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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