On Wed, Apr 3, 2019 at 8:26 PM Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear Greg,
In [10] and Out[10] of your answer below (thanks!) incited me to
believe that the geometry of double bonds
outside of the reactive center in the reaction product is not lost
for ever, contrarily to what my example showed.
So, I went back to my example and printed the SMILES
representations of the reagent and of the product.
The double bond are there and in good shape:
C/C=C(\C=C(C)\C=C(C)\C=C/C=C(/C)C(=O)[C@]12O[C@H]1[C@@](O)(CCO)N=C2O)C(=O)OC
for the reagent
C/C=C(\C=C(C)\C=C(C)\C=C/C=C(/C)C(=O)[C@]12O[C@H]1[C@@](O)(CCO)NC2=O)C(=O)OC
for the product.
So, what I conclude is that MolToInchi does not consider the
double bond geometry in the reaction product
but that MolToSmiles does it.
Apologies... I didn't read your original email closely enough and
answered the wrong question.
What's going on in your case is that the stereochemistry information
in the products of the reaction hasn't been updated.
This doesn't happen automatically (just as the products of reactions
are not automatically sanitized).
If you call Chem.AssignStereochemistry() on the products you get the
expected result:
In [38]: inchi1 =
"InChI=1S/C23H29NO7/c1-6-17(19(27)30-5)13-15(3)12-14(2)8-7-9-16(4)18(26)23-20(31-23)22(29,10-11-25)24-21(23)28/h6-9,1
...:
2-13,20,25,29H,10-11H2,1-5H3,(H,24,28)/b8-7-,14-12+,15-13+,16-9-,17-6+/t20-,22-,23-/m0/s1"
...: m1 = Chem.MolFromInchi(inchi1)
...: rxn =
AllChem.ReactionFromSmarts('[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]')
...: ps = rxn.RunReactants((m1,))
...: m2 = ps[0][0]
...: Chem.AssignStereochemistry(m2,force=True,cleanIt=True)
...: inchi2 = Chem.MolToInchi(m2)
...: print(inchi1)
...: print(inchi2)
...: print(inchi1 == inchi2)
InChI=1S/C23H29NO7/c1-6-17(19(27)30-5)13-15(3)12-14(2)8-7-9-16(4)18(26)23-20(31-23)22(29,10-11-25)24-21(23)28/h6-9,12-13,20,25,29H,10-11H2,1-5H3,(H,24,28)/b8-7-,14-12+,15-13+,16-9-,17-6+/t20-,22-,23-/m0/s1
InChI=1S/C23H29NO7/c1-6-17(19(27)30-5)13-15(3)12-14(2)8-7-9-16(4)18(26)23-20(31-23)22(29,10-11-25)24-21(23)28/h6-9,12-13,20,25,29H,10-11H2,1-5H3,(H,24,28)/b8-7-,14-12+,15-13+,16-9-,17-6+/t20-,22-,23-/m0/s1
True
The creation of new Mol objects from these two SMILES and the
subsequent
generation of InChI strings produces identical results
as expected, because the reagent and the product are tautomers.
By the way, does the last RDKit release correct the problem you
mentioned about MolFromSmiles
in you email dated February 14, 2019?
Part of it, but not everything. I will file a bug for the problem you
reported so that it doesn't get lost. Maybe I can find/fix it before
the next patch release.
