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From: Joerg K. W. <we...@in...> - 2005-01-18 10:00:41
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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 17:47:32
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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 W. <we...@in...> - 2005-01-10 09:20:53
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Sorry, now i've released a, as far as possible, tested and stable pre-alpha release, which fixes the bugs in the recursive caller hierarchy for calculating the atom and bond labels. Furthermore i've fixed the import/exort bugs for the newly introduced feature result classes. So all available feature should now be cached correctly when storing files, which support features, like the SDF. I would be happy if other peaople would have time to test and send bug reports to the tracking systems. But i'm, at least at the moment, quite happy with the achieved refactoring goal. Lets see what will come next ... i think we can switch to beta mode in the next two/three months. 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...> - 2005-01-07 13:23:51
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Hi, sorry, actual relases will be removed and a patch will be available tomorrow. 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...> - 2005-01-07 08:52:29
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Hi all, 1. Please note that i've consolidated and updated the copyright notices. Please check the dependencies. 2. The new JOELib2 release contains the hashed feature identifier calculation algorihm. 3. The (pre-alpha) JOELib2 API documentation is now also Online. Kind regards, Joerg Kurt Wegner -- 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...> - 2005-01-04 17:43:18
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Hi,
one additional comment:
1. please use for variables and methods as descriptive names as possible.
2. the two most critical PMD rules for readability are, IMHO:
- only one return statement per method !!!
- code complexity, introduce as much private/protected helper
methods or external helper classes for more general tasks.
Those classes can be singleton classes if they load parameters
or contain static helper methods.
Kind regards, Joerg
> Hi all,
>
> here a short summary of my developer environment and coding conventions.
> Nothing is fixed, so if you have better arguments, we switch to another
> convention.
>
> Please have a look at the other sources to get a feeling for the
> conventions.
>
> IDE:
> Is eclipse, because it has excellent refactoring tools, code formatting.
> http://www.eclipse.org/
>
> Coding:
> PMD, PMD, PMD: please use the PMD rules to check your sources. I've
> started really late to use this tool, but if anyone can measure software
> quality, then the guys from the PMD project. Its amazing how clever
> those rules are, and there is an eclipse plugin.
> http://pmd.sourceforge.net/
>
> Make-Tool:
> Apache ANT, because its all in once: compiling, maintaining, documentation
> http://ant.apache.org/
>
> Documentation:
> DocBook-XML based on Jade, so this is pretty complex, i know, so i've a
> working environment and its not necessary that every developer has a
> working environment. So, you are on your own if you want get this stuff
> to work, but of course you can ask me.
>
> 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...> - 2005-01-04 17:36:29
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Hi all, here a short summary of my developer environment and coding conventions. Nothing is fixed, so if you have better arguments, we switch to another convention. Please have a look at the other sources to get a feeling for the conventions. IDE: Is eclipse, because it has excellent refactoring tools, code formatting. http://www.eclipse.org/ Coding: PMD, PMD, PMD: please use the PMD rules to check your sources. I've started really late to use this tool, but if anyone can measure software quality, then the guys from the PMD project. Its amazing how clever those rules are, and there is an eclipse plugin. http://pmd.sourceforge.net/ Make-Tool: Apache ANT, because its all in once: compiling, maintaining, documentation http://ant.apache.org/ Documentation: DocBook-XML based on Jade, so this is pretty complex, i know, so i've a working environment and its not necessary that every developer has a working environment. So, you are on your own if you want get this stuff to work, but of course you can ask me. 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 15:16:19
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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 11:17:27
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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: Joerg K. W. <we...@in...> - 2004-12-16 14:32:39
