From owner-chemistry@ccl.net Mon Jul 31 17:43:00 2017 From: "Franck Giacomoni franck.giacomoni===clermont.inra.fr" To: CCL Subject: CCL: Inchi to SVG format with obabel Message-Id: <-52913-170731164238-9845-hoo+YMTr4CCyMHPK2FDiag]=[server.ccl.net> X-Original-From: "Franck Giacomoni" Date: Mon, 31 Jul 2017 16:42:36 -0400 Sent to CCL by: "Franck Giacomoni" [franck.giacomoni^clermont.inra.fr] Dear CCLers, Here is my challenge: I manage a compounds collection with different type of features for each of them. One is the INCHI. I need to produce a SVG image to illustrate molecule structure. OpenBabel (v2.4.1), under MACOS 10.11.6 generates SVG from INCHI but I met issue with particular molecule. Example: 5,6-dihydrouracil from https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15901 got two carbonyl groups (C=O). But with obabel produce a SVG with two imine groups (N=C). This form represent only less than 0.01% of possible tautomers. The used INCHI was : InChI=1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8) I observed the same issue with conversion from inchi to SMILES Obabel produces OC1=NC(=NCC1)O instead of the right form found on ChEBI : O=C1CCNC(=O)N1 Do you have explanation of this issue? Thank you very much for your help Franck From owner-chemistry@ccl.net Mon Jul 31 21:34:00 2017 From: "Geoffrey Hutchison geoff.hutchison++gmail.com" To: CCL Subject: CCL: Inchi to SVG format with obabel Message-Id: <-52914-170731195433-17546-pqbhfQEqxZxmF/sa/3T4bg]*[server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="Apple-Mail=_3127E8BC-C5FE-4894-A6B7-785001219C03" Date: Mon, 31 Jul 2017 19:54:24 -0400 Mime-Version: 1.0 (Mac OS X Mail 10.3 \(3273\)) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison a gmail.com] --Apple-Mail=_3127E8BC-C5FE-4894-A6B7-785001219C03 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Dear Franck, Well.. first off, there's an Open Babel discussion list = openbabel-discuss:_:lists.sourceforge.net = and associated forum = (forums.openbabel.org )=20 The big problem with converting a molecule from an InChI is that you've = basically thrown away most of the useful information (e.g., the = connection table). You know what atoms are bonded, but not single bonds = and double bonds. I'd be happy to discuss this further, but I'll point out that say the = NIH Chemical Resolver gives similar depictions: = https://cactus.nci.nih.gov/chemical/structure/InChI=3D1S/C4H6N2O2/c7-3-1-2= -5-4(8)6-3/h1-2H2,(H2,5,6,7,8)/image = On the other hand, if you have a better representation (e.g., the = original connection table, or even the chemical name) you'll get a = better depiction: https://cactus.nci.nih.gov/chemical/structure/5,6-dihydrouracil/image = But in general, the best place IMHO to ask Open Babel questions is on = the Open Babel discussion list. :-) Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh:_:pitt.edu web: http://hutchison.chem.pitt.edu/ > On Jul 31, 2017, at 4:42 PM, Franck Giacomoni = franck.giacomoni=3D=3D=3Dclermont.inra.fr = wrote: >=20 >=20 > Sent to CCL by: "Franck Giacomoni" = [franck.giacomoni^clermont.inra.fr] > Dear CCLers, >=20 > Here is my challenge: I manage a compounds collection with different = type of features for each of them. One is the INCHI. > I need to produce a SVG image to illustrate molecule structure. > OpenBabel (v2.4.1), under MACOS 10.11.6 generates SVG from INCHI but I = met issue with particular molecule. >=20 > Example: 5,6-dihydrouracil from = https://www.ebi.ac.uk/chebi/searchId.do?chebiId=3D15901 got two carbonyl = groups (C=3DO). But with obabel produce a SVG with two imine groups = (N=3DC). This form represent only less than 0.01% of possible tautomers.=20= >=20 > The used INCHI was : = InChI=3D1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8) >=20 > I observed the same issue with conversion from inchi to SMILES > Obabel produces OC1=3DNC(=3DNCC1)O instead of the right form found on = ChEBI : O=3DC1CCNC(=3DO)N1=20 >=20 > Do you have explanation of this issue? >=20 > Thank you very much for your help > Franck >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_3127E8BC-C5FE-4894-A6B7-785001219C03 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
Dear Franck,

Well.. first off, there's an Open Babel = discussion list openbabel-discuss:_:lists.sourceforge.net and = associated forum (forums.openbabel.org) 

The big problem with converting a = molecule from an InChI is that you've basically thrown away most of the = useful information (e.g., the connection table). You know what atoms are = bonded, but not single bonds and double bonds.

I'd be happy to discuss this further, = but I'll point out that say the NIH Chemical Resolver gives similar = depictions:
https://cactus.nci.nih.gov/chemical/structure/InChI=3D1S/C4H6N2= O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8)/image

On the other hand, if = you have a better representation (e.g., the original connection table, = or even the chemical name) you'll get a better depiction:
https://cactus.nci.nih.gov/chemical/structure/5,6-dihydrouracil= /image

But = in general, the best place IMHO to ask Open Babel questions is on the = Open Babel discussion list. :-)

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Department of = Chemistry
University of Pittsburgh
tel: = (412) 648-0492
email: geoffh:_:pitt.edu
web: http://hutchison.chem.pitt.edu/

On Jul 31, 2017, at 4:42 PM, Franck Giacomoni = franck.giacomoni=3D=3D=3Dclermont.inra.fr <owner-chemistry:_:ccl.net> wrote:


Sent to CCL by: "Franck  Giacomoni" [franck.giacomoni^clermont.inra.fr]
Dear CCLers,

Here is my = challenge: I manage a compounds collection with different type of = features for each of them. One is the INCHI.
I need to = produce a SVG image to illustrate molecule structure.
OpenBabel (v2.4.1), under MACOS 10.11.6 generates SVG from = INCHI but I met  issue with particular molecule.

Example: 5,6-dihydrouracil from https://www.ebi.ac.uk/chebi/searchId.do?chebiId=3D15901 = got two carbonyl groups (C=3DO). But with obabel produce a SVG with two = imine groups (N=3DC). This form represent only less than 0.01% of = possible tautomers.

The used INCHI was : =   = InChI=3D1S/C4H6N2O2/c7-3-1-2-5-4(8)6-3/h1-2H2,(H2,5,6,7,8)

I observed the same issue with conversion from = inchi to SMILES
Obabel produces OC1=3DNC(=3DNCC1)O instead = of the right form found on ChEBI : O=3DC1CCNC(=3DO)N1

Do you have explanation of this issue?

Thank you very much for your help
Franck



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