Dear Noel
Thanks a lot for your valuable hint and it works, I created a loop and
wrote the conformers as individual SDF file (code below), then I combine
all the individual SDF files into one using Openbabel GUI (not an ideal way
to do),
conformer.Setup(mol,5);
conformer.GetConformers(mol);
for(int i=1;i<6;i++) {
mol.SetConformer(i);
String fileName = "fileName"+ i +".sdf";
conv.WriteFile(mol,fileName); //
}
Is there a way that I could do it programmatically to combine all the
individual files into a single SDF file? any hints? Thank you.
On Wed, Dec 20, 2017 at 2:12 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Have you tried SetConformer(int n)? This switches the coordinates of the
> molecule between the available conformers.
>
> On 20 December 2017 at 12:35, Vinothkumar Mohanakrishnan <
> kmvin...@gmail.com> wrote:
>
>> Dear OpenBabelers
>>
>> I am using OpenBabel in my Java application.I would like to generate set
>> of conformers for my molecule using Openbabel and write the generated
>> conformers to an output file (SDF format).
>>
>> I am able to generate the conformers using GetConformers method in
>> OBConformerSearch class, Since, the return type of the method is void, I am
>> not able to get hold of the generated conformers and write them to the
>> output file. It would be great if I can have a list of generated conformers
>> which I can later write them in an SDF file?
>>
>> Below is the java code, by the way with this code, writes only one
>> generated conformer to the output file.
>>
>> System.loadLibrary("openbabel_java");
>>
>> OBMol mol = new OBMol();
>>
>> OBConformerSearch conformer = new OBConformerSearch();
>>
>> OBConversion conv = new OBConversion();
>>
>> conv.ReadFile(mol,"input.mol");
>>
>> conv.SetOutFormat("sdf");
>>
>> conformer.Setup(mol,5);
>>
>> conformer.GetConformers(mol);
>>
>> conv.WriteFile(mol, "conformers.sdf");
>>
>>
>> I have seen a similar post
>>
>> (
>> http://forums.openbabel.org/Generating-a-diverse-set-of-conf
>> ormers-td4656011.html
>> )
>> in python but there seems to be no answer.
>> Any suggestion in the right direction is highly appreciated. Thank you.
>>
>> --
>> Regards
>> Vinothkumar Mohanakrishnan
>>
>>
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>
--
Regards
Vinothkumar Mohanakrishnan
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