search

CDK-R / rinchi

An R wrapper around the InChI functionality provided by the rcdk
1 stars 2 forks source link

Sporadic errors on InChI conversion #1

Open rickhelmus opened 5 years ago

rickhelmus commented 5 years ago

Hello,

I'm trying to use rinchi::parse.inchi for the automatic conversion of large lists of InChI strings to SMILES. Most of the time this works OK, but sometimes no result is returned and a warning is displayed that parsing failed. Some examples are listed below. Converting them with OpenBabel works fine.

InChI=1S/C5H7NO3/c1-3(6)2-4(7)5(8)9/h8H,1-2,6H2/q-1
InChI=1S/C5H6O4/c1-3(6)2-4(7)5(8)9/h6,8H,1-2H2/q-1
InChI=1S/C3H4O3/c1-2(4)3(5)6/h5H,1H3/q-1
InChI=1S/C5H7NO3/c6-3-1-2-4(7)5(8)9/h1,3,8H,2,6H2/q-1
InChI=1S/C11H10O3/c12-10(11(13)14)8-4-7-9-5-2-1-3-6-9/h1-7,13H,8H2/q-1
InChI=1S/C5H6O3/c1-2-3-4(6)5(7)8/h2,7H,1,3H2/q-1
InChI=1S/C6H6O5/c1-2-3(5(8)9)4(7)6(10)11/h2-3,10H,1H2,(H,8,9)/q-1
InChI=1S/C14H16O4/c15-11-6-2-1-4-9(11)8-10-5-3-7-12(16)13(10)14(17)18/h1-7,11-12,15-16H,8,13H2,(H,17,18)/p-1
InChI=1S/C14H16O3/c15-13-8-4-2-6-11(13)9-10-5-1-3-7-12(10)14(16)17/h1-7,12,15H,8-9,13H2,(H,16,17)/p-1
InChI=1S/C14H16O3/c15-13-8-4-2-6-11(13)9-10-5-1-3-7-12(10)14(16)17/h1-6,8,13,15H,7,9,12H2,(H,16,17)/p-1

Any clues?

Thanks, Rick

stanstrup commented 4 years ago

I am seeing the same too. My examples also works in ChemDraw.

InChI=1S/C4H9N3O2/c1-7(4(5)6)2-3(8)9/h2H2,1H3,(H4,5,6,8,9)
InChI=1S/C10H7NO3/c12-9-5-8(10(13)14)11-7-4-2-1-3-6(7)9/h1-5H,(H,11,12)(H,13,14)/p-2
InChI=1S/C10H14N4O4.F6P/c1-2-17-9(15)8(7-11)13-18-10(12)14-3-5-16-6-4-14;1-7(2,3,4,5)6/h12H,2-6H2,1H3;/q;-1/p+1/b13-8+;
stanstrup commented 4 years ago

These examples give errors like:

Problems/mismatches: Mobile-H( Hydrogens: Number; Mobile-H groups: Missing, Attachment points; Charge(s): Do not match; Proton balance: Does not match)

when I try in Openbabel GUI.