Yes.
Sundar Thangapandian
> On Oct 13, 2017, at 3:08 PM, David Hall <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> 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
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>>>> _______________________________________________
>>>>>> OpenBabel-discuss mailing list
>>>>>> OpenBabel-discuss@lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>>>
>>>>>
>>>>
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> OpenBabel-discuss mailing list
>> OpenBabel-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