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Hi Xinshan, > I am a new user of the package, and I have a kind of > similar problem to Andreas'. Thanks for the info. you > have provided in this thread. One remaining question > I have regarding to Morgan routine is: will each > molecule end up the same unique numbering no matter > what initial values are assigned? The reason is that > I did a test to convert between SDF and SMILES back > and forth a couple times, and every time there is a > portion of molecules in the collection show different > SMILES strings compared to the previous rounds. Any > information is appreciated. There are still ties, and there are also publications using other canonizations. Of course Morgan is not perfect. If you are interested you can send a support request to the JOELib project. Please give details for the structures used (if possible), otherwise such things can get never fixed. Please note that canonization has at least polynominal runtime and this is not an easy task for molecular graphs. The best solution would be to create a test data set with uniqueSMILES -> index scrambling -> uniqueSMILES, then we can measure the improvement rate for better tie resolvers, but at the moment i've no time for such things. Any helping hand is highly welcome. 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: Peter Murray-R. <pm...@ca...> - 2004-12-16 13:42:28
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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 00:05:00
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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: Xinshan K. <jas...@ya...> - 2004-12-15 18:02:53
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Dear Joerg, I am a new user of the package, and I have a kind of similar problem to Andreas'. Thanks for the info. you have provided in this thread. One remaining question I have regarding to Morgan routine is: will each molecule end up the same unique numbering no matter what initial values are assigned? The reason is that I did a test to convert between SDF and SMILES back and forth a couple times, and every time there is a portion of molecules in the collection show different SMILES strings compared to the previous rounds. Any information is appreciated. Thanks, Jason ----------------------------------------- >Hi Andreas, > > morgan.renumber(tMol); returns the renumbered molecule (no salts!). > > In detail: > - Applying a modified BFS search which assigns the initial values > - The rest of the algorithm uses this numbers to get an unique > renumbering for this molecule. If renumbering ties occur, there are > several tie resolvers using different atom labels. > - Finally, the returned molecule should be uniquely renumbered, as far > as the morgan algorithm and the tie resolvers can grant this. > > If you put then this molecule into a SMILES generator, it should always > return the same SMILES, even, if the original molecules used another > numbering scheme. > > Kind regards, Joerg __________________________________ Do you Yahoo!? Take Yahoo! Mail with you! Get it on your mobile phone. http://mobile.yahoo.com/maildemo |
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From: Stefan K. <ste...@un...> - 2004-12-15 12:17:31
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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: Joerg K. W. <we...@in...> - 2004-12-15 09:51:02
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Hi all, >>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. 1. i've no experience with web services, can i execute those services you mentioned, because i got only XML code. I would be very interested for some help here. 2. i would prefer a neutral web-link, like sf.qsar.net/service or ... the name should be as general as possible and not mainly connected one specific library. 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: Christoph S. <c.s...@un...> - 2004-12-14 20:52:50
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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 16:19:15
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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 09:49:19
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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 16:32:52
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Hi Andreas,
morgan.renumber(tMol); returns the renumbered molecule (no salts!).
In detail:
- Applying a modified BFS search which assigns the initial values
- The rest of the algorithm uses this numbers to get an unique=20
renumbering for this molecule. If renumbering ties occur, there are=20
several tie resolvers using different atom labels.
- Finally, the returned molecule should be uniquely renumbered, as far=20
as the morgan algorithm and the tie resolvers can grant this.
If you put then this molecule into a SMILES generator, it should always=20
return the same SMILES, even, if the original molecules used another=20
numbering scheme.
Kind regards, Joerg
> If I use
>=20
> ------------------CODE BEGIN---------------------
> // create mol object out of this smiles string
> JOESmilesParser.smiToMol(mol, smiles, smiles);
> =09
> // clone the molecule
> // and recalculate
> // numbers
> JOEMol tMol =3D (JOEMol) mol.clone(false);
> morgan.calculate(tMol);
> JOEMol rMol =3D morgan.renumber(tMol); // (*)
> JOEMol rMol =3D tMol;
>=20
> // create mol to smiles converter=20
> m2s.init();
>=20
> // do some correction
> m2s.correctAromaticAmineCharge(rMol);
>=20
> // String buffer to hold the canonified string
> m2s.createSmiString(rMol, smilesb);
> return smilesb.toString();
> ------------------CODE BEGIN---------------------
>=20
> I get a NULL pointer exception at (*) with the following:
> Exception in thread "main" java.lang.NullPointerException
> at joelib.algo.morgan.Morgan.getBFS(Morgan.java:329)
> at joelib.algo.morgan.Morgan.renumber(Morgan.java:261)
> at SmilesCanonifier.canonify(SmilesCanonifier.java:35)
> at SmilesCanonifier.main(SmilesCanonifier.java:52)
> =09
> Without (*), however, it works quite well, too.
