Re: [Cdk-devel] CDK 1.1.x series

[Daniel Z. <zah...@dt...>]

On May 2, 2008, at 9:12 AM, Rajarshi Guha wrote:

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> On May 2, 2008, at 8:35 AM, Daniel Zaharevitz wrote:
>>
>> On May 2, 2008, at 7:06 AM, Daniel Zaharevitz wrote:
>>
>>>
>>> On May 2, 2008, at 1:34 AM, Rajarshi Guha wrote:
>>>>
>>>> - - add missing elements to atom type perception code
>>>
>>> I'm not sure if I sent you the final list, but I used the version  
>>> from a few months ago to run through all our open compounds  
>>> (~270K) and check to see if the computer representation of the  
>>> structure matched with the listed molecular formula. This  
>>> resulted in about 16K failures due to unparameterized atom. Most  
>>> of these were various heavy atoms, but there were some N, O, C  
>>> type failures as well. I can certainly send you that error set,  
>>> but it might be more useful to rerun with the current version.  
>>> Let me know what you would find useful.
>>>
>>>
>>
>> I just realized that it is easy to get to the unparameterized  
>> atoms. I put the comparison result as a comment in the update we  
>> sent to PubChem a few months ago. If you search in PubChem  
>> Substances for "Unparameterized Atom" with limits of Source = DTP/ 
>> NCI you will get the compounds that failed in the first pass.
>
> Can you send the query string to pull up those entries on PubChem?   
> just can't get it to recognize the word 'unparametrized'
>

This is cut and pasted from the text field. The quote marks are  
included in the query
"Unparameterized Atom"

It gets 15970 hits.


BTW, do you know of a way to share PubChem query results?

DanZ


/********************************************
    Daniel Zaharevitz
    Chief, Information Technology Branch
    National Cancer Institute
    zah...@dt...
********************************************/