Re: [Open Babel] gen3d doesn't convert all compounds

[Sundar]

Hi David and Geoff,

I ran the calculation again to reproduce the problem and realized that it
was my computer's memory that caused the program to abort not converting
all the compounds.
This time it converted all compounds. So no worries there. I still got
several following warnings though.
"*** Open Babel Warning  in CorrectStereoAtoms
  Could not correct 2 stereocenter(s) in this molecule (6674)
  with Atom Ids as follows: 7 9
Warning: Stereochemistry is wrong, using the distance geometry method
instead
"
The command I ran is
$ obabel 2D.sdf -O 3D.sdf --gen3d

But I still see 0. for z-coordinates for several compounds. Do you
still want those compounds to test yourself?

Thanks,
Jubilant

On Wed, Oct 25, 2017 at 9:39 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:

> > Are you able to provide files that show this? Or reduce it to single
> compounds that are being eliminated that can be shared?
>
> Even if it’s only a subset, that would be helpful.
>
> I’m working on a distance geometry method that should offer increased
> range. Either way, having examples is crucial.
>
> Thanks,
> -Geoff
>
>
>
> 
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Re: [Open Babel] gen3d doesn't convert all compounds

[Geoffrey Hutchison]

> Are you able to provide files that show this? Or reduce it to single 
> compounds that are being eliminated that can be shared?

Even if it’s only a subset, that would be helpful.

I’m working on a distance geometry method that should offer increased range. 
Either way, having examples is crucial.

Thanks,
-Geoff



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Re: [Open Babel] gen3d doesn't convert all compounds

[David Hall]

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  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  > wrote:
> Yes. 
> 
> Sundar Thangapandian
> 
> On Oct 13, 2017, at 3:08 PM, David Hall  > wrote:
> 
>> I assume your second command is actually using output2D.sdf as input?
>> 
>> -David
>> 
>> On Oct 13, 2017, at 3:46 PM, Sundar > > 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 >> > 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" >> > 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 >> > 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 >> > 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 ! 
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>>> 
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss 
>>> 
>>> 
>>> 
>>> 
>>> 
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>>> 
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss 
>>> 
> 

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Re: [Open Babel] gen3d doesn't convert all compounds

[Sundar Jubilant]

Yes. 

Sundar Thangapandian

> On Oct 13, 2017, at 3:08 PM, David Hall  wrote:
> 
> I assume your second command is actually using output2D.sdf as input?
> 
> -David
> 
>> On Oct 13, 2017, at 3:46 PM, Sundar  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  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"  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  
> 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  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
>> 
> 
 
>> 
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Re: [Open Babel] gen3d doesn't convert all compounds

[David Hall]

I assume your second command is actually using output2D.sdf as input?

-David

> On Oct 13, 2017, at 3:46 PM, Sundar  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  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"  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  
 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  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
> 
 
>>> 
> 
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Re: [Open Babel] gen3d doesn't convert all compounds

[Sundar]

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  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"  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 
>> 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  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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 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


>>>
>>
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Re: [Open Babel] gen3d doesn't convert all compounds

[Noel O'Boyle]

I'm a bit confused. Can you write out in full the commands you used?

On 13 Oct 2017 6:53 p.m., "Sundar"  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 
> 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  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
>>>
>>>
>>
>
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Re: [Open Babel] gen3d doesn't convert all compounds

[Sundar]

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  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  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
>>
>>
>
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Re: [Open Babel] gen3d doesn't convert all compounds

[Noel O'Boyle]

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  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
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
>
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[Open Babel] gen3d doesn't convert all compounds

[Sundar]

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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