Use "ok = $obconversion->SetInFormat("sdf")"
I presume this returns false.
Does a single .so build help?
- Noel
On 12 June 2013 19:42, Craig James <[email protected]> wrote:
> After struggling for two days to get my own swig Perl wrappers to work, I
> decided to start with OpenBabel's and work backwards. However, I can't even
> get OpenBabel's perl bindings to work. It seems to be the exact same
> problem: it can't find the plug-ins.
>
> One detail. The default configuration installed the OpenBabel.pm module in
> /usr/local/openbabel/lib, but since the module is called
> "Chemistry::OpenBabel", I had to create a subdirectory
> /usr/local/openbabel/lib/Chemistry, and move the OpenBabel.pm file to that.
> Once I did that, perl was able to find it.
>
> Functions that just manipulate the atoms and bonds directly work. But
> OBConversion just fails. This example prints the number of atoms and bonds,
> but won't print the SMILES:
>
> use lib '/usr/local/openbabel/lib';
> 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
> $numAtoms = $obMol->NumAtoms(); # now 5 atoms
> print "numAtoms: $numAtoms, numBonds: $numBonds\n";
>
> my $obConversion = new Chemistry::OpenBabel::OBConversion;
> $obConversion->SetInAndOutFormats("smi", "smi");
> my $smiles = $obConversion->WriteString($obMol);
>
> print "smiles: $smiles\n";
>
> Output is:
> numAtoms: 2, numBonds: 1
> ==============================
> *** Open Babel Error in RegisterOptionParam
> The number of parameters needed by option "a" in API differs from an
> earlier registration.
> smiles:
>
> And this example doesn't do anything; the ReadFile() returns "at end"
> immediately:
>
> use lib '/usr/local/openbabel/lib';
> use Chemistry::OpenBabel;
>
> my $obconversion = new Chemistry::OpenBabel::OBConversion;
> $obconversion->SetInFormat("sdf");
> my $obmol = new Chemistry::OpenBabel::OBMol;
>
> my $notatend = $obconversion->ReadFile($obmol,
> "../chemistry/test/test.smi");
> while ($notatend) {
> print "mwt: ", $obmol->GetMolWt(), "\n";
> $obmol->Clear();
> $notatend = $obconversion->Read($obmol);
> }
>
> There are no errors or warnings. Any thoughts?
>
> Thanks,
> Craig
>
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