have a working application it's relatively > easy to create a WS. YY > has created pages: > http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage > http://wwmm.ch.cam.ac.uk/moin/WebServiceDev > > P. > > > Peter Murray-Rust > Unilever Centre for Molecular Informatics > Chemistry Department, Cambridge University > Lensfield Road, CAMBRIDGE, CB2 1EW, UK > Tel: +44-1223-763069 > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT > Products from real users. > Discover which products truly live up to the hype. > Start reading now. > http://productguide.itmanagersjournal.com/ > _______________________________________________ > Qsar-devel mailing list > Qsa...@li... > https://lists.sourceforge.net/lists/listinfo/qsar-devel > ___________________________________ Nuovo Yahoo! Messenger: E' molto più divertente: Audibles, Avatar, Webcam, Giochi, Rubrica Scaricalo ora! http://it.messenger.yahoo.it |
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From: Peter Murray-R. <pm...@ca...> - 2004-12-12 16:19:18
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[Crossposted to several OpenSource lists - please reply thoughtfully. I will collate significant replies] We have been investigating Web Services as a means of distributing Open molecular functionality. YY has set up a range of services on our site: http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere I believe that web services provide a valuable approach for some of what we want to do. Rather than linking a library or executable into the code, a call is made to a WS. Thus, for example, we have set up an InChI server: http://wwmm.ch.cam.ac.uk/gridsphere/gridsphere?cid=generateinchi&JavaScript=enabled where the input is supplied as CML or legacy ASCII and the output returned as ASCII. Note that WS do not require graphical i/o or a human to click for the service - they can be called programmatically from a wide range of bindings (probably not FORTRAN) WS have several advantages: - the user doesn't have to install the code - the user doesn't have to maintain the code - complex architectures can be hidden behind the surface - it leads to cleaner component design - the developer may not have to worry about porting - it avoids the "jar explosion and version" problem that we have when using other systems - assuming the WS is open it can be cloned and installed elsewhere, thus adding redundancy - several generic systems (e.g. http://taverna.sf.net) are being developed to support component-based approaches including WS. - attractive when the operation is a relatively infrequent requirement - good for teaching There may be some disadvantages: - the user may not always be connected or the service is not available. Solution: install the service on your local machine and/or create mirrors - there may be a performance hit - is this is actually a problem? - the application requires the state to be maintained (WS are easier for stateless protocols). All our protocols are stateless. I think WS has a lot to offer our community. For example I'd like to use JOELib or CDK to calculate molecular properties. It's an effort to link these into a single bloated app as every time some library changes the whole lot has to be recompiled. With WS I can calculate the properties I want independently of the implementation. Are others in this community interested? What services would people like? Our own list includes but is not limited to: - calculate 2D coords for connection table - calculate 3D coords for molecule - MM, MD, MO calculations - calculate descriptors for molecule - calculate properties for molecules - legacy conversions - search databases - create SVG diagrams for molecules and reactions - create PNGs If you have a working application it's relatively easy to create a WS. YY has created pages: http://wwmm.ch.cam.ac.uk/moin/WebServiceUsage http://wwmm.ch.cam.ac.uk/moin/WebServiceDev P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |
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From: Peter Murray-R. <pm...@ca...> - 2004-12-08 09:49:22
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[Crossposted to several OpenSource lists - please reply thoughtfully. I will collate significant replies] I presented an invited lecture at the Royal Soc Chem yesterday on "The Chemical Semantic Web" and highlighted the impressive contribution of the Open Source movement in chemistry. I hope I managed to acknowledge most people's contributions. It generated a lively discussion in which, I think, the Open Source approach came out very positively. Two common negative questions were presented: "Who pays for it" the implication was that if there was no commercial development the software was second-class and there was no future for it. My response was that the code would be eagerly adopted by the bioinformatics community (strongly confirmed by Mike Ashburner) and we are starting to set up strong links with the Bioinformatics community on small molecules. This question came from the pharma industry and so I challenged them to put something back into the communal process. It's noticeable that the pharma industry is a consumer of our efforts but has not contributed anything in return and continues to pay for overpriced software products that do not use modern methodology. (I spent 15 years in Glaxo so I feel I have a right to criticise the industry). I know that pharma industry reads this list and I would be delighted if there were some who wished to support communal activity. [I would suggest they mail me directly and I will summarise replies. All replies will be assumed to be Open unless specifically indicated]. One approach would be to support a physical workshop on chemical open source. Particular topics could be: - markup languages - communal chemical ontologies (e.g. descriptors) - Open datasets - use of InChI (we are very excited about this) - graphical components - common code libraries - web services (I'll mail later) The only contribution that I know of from the pharma industry to chemoinformatics is the JME editor which is free, but despite repeated requests is not Open and not likely to be. It could be withdrawn at any time. "Open source