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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