Re: [OpenBabel-scripting] Open Babel for Java

[Noel O'B. <bao...@gm...>]

What is the current situation with OB/Java?

I've tried to follow the README in scripts/java but step 3 gave:
g++: libopenbabel.so: No such file or directory

Noel

On 07/11/06, richard apodaca <ric...@ya...> wrote:
> 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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