is unfair to commercial developers" I think this attitude is particularly strong in the US and perhaps Germany. The idea is that public funding should not be used to compete against commercial organisations. As Mike Ashburner replied, most Open software in bioinformatics is written by people on short term contracts often with no possibility of extension. I know that made contributors to these lists do not have jobs. I developed much of CML when I was unemployed after being made redundant from Glaxo. I would be more (slightly) more sympathetic to this view if the chemical software industry provided anything substantial to the community. I know of no support for Open efforts from the chemical software industry other than a very undersupported effort to get an Open Management Group spec for chemistry. I was invited to contribute CML as the core of this spec, but even then it was made clear that I would not even have my (foreign) travel expenses paid - even though I had no job. Note that "free" is not good enough and may even by counterproductive. Closed software often stifles development as there is no API and the software can be withdrawn at any time. That is why we are so keen to see a JChempaint component as a universal Open chemical editor for the web. In fact I think the tide is turning. The components that you are all developing are ideal for Web Services, which will have the potential to rapidly become a major player in the chemoinformatics market. Between the members of this community we have standards, data, transformers, algorithms, repositories, query languages, graphics and much more. I'll put forward a strategy in the next mail(s). Meanwhile - when you are hacking the latest set of bugs at 0200 in the morning, take heart - it really is appreciated - and yes - the day of Open Source for "chemistry" is dawning. In fact I think the centre of gravity of chemical software development is starting to shift towards bioscience [and materials] so that people will simply refer to the informatics of small molecules as "bioinformatics" Best P. Many thanks to those who have sponsored our Open Source development: Royal Soc. Chemistry, Nature Publishing Group, Cyprotex. More about this later. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |
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From: Joerg K. W. <we...@in...> - 2004-12-06 16:23:58
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Hi all, JOELib was heavily redesigned. The new version contains the following changes: - homogenized class names and package names - better interface/implementation separation for molecule/bond/atom - common assignment tasks (aromaticity, kekule, closure bonds, ...) are now treated as atom/bond labels, the caching is done by the feature caching, which was already available, e.g. for distance matrix, BCUT, RDF, ... This means that JOELib supports now 136 features, where 65 are ONLY the atom and bond labels, so by using features using them, e.g. RDF, we can easily calculate: 40atomlabels x 100RDF = 4000RDF, if we also use ... :-) Please note that this version is absolutely incompatible with previous releases, and it is still pre-alpha, so the interface and the implementation can still change, but not as heavily as already done. What are the problem: - Time!!! - So any helping hands updating the API documentation are highly welcome !!! - Furthermore some comments on the actual interface would be fine. !Rich! These version is available via CVS: cvs checkout joelib2 The pre-alpha distributions will be published at the web site. Kind regards, Joerg -- Dipl. Chem. Joerg K. Wegner Center of Bioinformatics Tuebingen (ZBIT) Department of Computer Architecture Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 29 78970 Fax: (+49/0) 7071 29 5091 E-Mail: mailto:we...@in... WWW: http://www-ra.informatik.uni-tuebingen.de -- Never mistake motion for action. (E. Hemingway) Never mistake action for meaningful action. (Hugo Kubinyi,2004) |
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From: rich a. <che...@ya...> - 2004-11-30 21:59:06
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I would like to propose changes to the Nucleus and RepresentationBuilder interfaces that will enable the specification of isotopically-labelled compounds. Nucleus: delete double getMass() add int getMassNumber() // returns -1 if Nucleus is natural abundance distribution RepresentationBuilder: add AtomHandle addAtom(String symbol, int massNumber) PeriodicTable would also be updated to enable the determination exact mass for a given isotope. If there are no objections in the next day, I will go ahead and make the changes. best, r __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
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From: E.L. W. <e.w...@sc...> - 2004-11-29 08:35:21
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=2D----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Saturday 27 November 2004 19:56, rich apodaca wrote: > I would like to propose some additional changes to the > Octet API (http://octet.sf.net). > > These methods would be removed from the Atom > interface: > > iterateNeighbors() > countNeighbors() > isConnectedTo(Atom atom) > countElectrons() > iterateBondingSystems() > countBondingSystems() > countReservedElectrons() > toNeighborArray() > toBondingSystemArray() > getConfiguration() > > ... and their equivalents would be placed into either > the Molecule or AtomGraph interface. For example, > Atom.getConfiguration() would become > Molecule.getConfiguration(Atom atom). AtomGraph > already has iterateNeighbors(Atom atom) and > countNeighbors(Atom atom). > > I believe these changes will result in a more > consistent, robust system. CDK uses the same approach... those kind of methods are in AtomContainer, and not in Atom itself. So no objection I guess. Egon =2D --=20 e.w...@sc... PhD-student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 =2D----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBqt8/d9R8I9Yza6YRAt4PAJ9UwlLDS3mFunCvA4ijbkIFf8vGowCgyHJ9 0McdtGkJXhFigkpEkxgpQWk=3D =3D0JdO =2D----END PGP SIGNATURE----- |
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