-greg
Best regards,
Jean-Marc
Le 03/04/2019 à 18:16, Greg Landrum a écrit :
Hi Jean-Marc,
Unfortunately not. The RDKit currently ignores stereo information
from "mapped bonds" (bonds for which both atoms are mapped) from
the reactants. If you include stereo info in the reaction itself,
that will be copied over in to the products, but that is not what
you're looking for. Here's an example:
In [4]: r1 =
AllChem.ReactionFromSmarts('[C:1][C:2]=[C:3][F:4]>>[C:1][C:2]=[C:3][Cl:4]')
In [5]:
Chem.MolToSmiles(r1.RunReactants((Chem.MolFromSmiles('CC=CF'),))[0][0])
Out[5]: 'CC=CCl'
In [6]:
Chem.MolToSmiles(r1.RunReactants((Chem.MolFromSmiles('C/C=C/F'),))[0][0])
Out[6]: 'CC=CCl'
In [7]: r2 =
AllChem.ReactionFromSmarts('[C:1]/[C:2]=[C:3]/[F:4]>>[C:1]/[C:2]=[C:3]/[Cl:4]')
In [8]:
Chem.MolToSmiles(r2.RunReactants((Chem.MolFromSmiles('C/C=C/F'),))[0][0])
Out[8]: 'C/C=C/Cl'
In [9]:
Chem.MolToSmiles(r2.RunReactants((Chem.MolFromSmiles('CC=CF'),))[0][0])
Out[9]: 'C/C=C/Cl'
In [10]:
Chem.MolToSmiles(r1.RunReactants((Chem.MolFromSmiles('C/C=C/CC=CF'),))[0][0])
Out[10]: 'C/C=C/CC=CCl'
It's more tolerant of atomic stereochemistry:
In [11]: r3 =
AllChem.ReactionFromSmarts('[C:1][C:2][F:3]>>[C:1][C:2][O:3]')
In [12]:
Chem.MolToSmiles(r3.RunReactants((Chem.MolFromSmiles('N[C@H](Cl)CF'),))[0][0])
Out[12]: 'N[C@H](Cl)CO'
In [13]:
Chem.MolToSmiles(r3.RunReactants((Chem.MolFromSmiles('C[C@H](F)Cl'),))[0][0])
Out[13]: 'C[C@H](O)Cl'
Figuring out a good solution for the double bond handling would
be a nice challenge for the next release.
Best,
-greg
On Wed, Apr 3, 2019 at 5:54 PM Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>>
wrote:
Dear all,
I have a molecule that comes from an InChI string, that is
decoded
as an iminol I would like to transform in its amide tautomer.
The same molecule contains also a series of doubles bonds.
The following code:
inchi1 =
"InChI=1S/C23H29NO7/c1-6-17(19(27)30-5)13-15(3)12-14(2)8-7-9-16(4)18(26)23-20(31-23)22(29,10-11-25)24-21(23)28/h6-9,12-13,20,25,29H,10-11H2,1-5H3,(H,24,28)/b8-7-,14-12+,15-13+,16-9-,17-6+/t20-,22-,23-/m0/s1"
m1 = Chem.MolFromInchi(inchi1)
rxn =
AllChem.ReactionFromSmarts('[C:1]([OH:2])=[N:3]>>[C:1](=[OH0:2])[NH:3]')
ps = rxn.RunReactants((m1,))
m2 = ps[0][0]
inchi2 = Chem.MolToInchi(m2)
print(inchi1)
print(inchi2)
print(inchi1 == inchi2)
prints:
[17:26:42] WARNING: Omitted undefined stereo
InChI=1S/C23H29NO7/c1-6-17(19(27)30-5)13-15(3)12-14(2)8-7-9-16(4)18(26)23-20(31-23)22(29,10-11-25)24-21(23)28/h6-9,12-13,20,25,29H,10-11H2,1-5H3,(H,24,28)/b8-7-,14-12+,15-13+,16-9-,17-6+/t20-,22-,23-/m0/s1
InChI=1S/C23H29NO7/c1-6-17(19(27)30-5)13-15(3)12-14(2)8-7-9-16(4)18(26)23-20(31-23)22(29,10-11-25)24-21(23)28/h6-9,12-13,20,25,29H,10-11H2,1-5H3,(H,24,28)/t20-,22-,23-/m0/s1
False
in which the /b layer has disappeared, leaving the double
bond geometry undefined.
Is there a way to preserve or to recover the lost information?
Jean-Marc
--
Dr. Jean-Marc Nuzillard
Institute of Molecular Chemistry, CNRS UMR 7312
Faculté des Sciences Exactes et Naturelles, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 33 3 26 91 82 10
Fax : 33 3 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
