From: Egon W. <eg...@sc...> - 2002-03-02 07:04:07
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Hi all, i'll have to say i'm getting lost in CDK... It is time for me to make a new release, but there are only a few changes... so i will skip the March release... next preview release will be in April... In the mean time i will stall these two activities that i promised: 1. the benzene ring detector based on P***** graph theory based detecting by multiplying the connectivity matrix (C)... after six multiplications (C*C*C*C*C*C) the aromatic carbons should be at the diagonal... (at least for benzene... have not tested larger aromatic fragments....) I hope a can find the reference... 2. the Cartoon3DRenderer... At this moment only a few conversion steps are missing... the renderer does not make a copy of the atomic coordinates, and does not have a conversion mechanism to screen coordinates yet... moreover, i have not connected the rotation (mouse) matrix in the proces yet.... Before i continue with these issues, however, i want to do some more project management: A. i want to write/find a doclet that can generate/calculate statistics on the use of Javadoc in our source code... B. I want to make a PDF file with the core and more important classes... For this, we need to classify all classes in several groups: 1. core class which are expected to be used directly by a CDK user 2. standard classes, which are expected to be used by a smaller sub group of CDK users 3. auxiliary classes, which are only used by CDK developers making new standard and core classes (or cleaning up stuff) Three PDFs will be generated; one for each class.... C. I want to write a taglet (new 1.4 stuff) that allows you to add new Javadoc tags... I'm going to add these tags: @license, @requiresjdk (see my message on 18-02)... A new @junit for referencing the JUnit class that tests this method/class... This should help us giving information on the amount of core/standard classes that are tested... But also: @keywords to make an index And probably @cdkclass to put classification (see B.) in source code... D. Generate statistics on the use of JUnit tests to validate our classes/methods... E. These keywords will be used to generate an index to quickly find a the CDK implementation of a procedure, entity, method, etc... F. Use Jase to generate up-to-date UML diagrams Ok, in the mean time I also am going to further work on my CML import stuff... There are several things that need to be done there: 1. test CML files in Jumbo 3.0 distro 2. make JUnit tests for regression tests 3. allow parsing of general XML stuff using xml namespaces to retrieve CML fragments If someone is interesting in continuing my stalled projects (aromiticity detection, Cartoon3dRenderer), please feel free to contact me... Also, feel free to comment on my intentions A-F... ok, enough for now... Egon |
From: Egon W. <eg...@sc...> - 2002-03-04 20:41:26
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On Monday 4 March 2002 13:55, Edgar Luttmann wrote: > Dear Egon, > > >i'll have to say i'm getting lost in CDK... > > that's what I also think from time to time. I just committed some > ArgoUML diagrams into the cdkarticle project, which you might have a > look at. Those should be stored in the cdk tree, but I'm not to happy > with them - yet. How did you generate them? Did you draw them by hand? Or used some tool to do the major job, and some cleaning up by hand? Have you seen my email about Jase (http://relativity.yi.org/jase/)? It can now also output SVG... which we can incorporate into DocBook as well... Anyway, as i could not check them out, i have not seen them yet... > One other thing, I'm confused about from time to time is some kind of > strategic plan for the CDK. I'm needing/ writing some typical Molecular > Modelling stuff and I'm confused if something like a grid framework or > some classes which are used for correcting errors in PDB files like > missing chain ID, correct numbering and so on should be placed in the > CDK. To solve all this I would appreciate some kind of "Strategic Plan > Paper" for the CDK. > > And I think something like that should come from the founders of the > project and should specify their vision of the project. I agree... While Christoph is in the far east, i will try to start such sort of document... Note that the developers guide is also supposed to help 'newer' developers get started... Anyway, the goal of CDK is to be a serious library of java classes to support java software solve typical chemical computational and informational problems... One part of CDK consists of the core classes which represent chemical entities, like bonds, atoms, molecules etc... Also in this class are more abstract entities, like connectivity tables etc A second part of CDK are helper classes to deal with (manipulate) these core classes... these can be grouped into a few subclasses: 1. viewers, IO etc that do not alter to content 2. procedural stuff to alter the core classes (think of cleaning up, drawing, modelling, etc) Note that none of the classes in this part are required by the first part... Extra stuff... This part consist of all other stuff that does not full into the other two. Note that none of the classes in this part are required by the first two parts... A fourth class is for project management which should include the Junit tests and the interactive test applications... I will make a nice list of classes belonging to which part... Note that package grouping should reflect this... E.g.: Core classes packages: org.openscience.cdk Standard classes packages: org.openscience.cdk.fingerprint org.openscience.cdk.renderer org.openscience.cdk.io Extra classes packages: org.openscience.cdk.nmr Project management test classes packages: org.openscience.cdk.applications org.openscience.cdk.tests Actually, the only thing that should not belong to CDK are user friendly applications.... org.openscience.cdk.applications is already a boarder line package, but is included as it serves for beta testing... Anyway, the things you suggest sound to fit perfectly well... the grid belongs to core, mol modelling probably would fit in standard... the PDB correction stuff would probably end up in extra... because of its rather specific nature... Since this classification is not very formal i send you the email about my recent efforts with JavaDoc stuff... it is a rather brainstorm thingy right now... i proper proposal will come in due time... Egon |
