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[Open Babel] PubChem XML molecular file format

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[Open Babel] PubChem XML molecular file format

Rich Apodaca
I've recently encountered the PubChem XML molecular file format. It does not
look like any form of CML I've seen before, so I was wondering if it was
related in some way. If not, does anyone know the reasoning behind using it
instead of, say, CML? What level of software support is there for PubChem's
format?

It then struck me that I don't remember ever seeing a comprehensive summary of
XML-based molecular file formats. So far, I'm only aware of these:

- CML1 & CML2
- PubChem
- CDML (BKChem)
- OctetML (still in development)

Are there any others?

thanks,
rich




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Re: [Open Babel] PubChem XML molecular file format

Jean Bréfort-3
Le vendredi 07 octobre 2005 à 01:03 -0500, Rich Apodaca a écrit :

> I've recently encountered the PubChem XML molecular file format. It does not
> look like any form of CML I've seen before, so I was wondering if it was
> related in some way. If not, does anyone know the reasoning behind using it
> instead of, say, CML? What level of software support is there for PubChem's
> format?
>
> It then struck me that I don't remember ever seeing a comprehensive summary of
> XML-based molecular file formats. So far, I'm only aware of these:
>
> - CML1 & CML2
> - PubChem
> - CDML (BKChem)
> - OctetML (still in development)
>
> Are there any others?

GChemPaint



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Re: [Open Babel] PubChem XML molecular file format

Jonathan Brecher
At 2:20 AM -0400 10/7/05, Jean Bréfort wrote:

>Le vendredi 07 octobre 2005 à 01:03 -0500, Rich Apodaca a écrit :
>>  I've recently encountered the PubChem XML molecular file format. It does not
>>  look like any form of CML I've seen before, so I was wondering if it was
>>  related in some way. If not, does anyone know the reasoning behind using it
>>  instead of, say, CML? What level of software support is there for PubChem's
>>  format?
>>
>>  It then struck me that I don't remember ever seeing a
>>comprehensive summary of
>>  XML-based molecular file formats. So far, I'm only aware of these:
>>
>>  - CML1 & CML2
>>  - PubChem
>>  - CDML (BKChem)
>>  - OctetML (still in development)
>>
>>  Are there any others?
>
>GChemPaint

CDXML (http://sdk.cambridgesoft.com/chemdraw/cdx/)
XDFile (http://www.mdl.com/downloads/public/ctfile/ctfile.jsp)

...and probably LOTS of others.  XML is a language, not a file format.


Jonathan Brecher
CambridgeSoft Corporation
[hidden email]


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Re: [Open Babel] PubChem XML molecular file format

Geoffrey Hutchison

On Oct 7, 2005, at 10:04 AM, Jonathan Brecher wrote:

>>>  - CML1 & CML2
>>>  - PubChem
>>>  - CDML (BKChem)
>>>  - OctetML (still in development)
>> GChemPaint
> CDXML (http://sdk.cambridgesoft.com/chemdraw/cdx/)
> XDFile (http://www.mdl.com/downloads/public/ctfile/ctfile.jsp)

CRK (http://crk.sourceforge.net/)
PDBML (http://pdbml.rcsb.org/)
ArgusLab (http://arguslab.com/)

To echo Jonathan's comments, I'm sure there are many, many XML-based  
formats now. If anything, XML makes it easier to write an in-house  
format or custom store for a proprietary format, etc.

Cheers,
-Geoff


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