Stereochemistry functions
Some inputs about stereochemistry from Paul:
and
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/445/cids/JSON?cids_type=same_parent_isotopes
will give the same list, the query CID will always come first in the list, but the ordering of the others is basically arbitrary.
...
“get me a stereochemistry neutral parent”
First get the parent, e.g.
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/44229196/cids/JSON?cids_type=parent
… and then take the result of that (cid 9899562) and get stereo variants with
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/9899562/cids/JSON?cids_type=same_isotopes
same as this if you want to just look at the list visually:
OR
with PUG REST in two steps.
First get the (7) stereo variants of the parent like above, but store the list for use in a second call:
{
"IdentifierList": {
"ListKey": "1550642116508648379",
"Size": 7,
"EntrezDB": "pccompound",
"EntrezWebEnv": "MCID_6093c529f6ba3b5f61217454",
"EntrezQueryKey": 1,
"EntrezURL": "https://www.ncbi.nlm.nih.gov/sites/entrez?cmd=HistorySearch&WebEnvRq=1&hinit=true&db=pccompound&WebEnv=MCID_6093c529f6ba3b5f61217454&query_key=1"
}
}
Then use that listkey to get stereo atom (sp3) and bond (sp2) information:
Note that CID 445 is the only one with fully undefined (undefined count = total) atom stereo:
{
"CID": 445,
"AtomStereoCount": 2,
"DefinedAtomStereoCount": 0,
"UndefinedAtomStereoCount": 2,
"BondStereoCount": 0,
"DefinedBondStereoCount": 0,
"UndefinedBondStereoCount": 0
}