I haven't yet looked into the Perl, but I've been doing some work on
the Java bindings and if you use the development code (trunk),
OBTest.java should compile and run okay, provided you use LD_PRELOAD
as follows:
LD_PRELOAD=whereever/libopenbabel.so java OBTest
On trunk, you will need to recreate the Java bindings with
-DRUN_SWIG=ON, and you should have a recent Swig executable on the
path.
- Noel
On 22 November 2011 10:08, Alexander Klenner
<alexander.garvin.klen...@scai.fraunhofer.de> wrote:
> That may not be of much help, but the same happens to me with Java bindings
> and the provided OBTest.java snippet.
>
> OBConversion c = new OBConversion();
> OBMol mol = new OBMol();
>
> System.out.println("Mol: "+mol);
> System.out.println(c.SetInFormat("SMILES"));
> System.out.println(c.ReadString(mol, "c1ccccc1"));
> System.out.println("Benzene has " + mol.NumAtoms()
> + " atoms.");
>
>
> The output there is also "Benzene has 0 atoms".
>
> Cheers,
>
> Alex
>
>
> --
> Alexander G. Klenner
> Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
> Schloss Birlinghoven, D-53754 Sankt Augustin
> Tel.: +49 - 2241 - 14 - 2736
> E-mail: alexander.garvin.klen...@scai.fraunhofer.de
> Internet: http://www.scai.fraunhofer.de
>
>
> ----- Original Message -----
> From: "Бодров Андрей" <andre-bo...@yandex.ru>
> To: openbabel-discuss@lists.sourceforge.net
> Sent: Monday, November 21, 2011 6:43:30 PM
> Subject: [Open Babel] Problem with ObConversion and Perl bindings.
>
>
>
> Hello OB Team,
>
>
> I am trying to use OpenBabel with Perl bindings in my project. OpenBabel
> compiled fine, and Perl bindings seem to work. Scripts which create molecules
> atom by atom work as expected. However, we have a problem when trying to use
> obConversion.
>
> I have tried to use obConversion in different ways (to read molecule from
> file, convert from Smiles string, and using different formats). None seem to
> work for me. The script just executes without any apparent error, but no
> molecule is loaded in obMol from the data provided.
>
> Here are examples
>
> PROGRAM LISTING #1 (works OK)
> -------------------------
>
> #!/usr/bin/perl
>
> use Chemistry::OpenBabel;
>
> my $obMol = new Chemistry::OpenBabel::OBMol;
>
> $obMol->NewAtom();
> $numAtoms = $obMol->NumAtoms(); # now 1 atom
>
> my $atom1 = $obMol->GetAtom(1); # atoms indexed from 1
> $atom1->SetVector(0.0, 1.0, 2.0);
> $atom1->SetAtomicNum(6); # carbon atom
>
> $obMol->NewAtom();
> $obMol->AddBond(1, 2, 1); # bond between atoms 1 and 2 with bond order 1
> $numBonds = $obMol->NumBonds(); # now 1 bond
> print "Atom count: " . $obMol->NumAtoms() . "\n";
> print "Bond count: $numBonds \n";
> $obMol->Clear();
>
> EXECUTION
> -------------------------
> myhost:~/build/test # perl 1.pl
> Atom count: 2
> Bond count: 1
>
> PROGRAM LISTING #2 (fails)
> -------------------------
>
> #!/usr/bin/perl
>
> use Chemistry::OpenBabel;
>
> my $obMol = new Chemistry::OpenBabel::OBMol;
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInAndOutFormats("smi", "mdl");
> $obConversion->ReadString($obMol, "C1=CC=CS1");
>
> $numAtoms = $obMol->NumAtoms(); # now 5 atoms
> print "$numAtoms\n";
> $obMol->AddHydrogens();
> $numAtoms = $obMol->NumAtoms(); # now 9 atoms
>
> my $outMDL = $obConversion->WriteString($obMol);
>
>
> EXECUTION
> -------------------------
> myhost:~/build/test # perl 2.pl
> 0
>
> It shows 0 despite I expect output 5.
>
> We have reproduced the error on two different machines (both are OpenSuSE
> 11.4, x86_64).
>
> Please also find attached a listing showing OpenBabel building steps.
>
> No ideas why this happens. I really appreciate your help.
>
>
> Thank you,
>
> Andrey
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security threats, fraudulent activity, and more. Splunk takes this
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