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Re: [Jmol-users] fun with Jmol -- xxxx.find("chemical",...)
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From: Otis R. <osr...@ic...> - 2016-05-09 16:38:33
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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. In the realm of Chemical Identifiers, molfile and SMILES are native to Jmol. Recently, Bob added an InChI app that returns standard InChI. It’s REALLY NEAT, but it’s a bit tricky to use. For “in-house” InChI, Jmol is going to Resolver. In the realm of Chemical Identifiers, molfile, SMILES, and JMEfile are native to JSME. While SMILES from different resources are variant, Bob implemented a process in Jmol that makes this point irrelevant! Jmol can communicate with JSME, Resolver, and your database with SMILES. It the latter case, it can compare SMILES it generates with SMILES in your database even if they were generated differently. Other issues to consider: OPSIN sits at the “front door” of Resolver. When you use Resolver, you are really putting additional power into OPSIN (https://cactus.nci.nih.gov/blog/?p=1523). Note that OPSIN is perfectly happy with incorrect IUPAC names (http://opsin.ch.cam.ac.uk/opsin/5-chlorohexane.png)! So I’m wondering if SMILES would not be a better choice for your comparison needs? For example: 1) Student draws JSME structure and enters (types) an IUPAC Name. 2) JSME SMILES is loaded into Jmol. 3) Student’s IUPAC Name is sent to Resolver for SMILES. Remember OPSIN at Resolver gets the 1st shot at reading this IUPAC name. All correctly structured names will be accepted. 4) Resolver returned SMILES is compared to Jmol SMILES. Alternatively, and more simply if you are OK with leaving the student grading out, would be to make JSME do all the work. The act of the student entering their IUPAC would return the IUPAC name for the JSME SMILES of the structure they drew. The comparison would be visual. By the way, if you give Resolver 5-chlorohexane, it simply says, “Ahem, I think you meant 2-chlorohexane” Or at least, you can make it say that! I can make some code suggestion if you want to go either route. Otis -- Otis Rothenberger ot...@ch... http://chemagic.org > On May 8, 2016, at 3:23 PM, Pierluigi Quagliotto <pie...@un...> wrote: > > Dear Bob, > > Last year I developed my teaching site: > > http://www.iorgchem.unito.it <http://www.iorgchem.unito.it/> > > I am trying to see if it is possible to implement the use of JSME as the 2D editor, JSMol as the 3D viewer and OPSIN as the naming "resolver". Since I am, however, a beginner as a programmer, I will have to test a lot the code I will produce, in order to see if I can obtain something useful. Since in my site the molecules used for quizzes are stored into a DB (prepared with MolDB6), I could imagine at least two possibilities: > > 1) to prepare one page in which students can use my DB with already available molecules for which the SMILES and Inchi are already present (calculated by MolDB6 when molecules are inserted into the DB). When students submit a name for the molecule, OPSIN would calculate the Inchi and by simple comparison with the given Inchi, it would be possible to know if the answer is correct or not. > > 2) to prepare a page in which the user / student can draw its own molecule and try to name it. In this case I would use directly JSmol to calculate the Inchi. by comparison with the OPSIN derived Inchi, the user would obtain the feedback about his answer. > > > My question is about the JSMol capabilities. I looked at your definition of the function of JSMol to obtain the Inchi. I would be certain that JSMol can convert a SMILES into Inchi, without using the NCI resolver. Am I right about this feature or the resort to NCI resolver is needed? This is a fantastic resource, but only molecules inside to its DB can be found and named. My goal would be to give everyone the possibility to find a name for a molecule, within the capabilities of OPSIN. It would be also interesting, if this idea could be implemented, to include OPSIN into the programs of the JSMol release, obviously if the JSMol and OPSIN licenses can agree each other. > > This should be a definite way to give JSmol all the power for organic chemistry teaching. > > Sorry for my long message, I am quite "verbose".... > > Many thanks for your attention and your huge effort to develop a wonderful piece of software! > > Pierluigi > > 2016-03-24 14:48 GMT+01:00 Robert Hanson <ha...@st... <mailto:ha...@st...>>: > Great, yes. > > I use this feature in class a lot when I am teaching organic chemistry. > > On Thu, Mar 24, 2016 at 4:05 AM, Pierluigi Quagliotto <pie...@un... <mailto:pie...@un...>> wrote: > Dear Bob, > > many thanks! > > I will update the JSMol version on my site and I will try to implement this feature. > > It should be amazing to have a naming feature that could give IUPAC names to every (almost...) structure we can draw. I will imagine this is quite difficult to implement. > > However this naming feature based on NCI database is very interesting, at least to give students and visitors of my site to have a chance to find a coorect name. The other option to have a name is to draw a structure, and naming it with the student ability and let the student to check it by using OPSIN to get the structure. if the name is correct the structure will be the same the student has drawn. A bit more complicated, but the students could improve their ability in writing formulas correctly and naming them. > > I will elt you know about the improving of my site. > > Thanks again and bye! > > Pierluigi > > 2016-03-23 19:42 GMT+01:00 Robert Hanson <ha...@st... <mailto:ha...@st...>>: > Nothing stops you from adding that to your pages, Pierluigi! :) > > In answer to the question, the name/SMILES, SMILES/name and SMILES/structure conversion is going through the NCI CACTVS resolver, which is just a fantastic resource. > > structure/SMILES conversion is done within Jmol unless it is > > print {*}.find("SMILES/NCI") > print {*}.find("SMILES/canonical") > > (these are just two ways of requesting the same thing) > > in which case it goes through NCI > > > Bob > > > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140> > _______________________________________________ > Jmol-users mailing list > Jmo...@li... <mailto:Jmo...@li...> > https://lists.sourceforge.net/lists/listinfo/jmol-users <https://lists.sourceforge.net/lists/listinfo/jmol-users> > > > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140> > _______________________________________________ > Jmol-users mailing list > Jmo...@li... <mailto:Jmo...@li...> > https://lists.sourceforge.net/lists/listinfo/jmol-users <https://lists.sourceforge.net/lists/listinfo/jmol-users> > > > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr <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 > > > ------------------------------------------------------------------------------ > Transform Data into Opportunity. > Accelerate data analysis in your applications with > Intel Data Analytics Acceleration Library. > Click to learn more. > http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140> > _______________________________________________ > Jmol-users mailing list > Jmo...@li... <mailto:Jmo...@li...> > https://lists.sourceforge.net/lists/listinfo/jmol-users <https://lists.sourceforge.net/lists/listinfo/jmol-users> > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z_______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users |
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