From: Egon W. <eg...@sc...> - 2002-03-04 22:10:36
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On Saturday 2 March 2002 08:03, Egon Willighagen wrote: > B. I want to make a PDF file with the core and more important classes... > > For this, we need to classify all classes in several groups: > > 1. core class which are expected to be used directly by a CDK user > 2. standard classes, which are expected to be used by a smaller sub > group of CDK users > 3. auxiliary classes, which are only used by CDK developers making new > standard and core classes (or cleaning up stuff) > > Three PDFs will be generated; one for each class.... Ok, i first tried a PDF of all classes, but that gave an out-of-memory error... but three PDFs for each category was already what i planned... Anyway, i need to incorporate the required FOP jars into the CDK cvs, but then you can do "ant -buildfile javadoc.xml core.pdf"... I'll put the resulting PDF online soon... Egon |
From: Egon W. <eg...@sc...> - 2002-03-17 09:36:53
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On Saturday 2 March 2002 08:03, Egon Willighagen wrote: > Before i continue with these issues, however, i want to do some more > project management: > > A. i want to write/find a doclet that can generate/calculate statistics on > the use of Javadoc in our source code... Working on that... a prelimenary version has been uploaded to CVS... The most interesting thing it does now is giving the number of classes without a JavaDoc description. This should be zero, but this is not the case for many packages... > B. I want to make a PDF file with the core and more important classes... > > Three PDFs will be generated; one for each class.... The core.pdf can be downloaded (PDF) or read (large webpage!) on the website... The others are still to come... > C. I want to write a taglet (new 1.4 stuff) that allows you to add new > Javadoc tags... > > I'm going to add these tags: > @license, @requiresjdk (see my message on 18-02)... > > A new @junit for referencing the JUnit class that tests this > method/class... This should help us giving information on the amount > of core/standard classes that are tested... > > But also: @keywords to make an index This one is done... I've added some keywords to several .java files... I'll put it online today... > And probably @cdkclass to put classification (see B.) in source code... > > D. Generate statistics on the use of JUnit tests to validate our > classes/methods... > > E. These keywords will be used to generate an index to quickly find a > the CDK implementation of a procedure, entity, method, etc... See above. > F. Use Jase to generate up-to-date UML diagrams See the Developers' Guide for more information. Egon |
From: Egon W. <eg...@sc...> - 2002-03-17 10:21:12
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On Sunday 17 March 2002 10:37, Egon Willighagen wrote: > > But also: @keywords to make an index > > This one is done... I've added some keywords to several .java files... > I'll put it online today... I still have to fix the missing alphabetic order of the keywords... > See the Developers' Guide for more information. Which is now online: http://cdk.sourceforge.net/guide.html Next week I will be on vacation, and will not read my email until next weekend... Please send comment before the next saturday, as I will continue this work then (probably...) Egon |
From: Egon W. <eg...@sc...> - 2002-03-24 22:36:53
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On Sunday 17 March 2002 11:21, Egon Willighagen wrote: > On Sunday 17 March 2002 10:37, Egon Willighagen wrote: > > > But also: @keywords to make an index > > > > This one is done... I've added some keywords to several .java files... > > I'll put it online today... > > I still have to fix the missing alphabetic order of the keywords... It's in alphabetic order now (case incensitive) and has links to the JavaDoc API pages: http://cdk.sourceforge.net/keywordindex.html At this moment there are 22 keywords being used. Much more need to be added to the Java source files. Moreover, I want to extend the syntax into: @keyword primary word, secondary word I.e., have a "," char being a separator for primary and secondary word. E.g. "@keyword atom, color" The item will then be putted in the list something like: atom color renderer.colors.CDKColors More about this soon... Egon |
From: Egon W. <eg...@sc...> - 2002-03-30 07:19:18
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On Monday 25 March 2002 00:37, Egon Willighagen wrote: > http://cdk.sourceforge.net/keywordindex.html > > At this moment there are 22 keywords being used. Much more need to be > added to the Java source files. > > Moreover, I want to extend the syntax into: > @keyword primary word, secondary word > > I.e., have a "," char being a separator for primary and secondary word. > E.g. "@keyword atom, color" > The item will then be putted in the list something like: > > atom > color renderer.colors.CDKColors done. Works like a charm. Please add more keywords for classes you have written. regards, Egon |