On Saturday 14 February 2004 14:46, M.Le_maudit wrote: > > > Ok, right now I'm working on "GamessReader " class and I uses the > > > "GamessReader" (1.2.2.3) from JMol (b6). > > > > > > If you're already working on this one, tell me and I'll choose another > > > one. > > > > How far have you progressed? > > Well, ... I have to confess that I'm not as fast as I expected. :-( > > Right now, the implemented methods are : > > Full implementation : > - GamessReader(Reader) > - accepts(ChemObject) > - getFormatName() > - close() > - scalesCoordinatesUnits(boolean) (*new) > - identifyAtomicSymbol(int) (*new) > - read(ChemObject) > - readCoordinates(boolean)
Excellent! > Not yet implemented: > - readFrequencies(ChemFrame) (from JMol b6 branch) I have not done that yet for the Gaussian readers... see below. > JUnit Tests: > - I want to write JUnit tests for the GamessReader class, but as it's the > first time I'm trying to write unit tests, I'm not sure about what "must" > and what "may" be tested. Do you have documentation readings to suggest ? There is nothing that you must, may or may not test... Just try to test whatever the class does as best as possibly. For example, add an assertion to see that the atom count read matches the number of atoms in the file. Same for bonds. I also normally test reading of coordinates by comparing it for one atom with that in the file (i.e. hard code the value in the file in the test...) Just look at the other IO tests... > Anyway, GamessReader is able to extract coordinate sets from a GAMESS log > file. (Yes, as I read in Gamess documentation, Gamess output files appear > to be punch files and what we're talking about GamessReader is log files.) > In order to store the extracted data, I'm using these objects : ChemFile, > ChemSequence, ChemModel, SetOfMolecules, Molecule, Atom, ... It seems to > work, but I'm not sure I use them the right way. Sounds ok. You could test it by compiling Jmol-HEAD and start it with: java -Dmodel=cdk -jar Jmol.jar then open up the DirBrowser, and try to load a Gamess file. > How and where may I store these information ? : > - Vibrations associated with a molecule. This has not been defined yet. Miguel, have you given thoughts to this? > - Energy information Miguel, are these currently stored? If not, again, how shall we do that? > - Symmetry information (The point group symmetry is extractible from the > file.) This is definately not done yet, but I will add a SpaceGroup class to CDK soon. > Concerning Atom symbol recognition, do you have tools to identify the > atomic symbol of an atom given its atomic number ? Yes, look at IsotopeFactory in the cdk.tools package. > If yes, which one are > they and how do I use them ? For the moment I'm using a specific method > within the GamessReader class, but I'm not satisfied with this design. > > At last, before committing changes to CVS, it would be kind of you to > seriously read all the modifications I've made and tell me all the things > that need to be improved about implementation and Javadoc. > By the way, there are questions asked directly in the source code (see TODO > tags). It would be nice if you could answer them. > > Thanks for your patience and for any enlightenments you'll provide. > I hope you'll be satisfied with the result's quality as I tried to do my > best. Ok. Can you send me the java file? Egon ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