> Only in some molecules it switches from (for example)
> 'C12CC3CC(CC(C3)C2)C1' to
> 'C12CC3CC(CC(C3)C1)C2',
> but that's not so problematic.
> Also, the missing salt support is no acute problem.
> What does (*) do, exactly?
>=20
> Greetings,
> Andreas
> =09
> On Tue, Nov 30, 2004 at 08:17:37AM +0100, Joerg K. Wegner wrote:
>=20
>>Hi Andreas,
>>
>>here is the code fragment used by joelib.io.types.Smiles. Please note=20
>>that the actual morgan algorithm can not deal with salts. A solution=20
>>would be to get all contiguous fragments in decreasing order (method=20
>>mol.contiguousFragments(List)) and apply the morgan algorithm to each=20
>>fragment. Then you must simply connect those fragments in the SMILES=20
>>String with frag1smiles.frag2smiles.frag3smiles
>>
>>Mmhh, its not a big deal but i'm at the moment heavily busy with the=20
>>JOELib2 refactoring. Anyway, here is the code:
>>
>>if (doCanonical)
>>{
>> JOEMol tMol =3D (JOEMol) mol.clone(false);
>> morgan.calculate(tMol);
>> JOEMol rMol =3D morgan.renumber(tMol);
>> m2s.correctAromaticAmineCharge(rMol);
>> m2s.createSmiString(rMol, smilesb);
>>}
>>else
>>{
>> m2s.correctAromaticAmineCharge(mol);
>> m2s.createSmiString(mol, smilesb);
>>}
>>
>>MfG, Joerg
>>
>>
>>>with the following code I read in a SMILES, build a molecule out of=20
>>>it and reencode it as a string:
>>>
>>>----------------- BEGIN CODE --------------------------------
>>>
>>>import joelib.molecule.*;
>>>import joelib.smiles.*;
>>>
>>>public class SmilesCanonifier {
>>> =20
>>> public String canonify(String smiles) {
>>> JOEMol mol=3Dnew JOEMol();
>>> JOEMol2Smi m2s =3D new JOEMol2Smi(); m2s.init();
>>> StringBuffer smilesb =3D new StringBuffer(1000);
>>>
>>> // create mol object out of this smiles string
>>> JOESmilesParser.smiToMol(mol, smiles, smiles);
>>>
>>> // create mol to smiles converter
>>> m2s.init();
>>> // do some correction
>>> m2s.correctAromaticAmineCharge(mol);
>>>
>>> // String buffer to hold the canonified string
>>> m2s.createSmiString(mol, smilesb);
>>> return smilesb.toString();
>>> }
>>>
>>> public static void main(String args[]) {
>>> String smiles =3D args[0];
>>> System.out.println(smiles);
>>> SmilesCanonifier sc =3D new SmilesCanonifier();
>>> System.out.println(sc.canonify(smiles));
>>> }
>>>}
>>>
>>>----------------- END CODE ----------------------------------
>>>
>>>When I try this on a SMILES s0 I get an equivalent output smiles s1.
>>>When I try it on s1, I get an equivalent output smiles s2, which is=20
>>>different from s1.
>>>When I try it on s2, I get an equivalent output smiles s3, which is=20
>>>the same as s1, s3=3Ds1.
>>>When I try it on s3=3Ds1, I get an equivalent output smiles s4, which=20
>>>is the same as s2, s4=3Ds2.
>>>
>>>The process repeats from now on, switching between two SMILES=20
>>>versions.
>>>Is there no canonical version? Otherwise, how can I get one?
>>>
>>>Greetings,
>>>Andi
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>SF email is sponsored by - The IT Product Guide
>>>Read honest & candid reviews on hundreds of IT Products from real=20
>>>users.
>>>Discover which products truly live up to the hype. Start reading=20
>>>now. http://productguide.itmanagersjournal.com/
>>>_______________________________________________
>>>Joelib-help mailing list
>>>Joe...@li...
>>>https://lists.sourceforge.net/lists/listinfo/joelib-help
>>>
>>
>>
>>--=20
>>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)
>>
>>
>>
>>-------------------------------------------------------
>>SF email is sponsored by - The IT Product Guide
>>Read honest & candid reviews on hundreds of IT Products from real=20
>>users.
