Re: [Cdk-user] Question about 3D SDF file from SMILES string

2018-05-20 Thread Xuan Cao 
Thank you!

On Sun, May 20, 2018, 12:49 PM John Mayfield, 
wrote:

> Sorry, intended that you replace "{smiles}" with your structure :-)
>
> On 20 May 2018 at 19:45, Egon Willighagen 
> wrote:
>
>>
>> Maybe a temporary glitch?
>> https://cactus.nci.nih.gov/chemical/structure/CCC/sdf works for me right
>> now...
>>
>> Egon
>>
>> On Sun, May 20, 2018 at 4:20 PM Xuan Cao 
>> wrote:
>>
>>> Hi John,
>>>
>>> Thank you for your reply! I will look into that!
>>>
>>> BTW, the link is not working (404).
>>>
>>> Xuan
>>>
>>> On 20 May 2018 at 02:16, John Mayfield 
>>> wrote:
>>>
 There is some support in the *builder3d *modules but there are better
 options out there. One day I'll find some time to update that code but
 depending on how many structure you need to convert the NCI resolver uses
 Corina (via CACTVS) IIRC.

 https://cactus.nci.nih.gov/chemical/structure/{smiles}/sdf

 John

 On 20 May 2018 at 06:08, Xuan Cao  wrote:

> Hi everyone!
>
> I am just wondering does CDK have the feature that convert SMILES
> string to 3D SDF file, or convert 2D SDF file to 3D SDF file?
>
> I see that there are some stand-alone programs that do the convert (2D
> to 3D), but I prefer using CDK if it has the feature.
>
> Thank you so much!
>
> Xuan
>
>
> --
> 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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>
>

>>>
>>> --
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>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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>>>
>>
>>
>> --
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Homepage: http://egonw.github.com/
>> LinkedIn: http://se.linkedin.com/in/egonw
>> Blog: http://chem-bla-ics.blogspot.com/
>> PubList: https://www.zotero.org/egonw
>> ORCID: -0001-7542-0286 
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>
>
>
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Re: [Cdk-user] Question about 3D SDF file from SMILES string

2018-05-20 Thread John Mayfield 
Sorry, intended that you replace "{smiles}" with your structure :-)

On 20 May 2018 at 19:45, Egon Willighagen 
wrote:

>
> Maybe a temporary glitch? https://cactus.nci.nih.gov/chemical/structure/
> CCC/sdf works for me right now...
>
> Egon
>
> On Sun, May 20, 2018 at 4:20 PM Xuan Cao  wrote:
>
>> Hi John,
>>
>> Thank you for your reply! I will look into that!
>>
>> BTW, the link is not working (404).
>>
>> Xuan
>>
>> On 20 May 2018 at 02:16, John Mayfield 
>> wrote:
>>
>>> There is some support in the *builder3d *modules but there are better
>>> options out there. One day I'll find some time to update that code but
>>> depending on how many structure you need to convert the NCI resolver uses
>>> Corina (via CACTVS) IIRC.
>>>
>>> https://cactus.nci.nih.gov/chemical/structure/{smiles}/sdf
>>>
>>> John
>>>
>>> On 20 May 2018 at 06:08, Xuan Cao  wrote:
>>>
 Hi everyone!

 I am just wondering does CDK have the feature that convert SMILES
 string to 3D SDF file, or convert 2D SDF file to 3D SDF file?

 I see that there are some stand-alone programs that do the convert (2D
 to 3D), but I prefer using CDK if it has the feature.

 Thank you so much!

 Xuan

 
 --
 Check out the vibrant tech community on one of the world's most
 engaging tech sites, Slashdot.org! http://sdm.link/slashdot
 ___
 Cdk-user mailing list
 Cdk-user@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/cdk-user


>>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot__
>> _
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>
>
> --
> E.L. Willighagen
> Department of Bioinformatics - BiGCaT
> Maastricht University (http://www.bigcat.unimaas.nl/)
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: https://www.zotero.org/egonw
> ORCID: -0001-7542-0286 
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
--
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Re: [Cdk-user] Question about 3D SDF file from SMILES string

2018-05-20 Thread Egon Willighagen 
Maybe a temporary glitch?
https://cactus.nci.nih.gov/chemical/structure/CCC/sdf works for me right
now...

Egon

On Sun, May 20, 2018 at 4:20 PM Xuan Cao  wrote:

> Hi John,
>
> Thank you for your reply! I will look into that!
>
> BTW, the link is not working (404).
>
> Xuan
>
> On 20 May 2018 at 02:16, John Mayfield 
> wrote:
>
>> There is some support in the *builder3d *modules but there are better
>> options out there. One day I'll find some time to update that code but
>> depending on how many structure you need to convert the NCI resolver uses
>> Corina (via CACTVS) IIRC.
>>
>> https://cactus.nci.nih.gov/chemical/structure/{smiles}/sdf
>>
>> John
>>
>> On 20 May 2018 at 06:08, Xuan Cao  wrote:
>>
>>> Hi everyone!
>>>
>>> I am just wondering does CDK have the feature that convert SMILES string
>>> to 3D SDF file, or convert 2D SDF file to 3D SDF file?
>>>
>>> I see that there are some stand-alone programs that do the convert (2D
>>> to 3D), but I prefer using CDK if it has the feature.
>>>
>>> Thank you so much!
>>>
>>> Xuan
>>>
>>>
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>>
>>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
--
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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Re: [Cdk-user] Question about 3D SDF file from SMILES string

2018-05-20 Thread Xuan Cao 
Hi John,

Thank you for your reply! I will look into that!

BTW, the link is not working (404).

Xuan

On 20 May 2018 at 02:16, John Mayfield  wrote:

> There is some support in the *builder3d *modules but there are better
> options out there. One day I'll find some time to update that code but
> depending on how many structure you need to convert the NCI resolver uses
> Corina (via CACTVS) IIRC.
>
> https://cactus.nci.nih.gov/chemical/structure/{smiles}/sdf
>
> John
>
> On 20 May 2018 at 06:08, Xuan Cao  wrote:
>
>> Hi everyone!
>>
>> I am just wondering does CDK have the feature that convert SMILES string
>> to 3D SDF file, or convert 2D SDF file to 3D SDF file?
>>
>> I see that there are some stand-alone programs that do the convert (2D to
>> 3D), but I prefer using CDK if it has the feature.
>>
>> Thank you so much!
>>
>> Xuan
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>>
>
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Re: [Cdk-user] Question about 3D SDF file from SMILES string

2018-05-20 Thread John Mayfield 
There is some support in the *builder3d *modules but there are better
options out there. One day I'll find some time to update that code but
depending on how many structure you need to convert the NCI resolver uses
Corina (via CACTVS) IIRC.

https://cactus.nci.nih.gov/chemical/structure/{smiles}/sdf

John

On 20 May 2018 at 06:08, Xuan Cao  wrote:

> Hi everyone!
>
> I am just wondering does CDK have the feature that convert SMILES string
> to 3D SDF file, or convert 2D SDF file to 3D SDF file?
>
> I see that there are some stand-alone programs that do the convert (2D to
> 3D), but I prefer using CDK if it has the feature.
>
> Thank you so much!
>
> Xuan
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
--
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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