Hi,
On Sun, May 4, 2008 at 6:24 AM, demigodntu <[EMAIL PROTECTED]> wrote:
> part of my code looks like:
>
> try {
> FileReader fr = new FileReader("***.xyz");
Make sure that ***.xyz is a single file, not a filter... you'll have
to do looping over a set of files differently.
> XYZReader xyzreader = new XYZReader(fr);
> ichemobject2 = xyzreader.read(ichemobject);
> }
> catch (Exception e){
> System.out.print("Exception");
> }
What IChemObject are you passing to the read() method?
You can use accepts() to test if a certain IChemObject is supported, e.g.:
xyzreader.accepts(Molecule.class);
>From
>http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/trunk/src/main/org/openscience/cdk/io/XYZReader.java?revision=10370&view=markup
you can see that only IChemFile is supported, so you would do:
FileReader fr = new FileReader("someFile.xyz");
XYZReader xyzreader = new XYZReader(fr);
IChemFile chemFile = xyzreader.read(new ChemFile());
> There is always an exception.
What's the exception you get?
> I'm wondering what kind of ichemobject shall I use as the parameter and
> where does it come from.
The interfaces are defined in org.openscience.cdk.interfaces, and
there are three implementations, in org.openscience.cdk,
org.openscience.cdk.debug and org.openscience.cdk.nonotify.
> Actually I don't quite understand why the input parameter in
> xyzreader.read(ichemobject) was needed.
For user convenience... the alternative would be to always return a
IChemFile. But many file formats really contains a IMolecule, and is
thus added as shortcut...
The unit tests Rajarshi mentions, can be found at:
http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/trunk/src/test/org/openscience/cdk/io/XYZReaderTest.java?revision=10775&view=markup
Egon
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