Re: [Open Babel] conformer generation

2013-02-11 Thread Geoffrey Hutchison 

> This gives me a file with only one 3D structure, which is actually the one 
> obtained from the gen3d option. For some reason no conformers are generated. 
> I also tried the FF derived searches at no success.

IIRC, you can't perform both the gen3d and the conformer search in one step 
from the command-line. Either write a short script with Pybel, or save the 
output from gen3d and *then* run the conformer search.

Hope that helps,
-Geoff

---
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University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutchison.chem.pitt.edu/

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[Open Babel] Cannot create objects using C++ API

2013-02-11 Thread Peter 
Hi,

I am new to openbabel and am trying to write short C++ applications using
openbabel. The openbabel installation went on fine. 
Now I am trying to test a short code:
e.g.
#include 
#include 
#include 
using namespace std;

int main(int argc,char **argv){
  OBConversion conv(&cin,&cout);
  if(conv.SetInAndOutFormats("SDF","MOL2")){
OBMol mol;
if(conv.Read(&mol))
  conv->Write(&mol);
  }
  return(1);
}

Compiling this using : g++ -L/usr/local/lib -l openbabel -I
/usr/local/include/openbabel-2.0 main.cpp -o test.o
would raise errors, as:
main.cpp:7: error: ‘OBConversion’ was not declared in this scope
main.cpp:7: error: expected ‘;’ before ‘conv’
main.cpp:8: error: ‘conv’ was not declared in this scope
main.cpp:9: error: ‘OBMol’ was not declared in this scope


When I change it to:
OpenBabel::OBConversion conv(&cin,&cout);
OpenBabel::OBMol mol;
The error 
main.cpp:11: error: base operand of ‘->’ has non-pointer type
‘OpenBabel::OBConversion’


Any help/suggestion is appreciated.

Thanks,
Peter




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Re: [Open Babel] Cannot create objects using C++ API

2013-02-11 Thread David van der Spoel 
On 2013-02-12 07:54, Peter wrote:
> Hi,
>
> I am new to openbabel and am trying to write short C++ applications using
> openbabel. The openbabel installation went on fine.
> Now I am trying to test a short code:
> e.g.
> #include 
> #include 
> #include 
> using namespace std;
>
> int main(int argc,char **argv){
>OBConversion conv(&cin,&cout);
>if(conv.SetInAndOutFormats("SDF","MOL2")){
>  OBMol mol;
>  if(conv.Read(&mol))
>conv->Write(&mol);
>}
>return(1);
> }
>
> Compiling this using : g++ -L/usr/local/lib -l openbabel -I
> /usr/local/include/openbabel-2.0 main.cpp -o test.o
> would raise errors, as:
> main.cpp:7: error: ‘OBConversion’ was not declared in this scope
> main.cpp:7: error: expected ‘;’ before ‘conv’
> main.cpp:8: error: ‘conv’ was not declared in this scope
> main.cpp:9: error: ‘OBMol’ was not declared in this scope
>
>
> When I change it to:
> OpenBabel::OBConversion conv(&cin,&cout);
> OpenBabel::OBMol mol;
> The error
> main.cpp:11: error: base operand of ‘->’ has non-pointer type
> ‘OpenBabel::OBConversion’
>
You need to replace it by a .

>
> Any help/suggestion is appreciated.
>
> Thanks,
> Peter
>
>
>
>
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> View this message in context: 
> http://forums.openbabel.org/Cannot-create-objects-using-C-API-tp4655946.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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