On Mon, May 9, 2016 at 4:30 PM, Otis Rothenberger <osrot...@icloud.com>
wrote:
> I’ve hinted at this before, but Pierluigi’s note gives me cause to be
> specific: Let’s not forget PubChem as a source of data other than 3d
> coordinates!
>
> Over the years, Jmol has become research and teaching powerful - no VERY
> powerful. Resolver was a logical partner for Jmol because it is also
> powerful. But let’s not forget PubChem. This is particularly true if your
> teaching interests are like mine: Basic general and organic chemistry small
> molecules. In this small molecule situation, many, if not most, molecules
> of interest are going to be in PubChem. So what? Well for one thing,
> important look-up information is curated in PubChem. This is really what
> Marcus was striving for with his name look-up index help request, and this
> is what resulted in the ill fated Volhardt project conducted by two hacks
> with copies of Volhardt in their hands.
>
> Getting PubChem data (e.g. curated calculated IUPAC names) is fast and
> easy:
>
>
> http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSON?callback=corsPubChempcdM&smiles=CCOCCC
>
> Parsing is a bit of a hassle,
...I don't think so. JSON is a subset of Jmol scripting.
*$ x =
eval(load("http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSON?callback=corsPubChempcdM&smiles=CCOCCC
<http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSON?callback=corsPubChempcdM&smiles=CCOCCC>"))$
print x.PC_Compounds[1].props.select("(value) where urn.label='IUPAC
name'")..1.sval*
1-ethoxypropane
*$ print x.PC_Compounds[1].props.select("(value) where
urn.label='InChI'")..1.sval*
InChI=1S/C5H12O/c1-3-5-6-4-2/h3-5H2,1-2H3
*$ print
x.PC_Compounds[1].props.select("(urn,value)").select("label,name,fval,sval,ival")*
{
"ival" : 1
}
{
"label" : "Compound"
"name" : "Canonicalized"
}
{
"fval" : 19.9
}
{
"label" : "Compound Complexity"
}
{
"ival" : 1
}
{
"label" : "Count"
"name" : "Hydrogen Bond Acceptor"
}
{
"ival" : 0
}
{
"label" : "Count"
"name" : "Hydrogen Bond Donor"
}
{
"ival" : 3
}
{
"label" : "Count"
"name" : "Rotatable Bond"
}
{
}
{
"label" : "Fingerprint"
"name" : "SubStructure Keys"
}
{
"sval" : "1-ethoxypropane"
}
{
"label" : "IUPAC Name"
"name" : "Allowed"
}
{
"sval" : "1-ethoxypropane"
}
{
"label" : "IUPAC Name"
"name" : "CAS-like Style"
}
{
"sval" : "1-ethoxypropane"
}
{
"label" : "IUPAC Name"
"name" : "Preferred"
}
{
"sval" : "1-ethoxypropane"
}
{
"label" : "IUPAC Name"
"name" : "Systematic"
}
{
"sval" : "1-ethoxypropane"
}
{
"label" : "IUPAC Name"
"name" : "Traditional"
}
{
"sval" : "InChI=1S/C5H12O/c1-3-5-6-4-2/h3-5H2,1-2H3"
}
{
"label" : "InChI"
"name" : "Standard"
}
{
"sval" : "NVJUHMXYKCUMQA-UHFFFAOYSA-N"
}
{
"label" : "InChIKey"
"name" : "Standard"
}
{
"fval" : 1.3
}
{
"label" : "Log P"
"name" : "XLogP3-AA"
}
{
"fval" : 88.08881
}
{
"label" : "Mass"
"name" : "Exact"
}
{
"sval" : "C5H12O"
}
{
"label" : "Molecular Formula"
}
{
"fval" : 88.14818
}
{
"label" : "Molecular Weight"
}
{
"sval" : "CCCOCC"
}
{
"label" : "SMILES"
"name" : "Canonical"
}
{
"sval" : "CCCOCC"
}
{
"label" : "SMILES"
"name" : "Isomeric"
}
{
"fval" : 9.2
}
{
"label" : "Topological"
"name" : "Polar Surface Area"
}
{
"fval" : 88.08881
}
{
"label" : "Weight"
"name" : "MonoIsotopic"
}
The data extraction from the JSONP above is tricky because these PubChem
> data files *are not consistent from compound to compound*.
>
>
Then you should contact PubChem and get them to fix that.
Bob
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