Re: [OpenBabel-scripting] Open Babel for Java

[richard a. <ric...@ya...>]

Hi Geoff,

What a coincidence!

In looking through the Java that your openbabel-java.i
file generated (svn trunk rev 1584), I see the cause
of the large filenames. The %module directive uses
net.sourceforge.openbabel as the name. Change this to:

%module openbabel

The problems with long filenames will disappear. But
that's not the biggest problem. The autogenerated java
also wouldn't compile because it was defining things
like:

public interface net.sourceforge.openbabelJNI
{
...
}

when it really should have been generating:

package net.sourceforge.openbabel;

public interface JNI
{
...
}

and so on. Packages are more of a hassle than they're
worth at this point. We can always get that part
tidied up later.

So when I run swig with the '%module openbabel'
directive, I get to the same place I was before. That
is, 32 java compile errors are produced. They involve
these class definitions that can't be found:

OBBitVec
matrix3x3
OBAromaticTyper
OBAtomTyper
OBChainsParser

In addition, 2 of these errors are apparently related
to method duplication:

OBSmartsPattern.java:107:
RestrictedMatch(OBMol,SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t,boolean)
is already defined in OBSmartsPattern
  public boolean RestrictedMatch(OBMol mol, OBBitVec
bv, boolean single) {

...

OBSmartsPattern.java:111:
RestrictedMatch(OBMol,SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t)
is already defined in OBSmartsPattern
  public boolean RestrictedMatch(OBMol mol, OBBitVec
bv) {

...

cheers,
Rich

--- Geoffrey Hutchison <ge...@ge...>
wrote:

> 
> On Nov 5, 2006, at 9:03 PM, richard apodaca wrote:
> 
> > I know Java is technically not a scripting
> language,
> > but I was wondering if anyone was interested in
> trying
> > to get a Java interface to OB working.
> 
> Actually, there are SWIG generated files for Java in
> the current SVN  
> head (much like you describe).
> 
> I had to do some renaming though -- the filenames
> are so huge that  
> they can't be archived by tar (i.e., for generating
> snapshots and  
> releases). I haven't updated the Makefile to do this
> automatically yet.
> 
> > (6) on line 1 of openbabel_java.cpp, add #include
> > <math.h>
> 
> Actually, you can automate this by adding to
> openbabel-java.i
> 
> > [produces 32 errors about missing classes such as
> > OBChainsParser, OBBitVec, matrix3x3,
> OBAromaticTyper,
> > and so on.]
> 
> If you can get me a full list, I'll definitely hack
> the SWIG  
> interface file to generate these.
> 
> Cheers,
> -Geoff
> 


____________________________
Richard Apodaca
Blog: http://depth-first.com



 
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