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phetsims / build-a-molecule

"Build a Molecule" is an educational simulation in HTML5, by PhET Interactive Simulations.
GNU General Public License v3.0
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More examples of incorrect nomenclature #153

Closed arouinfar closed 4 years ago

arouinfar commented 4 years ago

In #149 we discovered that the database had an incorrect entry for ethenone. Since that issue contained some tangential discussion, @Denz1994 and I decided to open a new issue to document other examples. There are more than 9000 named molecules in otherMoleculesData.js, and it's unreasonable to check them all by hand. However, a good rule of thumb would be for QA to cross-reference the pubchem database whenever they encounter a named molecule they are unfamiliar with.

This structure is not butane (C4H10). @Denz1994 confirmed there is error in otherMoleculeData.js which begins with butane|C4H9|137553|...

(As a side note the 3rd datapoint in the entry is the PubChem CID, which reveals this entry belongs to 2-butyl radical. This echos a bit of #150).

Denz1994 commented 4 years ago

The entry for C4H9|Butane was removed. The PubChem entry for Butane includes an alternate listing for Butane as C4H10|n-Butane, which is currently being used.

I think #148 needs to be fixed before we can create it though. I was only able to create isobutane. image

Denz1994 commented 4 years ago

Also worth noting, the full source of molecules can be found here: Collection Molecules and Other Molecules

The Collection Molecules data is formated so it is read like so: moleculeName|generalFormula|compoundCID|2d3dOrBoth|totalAtoms|totalBonds|{Element n xyz}.

You can navigate the data set with a search for the {moleculeName}| for example.

arouinfar commented 4 years ago

@Denz1994 we should have two entries for C4H10: n-butane and isobutane. The Java sim currently handles both cases correctly. The C4H9 entry for butane is the incorrect one.

Denz1994 commented 4 years ago

@Denz1994 we should have two entries for C4H10: n-butane and isobutane. The Java sim currently handles both cases correctly. The C4H9 entry for butane is the incorrect one.

Confirmed in otherMoleculesData.js we have both n-butane and isobutane as C4H10.

Denz1994 commented 4 years ago

It was discussed during the design meeting on 01/31/20:

We haven't gotten reports of problematic molecules. We should leave up to users to report on any molecules that are incorrect. QA shouldn't have to check against each molecule for its existence.

Denz1994 commented 4 years ago

@ariel-phet mentioned:

If QA finds an obvious problem with the name of a molecule that is built during testing, then it should be reported. But other than that we will defer to user reports.

I will close this issue and any erroneous molecules that are noted during testing a separate issue should be opened. Closing this issue.