(ccing the list)
---------- Forwarded message ----------
From: Geoffrey Wood <ge.ff...@gmail.com>
Date: 28 May 2015 at 13:15
Subject: Re: [Open Babel] perl api
To: Noel O'Boyle <baoille...@gmail.com>
Hi Noel,
I'm not sure exactly how to extract the value of $genOp within the
perl script. Obviously printing it doesn't work as I just get a hash
reference. If I extract the description of what it is:
my $desc=$genOp->Description();
print "$desc\n";
$genOp->Do($obmol2);
Then this prints " Generate 3D coordinates"
So it seems to be set.
Geoff.
On Thu, May 28, 2015 at 4:23 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
>
> Is $genOp NULL if you test it just before calling "Do"?
>
> On 27 May 2015 at 23:02, Geoffrey Wood <ge.ff...@gmail.com> wrote:
> > Hi Geoff,
> >
> > I downloaded the master again for the latest updates and I've been running
> > into a problem that has been documented before. That is, a "segmentation
> > fault" when it trys to generate 3D coordinates from a smiles string. The
> > rest of the code that I have looking at VectoInts etc works fine but the
> > offending part of the code looks like:
> >
> > my $obconversion2 = Chemistry::OpenBabel::OBConversion->new(); #
> > conversion object
> >
> > my $obmol2 = Chemistry::OpenBabel::OBMol->new(); # molecule
> >
> > my $genOp = Chemistry::OpenBabel::OBOp::FindType("gen3D");
> >
> > $obconversion2->SetInAndOutFormats("smi","xyz"); # conversion formats
> >
> > $obconversion2->ReadString($obmol2,"CCC"); # convert
> >
> > $genOp->Do($obmol2);
> >
> >
> >
> > With the final line causing the segmentation fault.
> >
> >
> > Any help here would be great as I have spent the last couple of days trying
> > to revert back to what I originally had without any success. This is what
> > I'm passing to cmake (perl 5.20.0; gcc 4.8.3, swig 3.0.5):
> >
> > CXX=/home/woodg07/software/gccBuild/bin/g++
> > CC=/home/woodg07/software/gccBuild/bin/gcc cmake ../openbabel-master/
> > -DCMAKE_INSTALL_PREFIX=/home/woodg07/software/openBabel/ -DRUN_SWIG=TRUE
> > -DPERL_BINDINGS=TRUE -DSWIG_EXECUTABLE=/home/woodg07/software/swig/bin/swig
> > -DEIGEN3_INCLUDE_DIR=/home/woodg07/software/eigen3/include/eigen3/
> >
> >
> >
> >
> > On Mon, May 4, 2015 at 5:45 PM, Geoffrey Wood <ge.ff...@gmail.com> wrote:
> >>
> >> Using version 2.3.1 with the perl bindings I used to have a piece of code
> >> that went something like:
> >>
> >> my $obrotorList = new Chemistry::OpenBabel::OBRotorList; # rotor list
> >> object
> >>
> >> $obrotorList->Setup($obmol);
> >>
> >> $obrotorList->FindRotors($obmol);
> >>
> >>
> >> my $nRotors = $obrotorList->Size(); # number of rotors found
> >>
> >> if ($nRotors > 0 )
> >>
> >> {
> >>
> >> my $rotor = new Chemistry::OpenBabel::OBRotor; # create new rotor
> >> object
> >>
> >> my $it=$obrotorList->BeginRotors(); # an STL iterator
> >>
> >> $rotor=$obrotorList->BeginRotor($it); # get first rotor in list
> >>
> >> my $increment=0;
> >>
> >> for (my $j = 0 ; $j < $nRotors ; $j++)
> >>
> >> {
> >>
> >> my $v_i = new Chemistry::OpenBabel::VectorInt; # vector of
> >> integers for dihedral atoms
> >>
> >> $v_i = $rotor->GetDihedralAtoms();
> >>
> >> if($v_i->size() == 4 ) # make sure that the dihedral has atoms ---
> >> babel returns 0's for methyls
> >>
> >> {
> >>
> >> }
> >>
> >> }
> >>
> >>
> >> After updating my release to the master I've found that this code doesn't
> >> work anymore, inparticular the line:
> >>
> >> $v_i->size()
> >>
> >> gives the error:
> >>
> >> Can't locate object method "size" via package
> >> "Chemistry::OpenBabel::VectorInt"
> >>
> >> I cannot work out why this is happening, the get function still works,
> >> i.e. $v_i->get(0) for example.
> >>
> >> I did notice that in the OpenBabel.pm file a number of new lines have been
> >> added to class definitions:
> >>
> >> like: *size = *Chemistry::OpenBabelc::VectorInt_size;
> >>
> >> Could someone help me out here?
> >>
> >>
> >> Thanks in advance, Geoff.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >
> > ------------------------------------------------------------------------------
> >
> > _______________________________________________
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> > OpenBabel-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
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