Converting from compound name to chemical structure

Asked by over 1 year ago

Hi all,

Following on from an earlier question (http://blueobelisk.shapado.com/questions/synomyns-of-compounds)

I was wondering if anybody could help me figure out a comprehensive way of converting compound names to smiles structures.

The best I have so far is this python script:

from cinfony import webel

import urllib2

namelist=[‘rapamycin’,‘aspirin]

for name in namelist:

try:

compound = webel.readstring(“name”, name)

print compound.smiles

except urllib2.HTTPError:

print “Failed to resolve %s” % (name)

compound = “NA”

My problem with this approach is that it doesn’t identify the structure of 'rapamycin’

This could be fixed by using the chemspider resovler (http://cactus.nci.nih.gov/blog/?p=1386) such as

http://cactus.nci.nih.gov/chemical/structure/Rapamycin/smiles?resolver=namebychemspider

Any pointers on how to modify my script to use this resolver, or even an alternative approach completely, greatly received

Cheers,

Iain

3 answers

**Noel O'Boyle [ Admin ] from Unknown** Dec 6, 2011 (Edited Dec 7, 2011)

I’ll log this as a feature request for webel. In the meanwhile, you’ll have to do it manually:
>>> print urllib2.urlopen(“http://cactus.nci.nih.gov/chemical/structure/rapamycin/smiles?resolver=name_by_chemspider”).read() C3([C@@H]1CCCCN1C(=O)C([C@@]2(O[C@@H](CC[C]2[CH2])C[C](C(=[C][C]=[C][C]=[C][C](C [C](C([C]([C](C(=[C][C](C(C[C@H](O3)[C](C[C@@H]4CC[C]([C](C4)O[CH2])[O])[CH2])=O )[CH2])[CH2])[O])O[CH2])=O)[CH2])[CH2])[CH2])O[CH2])[O])=O)=O

NN comments

Note that this version lost double bond stereochemistry (compare with the KEGG version above).

Dec 8, 2011

Daniel’s comment below would be an even better feature request for webel.

Dec 12, 2011

**wdiwdi [ Editor ] from Frankfurt am Main, Deutschland** Dec 5, 2011 (Edited Dec 8, 2011)

2 line Cactvs script:

lappend cactvs(lookuphosts) kegg
ens get [ens create rapamycin] E_SMILES

Result:

N24[C@H](C(OC([C](CC1C[C@H]([C@H](O)CC1)OC)C)CC([C](\C=C(\[C@H]([C@H](C([C](C[C](/C=C/C=C/C=C(/[C@H](C[C@H]3O[C@@](C(C2=O)=O)([C](CC3)C)O)OC)C)C)C)=O)OC)O)C)C)=O)=O)CCCC4

(I suggest to always use KEGG as first-line resolver for this kind of biological compound - the structures are more reliable than Chemspider or PubChem - though of course the database is smaller)

NN comments

**Daniel Lowe [ Editor ] from Cambridge, United Kingdom** Dec 8, 2011 (Edited Dec 8, 2011)

Your modified request I believe will only be using ChemSpider for name resolving.
You may get higher recall if you include the chemical identifier resolver’s database. As you can choose the order the resolvers are used in you can make a request such that the structure will always be returned from ChemSpider if the name is present there. There’s a nice guide on how to do this in Markus' blog:
http://cactus.nci.nih.gov/blog/?p=1386

NN comments

Cactvs has built-in support for name resolution by the NCI resolver, KEGG, ChemSpider (direct, not via NCI) and OPSIN. The sequence of contacting these is straightforward to configure.

Dec 8, 2011

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Converting from compound name to chemical structure

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**Noel O'Boyle [ Admin ] from Unknown** Dec 6, 2011 (Edited Dec 7, 2011)

**wdiwdi [ Editor ] from Frankfurt am Main, Deutschland** Dec 5, 2011 (Edited Dec 8, 2011)

**Daniel Lowe [ Editor ] from Cambridge, United Kingdom** Dec 8, 2011 (Edited Dec 8, 2011)

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Converting from compound name to chemical structure

3 answers

Noel O'Boyle [ Admin ] from Unknown Dec 6, 2011 (Edited Dec 7, 2011)

wdiwdi [ Editor ] from Frankfurt am Main, Deutschland Dec 5, 2011 (Edited Dec 8, 2011)

Daniel Lowe [ Editor ] from Cambridge, United Kingdom Dec 8, 2011 (Edited Dec 8, 2011)

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**Noel O'Boyle [ Admin ] from Unknown** Dec 6, 2011 (Edited Dec 7, 2011)

**wdiwdi [ Editor ] from Frankfurt am Main, Deutschland** Dec 5, 2011 (Edited Dec 8, 2011)

**Daniel Lowe [ Editor ] from Cambridge, United Kingdom** Dec 8, 2011 (Edited Dec 8, 2011)