Are you able to provide files that show this? Or reduce it to single compounds
that are being eliminated that can be shared?
> On Oct 24, 2017, at 8:53 PM, Sundar <jubilantsun...@gmail.com> wrote:
>
> Hi,
>
> I am refreshing this thread for an answer.
>
> obabel input.smi -h -r -b -c --unique --gen2d --partialcharge mmff94 -O
> output2D.sdf
> obabel output2D.sdf --gen3d -O output3D.sdf
>
> output2D.sdf contains 7581 compounds exactly as in input.smi but
> output3D.sdf only has 881 compounds.
>
> Can someone tell me why this happens?
>
> I had several warnings on Stereochemistry of the molecules and using distance
> geometry method instead.
>
> Thanks,
> Sundar
>
> On Fri, Oct 13, 2017 at 5:56 PM, Sundar Jubilant <jubilantsun...@gmail.com
> <mailto:jubilantsun...@gmail.com>> wrote:
> Yes.
>
> Sundar Thangapandian
>
> On Oct 13, 2017, at 3:08 PM, David Hall <li...@cowsandmilk.net
> <mailto:li...@cowsandmilk.net>> wrote:
>
>> 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
>> <mailto: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
>>> <mailto: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
>>> <mailto: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
>>> <mailto: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
>>> <mailto: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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