On Jun 11, 2015, at 2:20 PM, Laëtitia Bomble wrote:
> Is there a rdkit tool to get IUPAC name of a molecule?
No, there isn't. If you only have a few names, and/or are
willing to wait for a web service, you can use the NCI
resolver at
http://cactus.nci.nih.gov/chemical/structure
For example, the following URL returns the IUPAC name
for caffeine:
http://cactus.nci.nih.gov/chemical/structure/C%5BN%5D1C=NC2=C1C(=O)N(C(=O)N2C)C/iupac_name
1,3,7-trimethylpurine-2,6-dione
I've appended a small program which uses that service. Here's
an example of how to use it:
% python nci_iupac_name.py c1ccccc1O CO
'InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3' 'ascorbic
acid'
c1ccccc1O PHENOL
CO methanol
InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
1,3,7-trimethylpurine-2,6-dione
ascorbic acid 2-(1,2-dihydroxyethyl)-4,5-dihydroxyfuran-3-one
Andrew
[email protected]
# Interface to the NCI services to get an IUPAC name
# given a SMILES, InChI, or other compound name/structure.
# Example:
# % python nci_iupac_name.py c1ccccc1O CO 'InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3' 'ascorbic acid'
# c1ccccc1O PHENOL
# CO methanol
# InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 1,3,7-trimethylpurine-2,6-dione
ascorbic acid 2-(1,2-dihydroxyethyl)-4,5-dihydroxyfuran-3-one
import sys
import urllib2
def fetch_nci_iupac_name(name):
quoted_name = urllib2.quote(name)
try:
f = urllib2.urlopen("http://cactus.nci.nih.gov/chemical/structure/%s/iupac_name";
% (quoted_name,))
iupac_name = f.read()
except urllib2.HTTPError, err:
code = err.getcode()
if code == 404:
# Not a valid structure
return None
raise
return iupac_name
def main(argv=None):
if argv is None:
argv = sys.argv
for name in argv[1:]:
iupac_name = fetch_nci_iupac_name(name)
if iupac_name is None:
iupac_name = "*"
sys.stdout.write("%s\t%s\n" % (name, iupac_name))
if __name__ == "__main__":
main()
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