I assume your second command is actually using output2D.sdf as input?
-David
> On Oct 13, 2017, at 3:46 PM, Sundar <jubilantsun...@gmail.com> wrote:
>
> Sure.
> Here it goes.
>
> obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O
> output2D.sdf
> obabel output3D.sdf --gen3d -O output3D.sdf
>
> output2D.sdf contains 7581 compounds exactly as in input.smi but
> output3D.sdf only has 881 compounds.
>
> Thanks,
> Sundar
>
>
>> On Fri, Oct 13, 2017 at 2:18 PM, Noel O'Boyle <baoille...@gmail.com> wrote:
>> I'm a bit confused. Can you write out in full the commands you used?
>>
>>> On 13 Oct 2017 6:53 p.m., "Sundar" <jubilantsun...@gmail.com> wrote:
>>> Hi Noel,
>>>
>>> No. I used --unique option to generate 2D coformations from smiles and got
>>> ~7000 compounds.
>>> While generating 3D from the 2D I only used --gen3d
>>>
>>> Thanks,
>>> Jubilant
>>>
>>>> On Fri, Oct 13, 2017 at 11:28 AM, Noel O'Boyle <baoille...@gmail.com>
>>>> wrote:
>>>> Hi there,
>>>>
>>>> The "--unique" option removes duplicates. My guess is that you have only
>>>> 800 unique compounds.
>>>>
>>>> Regards,
>>>> - Noel
>>>>
>>>>> On 13 October 2017 at 11:58, Sundar <jubilantsun...@gmail.com> wrote:
>>>>> Hi everyone,
>>>>>
>>>>> I am pretty new to OB. I am trying to convert a database of compounds
>>>>> (~7000) from smiles to 3D.
>>>>> I first converted them into 2D using -h -r --unique -b -c --partialcharge
>>>>> mmff94
>>>>> followed by --gen3d.
>>>>> It only converted ~800 compounds saying nothing about other conformers.
>>>>> Any idea it behaves this way?
>>>>>
>>>>> -Jubilant
>>>>>
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>>>
>
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