>>Discover which products truly live up to the hype. Start reading now.=20
>>http://productguide.itmanagersjournal.com/
>>_______________________________________________
>>Joelib-help mailing list
>>Joe...@li...
>>https://lists.sourceforge.net/lists/listinfo/joelib-help
>=20
>=20
> Viele Gr=FC=DFe,
> Andi
--=20
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)
|
|
From: Joerg K. W. <we...@in...> - 2004-12-06 16:28:20
|
Hi Ambrish, > the error is > reader = new SimpleReader(input, inType); whats the detailed error message, this is only a code fragment. 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) |
|
From: Joerg K. W. <we...@in...> - 2004-12-06 16:23:57
|
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) |
|
From: Ambrish R. <che...@ya...> - 2004-12-03 16:14:53
|
Hi there is a problem in compiling can anyone help the error is reader = new SimpleReader(input, inType); Does anyone knows the solution.... Please reply back immediately Thanks Ambrish "Joerg K. Wegner" <we...@in...> wrote: Hi Ambrish, 1. please use the mailing list, such things are interesting for all users. I forward it automatically, hope you don't mind. > 4. i have put all the necessary jar files in JOELib\lib. > but when i run Test.java i get errors like > package joelib.molecule does not exist import joelib.molecule.JOEAtom; > package joelib.data does not exist import joelib.data.JOEPairData; > and similar errors. The compiler does not find the sources and/or the build directory or the joelib.jar. Do you have set also JOELIBDIR? 2. Installation is the most critical step. I strongly recommend to use 'cygwin' instead of the DOS prompt. Unfortunately this is tricky to install. Then you can work with the shell scripts build.sh. Sorry, i might have no quick fix for this problem, so i tell you possible solutions and you can decide which one might be the fastest: 2.1. Use the joelib.jar-file (only if you don't need the interface classes, like CDK, Java3D, Ghemical, ...) 2.2. Use Windows with BAT-files. Problem: The classpath must be checked by hand, that it includes all required .jar files and directories. Please check if you have set: JAVA_HOME ANT_HOME JOELIBDIR 2.3. Use Windows/Cygwin or Linux, then you can use the shell scripts SH. They will find all required jar files in the lib directory automatically. So, this is much easier than fixing them by hand. If you are a Windows user, installing Cygwin might be a problem, because the installation menu is not optimal. Please check if you have set: JAVA_HOME ANT_HOME JOELIBDIR 2.4. Install ANT and add it to your PATH environment. If this was done you can use: 'joelib/ant/ant compile'. That's what is done, by the build.sh anyway. Then you must not set JOELIBDIR, because only the shell scripts require this environment option. > I am soory to bother you so much but i need ur help immediately as i have to complete my project before 10th December. > Can you please tell me in detail how to start using and copiling all the packages.... > Looking forrward for an early reply. > Ambrish > Bioinformatics Centre Sorry, for this late reply. Kind regards, Joerg > > > "Joerg K. Wegner" wrote: > Hi Ambrish, > > 1. LOG4J requires its property file in the classpath. If you use the > source code distribution (strongly recommended) this will be copied > automatically to > joelib/build/log4j.properties > > 2. Seems that there are the required libraries missing which are located > under joelib/lib/log4j.jar > > Please check carefully if the properties and the libraries are part of > your classpath. > You can resolve such things dynamically via ANT or the included shell > scripts. For Windows and your own potential application you must check > such things 'by hand'. > > Kind regards, Joerg > > > >>hi >>thanx for the prompt reply..... >>i am having problem s like >>1.package org.apache.log4j does not exist import org.apache.log4j.Category; >>2. private static Category logger = Category.getInstance( >> >>I tried to configure log4j but still the problem persists. i also searched for the solution but got some hits like This class has been deprecated and replaced by the Logger subclass >>should i replace that in my program. >> >> >> >> >> >>"Joerg K. Wegner" wrote: >>Hi Ambrish, >> >> >> >>>i am a new user to JOELib but am not able to make out how to get started with the package.... >>>Can somebody write to me in detail how to start and if i want to write a program using this package where will i have to store the program i.e whether in same directory? >> >>I recommend to start with all examples in joelib/src/joelib/test >>Have a look at them and try to understand them, then you will know the >>basic functionalities. >> >> >> >>>Also i am getting problem with setting with JOELib enviornment. >> >>That's to sloppy fomulated. >>What are your problems: Java, ANT, eclipse, properties files, >>protonation model, atom typer, ... >> >>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) __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
