I recompiled everything with the same results.
On Thu, May 28, 2015 at 9:09 AM, Geoffrey Wood <ge.ff...@gmail.com> wrote:
> Hi Noel,
>
> We have a number of gcc's installed on the system they are maintained
> through modules. I have tried with 4.4.x, which is what the operating
> system shipped with. We also have 4.9.2 available but I didn't try that
> yet....will do that now and let you know.
>
>
> On Thu, May 28, 2015 at 8:58 AM, Noel O'Boyle <baoille...@gmail.com>
> wrote:
>
>> Does it work with system gcc?
>>
>> 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.
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>>
>
>
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