After trial and error I found that reverting back to version 2.3.1 solves
this issue. 2.3.2 and the development version have this bug.
Thanks.
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I tried using the solution below but am still getting the segmentation fault
error. Has anyone else had success with this?
my
$x="InChI=1S/C15H12N2O/c16-15(18)17-13-7-3-1-5-11(13)9-10-12-6-2-4-8-14(12)17/h1-10H,(H2,16,18)";
push(@inchis,$x);
my $obMol = Chemistry::OpenBabel::OBMol->new();
my $obC
Never mind. Problem solved! I ended up having to rearrange some statements
to make it work, shown as follows:
*my $obMol = Chemistry::OpenBabel::OBMol->new();my $obConversion =
Chemistry::OpenBabel::OBConversion->new();my $genOp =
Chemistry::OpenBabel::OBOp::FindType("gen3D");$obConversi
I finally figured out how to call the the OBOp class with the following
code:
my $genOp = Chemistry::OpenBabel::OBOp::FindType("gen3d");
$genOp->Do($obMol);
However, this brought up a new problem, where I get the error message,
"Segmentation fault." This appears to be an issue with the binding, i
> I'm using version 2.2.3 of Open Babel.
I don't remember, but it's entirely possible OBOp is not included in the Perl
wrapper for that version. It's now over 4 years old.
The latest version is 2.3.2:
http://openbabel.org/wiki/Install
Hope that helps,
-Geoff
I'm using version 2.2.3 of Open Babel.
Wallace
On Thu, Nov 14, 2013 at 2:11 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > And, I got this error: "Can't locate object method "new" via package
> "Chemistry::Openbabel::OBOp" (perhaps you forgot to load
> "Chemistry::Openbabel::OB
> And, I got this error: "Can't locate object method "new" via package
> "Chemistry::Openbabel::OBOp" (perhaps you forgot to load
> "Chemistry::Openbabel::OBOp"?) at convert_iuphar.pl line 30." This is the
> same way I call OBConversion and OBMol, so I'm not sure why it's not working.
> Either
Okay, so I tried using the following statement in my code for the
constructor:
my $op = Chemistry::Openbabel::OBOp->new();
And, I got this error: "Can't locate object method "new" via package
"Chemistry::Openbabel::OBOp" (perhaps you forgot to load
"Chemistry::Openbabel::OBOp"?) at convert_iuphar
OBOp should be in Chemistry::OpenBabel just like OBConversion. If not,
there's a problem at our end.
- Noel
On 13 November 2013 17:18, Wallace Chan wrote:
> Thanks for the reply, Noel. I apologize for being a complete novice, but do
> you have to open OBOp as a separate package? I usually use th
Thanks for the reply, Noel. I apologize for being a complete novice, but do
you have to open OBOp as a separate package? I usually use the line "use
Chemistry::OpenBabel" at the top, but do I have to do this separately for
OBOp? I don't have to do this for OBMol or OBConversion, so I was just
wonde
I don't have the exact code to hand, but it's something like the
following in Python:
myop = OBOp.FindType("gen3d")
success = myop.Do(myOBMol)
- Noel
On 7 November 2013 18:13, Wallace Chan wrote:
> Dear All,
>
> I am having some frustration trying to generate a 3D SDF file from an InChI
> ID.
Dear All,
I am having some frustration trying to generate a 3D SDF file from an InChI
ID. I am able to get it from InChI to SDF without the coordinate
information. I am aware that I have to use the 'gen3d' option but am
unaware of how to do so. Looking around the internet, I see others using
OPOb,
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