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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