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 <walla...@umich.edu> 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 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
> wondering this.
>
> When I call OBConversion to do a task, I do the following as an example:
>
> my $obConversion = Chemistry::OpenBabel::OBConversion->new();
> $obConversion->SetInAndOutFormats("inchi", "sdf");
> foreach my $inchi (@inchis)
> {
> $obConversion->ReadString($obMol, $inchi);
> print $obConversion->WriteString($obMol);
> }
>
> The above is just a snippet of code and not he whole thing. When I do run my
> code, I am able to SDF files without any coordinate information. My problem
> really is how to use the 'gen3d' function with OBOp in Perl. Any help woudl
> be greatly appreciated!
>
>
>
>
> On Fri, Nov 8, 2013 at 2:25 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> 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 <walla...@umich.edu> wrote:
>> > 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,
>> > but I
>> > can't seem to call that class. I have Chemistry::OpenBabel installed,
>> > latest
>> > version. Any help would be greatly appreciated.
>> >
>> > --
>> > Wallace Chan
>> > Zhang Lab
>> > Department of Biological Chemistry
>> > University of Michigan
>> > walla...@umich.edu
>> >
>> >
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>
>
>
>
> --
> Wallace Chan
> Zhang Lab
> Department of Biological Chemistry
> University of Michigan
> walla...@umich.edu
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