Dear All,
many thanks for your kind attention and all time you lost to give me some
info about the whole problem,
The delay in answering you was due to the fact that I tried to inspect the
code in your pages. You did a lot of work to obtain this. In order to make
something similar probably I would need to spend a year only in increasing
my programming abilities.
I had a look to the pages Otis and Bob linked, referring also to the new
topic "Let's Not Forget PubChem".
First of all, I was not fully aware of the integration of OPSIN into the
Resolver. The integration now is at the 1.2 version, while on the OPSIN
site it is claimed that OPSIN 2.1.0 was released in March, 2016.
I tried the page Otis has just set-up and this is a very interesting way to
help student in determining the name by using both the Resolver and
PubChem. Unfortunately, by writing a few structures the Resolver or even
both the Resolver and PubChem failed to attribute a name. I have used also
structures from my DB and some of them could not be solved by both sites..
1) 7-ethyl-3,5-dimethyl-4-propyldodecane
2) 3-chloro-3-ethyl-4-methylpentanoic acid
were not solved by both sites.
Using the Bob page: http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm
and giving these names to solve to NCI-resolver, the molecular
structure were produced correctly.
I would imagine that this occurs since the request from this page is solved
by the OPSIN call in Resolver, while sending a molecule by JSME is not
found, since the search is performed with other ways.
a fun view on PubChen is that the 2-chlorohexane that was correctly solved
by the Resolver, (bypassing the errors featured by OPSIN, that can name the
product also as 5-chlorohexane) is named as 2-chloranylhexane by PubChem.
By using the Bob Inchi page, both 2- and 5-chlorohexane are introduced,
giving, obviously, the same molecule. In view to present to students this
opportunity to find names, these errors can give some troubles to students.
Luckily, I tried directly on the OPSIN site and these structure were solved
and all representation were produced, starting from the name that I
indicated on my site as the solution.
I read on the Resolver site that OPSIN is the first trial to solve the
problem and after the Resolver works around the problem to solve it using
other ways. This should let the possibility that the structure that now
made the two sites to fail, should give good results, once the Resolver
will update to this version of OPSIN.
A JSME / JSMol page could be imagined in which beside the names coming from
different sources, like Resolver and PubChem, in which the different
aspects showed in the Bob and Otis pages can be combined, to let people
aware that Organic Nomenclature is a real puzzle also for actual open
source cheminformatics.
I will try to have a deeper look on the code you produced, just to know
more about it and I will let you know. Your help will be needed for sure.
Many thanks again!
Pierluigi
2016-05-10 10:40 GMT+02:00 Pierluigi Quagliotto <
pierluigi.quaglio...@unito.it>:
> Dear All,
>
> many thanks for your kind attention and all time you lost to give me some
> info about the whole problem,
>
> I had a look to the pages Otis and Bob linked, referring also to the new
> topic "Let's Not Forget PubChem".
>
> First of all, I was not fully aware of the integration of OPSIN into the
> Resolver. The integration now is at the 1.2 version, while on the OPSIN
> site it is claimed that OPSIN 2.1.0 was released in March, 2016.
>
> I tried the page Otis has just set-up and this is a very interesting way
> to help student in determining the name by using both the Resolver and
> PubChem. Unfortunately, by writing a few structures the Resolver or even
> both the Resolver and PubChem failed to attribute a name. I have used also
> structures from my DB and some of them could not be solved by both sites..
>
>
> 1) 7-ethyl-3,5-dimethyl-4-propyldodecane
>
> 2) 3-chloro-3-ethyl-4-methylpentanoic acid
>
>
>
> Luckily, I tried directly on the OPSIN site and these structure were
> solved and all representation were produced, starting from the name that I
> indicated on my site as the solution.
> I read on the Resolver site that OPSIN is the first trial to solve the
> problem and after the Resolver works around the problem to solve it using
> other ways. This should let the possibility that the structure that now
> made the two sites to fail, should give good results, once the Resolver
> will update to this version of OPSIN.
>
> 2016-05-09 20:48 GMT+02:00 Robert Hanson <hans...@stolaf.edu>:
>
>> I note that JSmol now includes a client-side InChI calculator. See
>>
>> http://chemapps.stolaf.edu/jmol/jsmol/inchi.htm
>>
>> for more.
>>
>> Bob
>>
>> On Mon, May 9, 2016 at 12:51 PM, Otis Rothenberger <osrot...@icloud.com>
>> wrote:
>>
>>> One more JSME point on this subject. The JSME call backs that I
>>> mentioned in this chain can handle the IUPAC dynamically as the structure
>>> is edited. Again, here are all the new callbacks:
>>>
>>> BeforePaste, AfterPaste, AfterStructureModified, AtomHighlight,
>>> BondHighlight, AtomClicked, BondClicked
>>>
>>> Any on these callbacks could be use to communicate with Resolver and
>>> place the IUPAC directly in JSME - i.e. the info holder bottom left. The
>>> logical callbacks for IUPAC would be AfterStructureModified and/or
>>> AfterPaste. Returned ResolverData after AJAX can be shown via:
>>>
>>> document.JME.showInfo(ResolverData)
>>>
>>> VERY IMPORTANT RESOLVER POINT IN ALL OF THIS:
>>>
>>> Resolver is not calculating these IUPAC’s. It is looking them up! This
>>> goes back to the Herculean (to me) task of indexing all Volhardt compounds.
>>> In Markus’ own words from his again viewable blog:
>>>
>>>
>>> “We took great care during the implementation of the name index for this
>>> web service, however, we are aware of that it is far from perfect and has
>>> quite few errors in it. Unfortunately, these errors are not easy to to
>>> find if you have to deal with millions of names and their proper assignment
>>> to the correct chemical structure. If you find any mistakes, please tell
>>> us. Our plan is to improve the name index over the time but we are of
>>> course happy about any contributions helpful for this process. Thanks!”
>>>
>>> And yes, he is talking about trivial AND IUPAC names above.
>>>
>>>
>>> Otis
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.org
>>> http://chemagic.org
>>>
>>> On May 9, 2016, at 1:24 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>>>
>>>
>>>
>>> On Mon, May 9, 2016 at 11:39 AM, Otis Rothenberger <osrot...@icloud.com>
>>> wrote:
>>>
>>>> Hi Pierluigi-
>>>>
>>>> For reasons that I do not fully understand, OPSIN returns InChI - not
>>>> standard InChI. It does, however, return standard InChIKey! In general, I’d
>>>> be very nervous about comparing InChI strings created by different
>>>> resources.
>>>>
>>>>
>>> NCI Resolver returns both. You just have to ask for the right one.
>>>
>>> https://cactus.nci.nih.gov/chemical/structure/biphenol/stdinchi
>>>
>>> not
>>>
>>> https://cactus.nci.nih.gov/chemical/structure/biphenol/inchi
>>>
>>> I made that correction in Jmol some time back.
>>>
>>> Jmol has a broad range of comparison functions that do exactly what you
>>> want to do. Take a look at the find() and compare() functions. Also note
>>> the JSME needs to be carefully set up to deliver the right sort of SMILES.
>>> See jsmol/jsmetest.htm and jsmol/jsmetest2.htm in the distribution.
>>>
>>>
>>>
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>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Department of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>>
>>
>> ------------------------------------------------------------------------------
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>> tiers of
>> your business applications. It resolves application problems quickly and
>> reduces your MTTR. Get your free trial!
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>>
>
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