|
From: Joerg K. W. <we...@in...> - 2004-11-29 17:48:30
|
Hi Ambrish, 1. please use the mailing list, such things are interesting for all users. I forward it automatically, hope you don't mind. > 4. i have put all the necessary jar files in JOELib\lib. > but when i run Test.java i get errors like > package joelib.molecule does not exist import joelib.molecule.JOEAtom; > package joelib.data does not exist import joelib.data.JOEPairData; > and similar errors. The compiler does not find the sources and/or the build directory or the joelib.jar. Do you have set also JOELIBDIR? 2. Installation is the most critical step. I strongly recommend to use 'cygwin' instead of the DOS prompt. Unfortunately this is tricky to install. Then you can work with the shell scripts build.sh. Sorry, i might have no quick fix for this problem, so i tell you possible solutions and you can decide which one might be the fastest: 2.1. Use the joelib.jar-file (only if you don't need the interface classes, like CDK, Java3D, Ghemical, ...) 2.2. Use Windows with BAT-files. Problem: The classpath must be checked by hand, that it includes all required .jar files and directories. Please check if you have set: JAVA_HOME ANT_HOME JOELIBDIR 2.3. Use Windows/Cygwin or Linux, then you can use the shell scripts SH. They will find all required jar files in the lib directory automatically. So, this is much easier than fixing them by hand. If you are a Windows user, installing Cygwin might be a problem, because the installation menu is not optimal. Please check if you have set: JAVA_HOME ANT_HOME JOELIBDIR 2.4. Install ANT and add it to your PATH environment. If this was done you can use: 'joelib/ant/ant compile'. That's what is done, by the build.sh anyway. Then you must not set JOELIBDIR, because only the shell scripts require this environment option. > I am soory to bother you so much but i need ur help immediately as i have to complete my project before 10th December. > Can you please tell me in detail how to start using and copiling all the packages.... > Looking forrward for an early reply. > Ambrish > Bioinformatics Centre Sorry, for this late reply. Kind regards, Joerg > > > "Joerg K. Wegner" <we...@in...> wrote: > Hi Ambrish, > > 1. LOG4J requires its property file in the classpath. If you use the > source code distribution (strongly recommended) this will be copied > automatically to > joelib/build/log4j.properties > > 2. Seems that there are the required libraries missing which are located > under joelib/lib/log4j.jar > > Please check carefully if the properties and the libraries are part of > your classpath. > You can resolve such things dynamically via ANT or the included shell > scripts. For Windows and your own potential application you must check > such things 'by hand'. > > Kind regards, Joerg > > > >>hi >>thanx for the prompt reply..... >>i am having problem s like >>1.package org.apache.log4j does not exist import org.apache.log4j.Category; >>2. private static Category logger = Category.getInstance( >> >>I tried to configure log4j but still the problem persists. i also searched for the solution but got some hits like This class has been deprecated and replaced by the Logger subclass >>should i replace that in my program. >> >> >> >> >> >>"Joerg K. Wegner" wrote: >>Hi Ambrish, >> >> >> >>>i am a new user to JOELib but am not able to make out how to get started with the package.... >>>Can somebody write to me in detail how to start and if i want to write a program using this package where will i have to store the program i.e whether in same directory? >> >>I recommend to start with all examples in joelib/src/joelib/test >>Have a look at them and try to understand them, then you will know the >>basic functionalities. >> >> >> >>>Also i am getting problem with setting with JOELib enviornment. >> >>That's to sloppy fomulated. >>What are your problems: Java, ANT, eclipse, properties files, >>protonation model, atom typer, ... >> >>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) |
|
From: Joerg K. W. <we...@in...> - 2004-11-16 15:30:20
|
Hi all, i don't know if i've already announced that JOELib is presented at the eChemInfo 2004, so here we go: eChemInfo 2004 http://echeminfo.colayer.net/ 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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