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Describe the bug Here's a demo:
In [15]: print(mb) RDKit 3D 0 0 0 0 0 0 0 0 0 0999 V3000 M V30 BEGIN CTAB M V30 COUNTS 5 4 0 0 0 M V30 BEGIN ATOM M V30 1 C 0.900794 -0.086835 0.009340 0 M V30 2 C -0.552652 0.319534 0.077502 0 M V30 3 F -0.861497 0.413307 1.437370 0 M V30 4 Cl -0.784572 1.925710 -0.672698 0 M V30 5 O -1.402227 -0.583223 -0.509512 0 M V30 END ATOM M V30 BEGIN BOND M V30 1 1 1 2 M V30 2 1 2 3 M V30 3 1 2 4 M V30 4 1 2 5 M V30 END BOND M V30 END CTAB M END In [16]: nm = Chem.MolFromMolBlock(mb) In [17]: nm.Debug() Atoms: 0 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 0 2 9 F chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0 3 17 Cl chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 4 arom?: 0 chi: 0 Bonds: 0 0->1 order: 1 conj?: 0 aromatic?: 0 1 1->2 order: 1 conj?: 0 aromatic?: 0 2 1->3 order: 1 conj?: 0 aromatic?: 0 3 1->4 order: 1 conj?: 0 aromatic?: 0
if we call AssignStereochemistryFrom3D() then the chiral center is recognized:
AssignStereochemistryFrom3D()
In [18]: Chem.AssignStereochemistryFrom3D(nm) In [19]: nm.Debug() Atoms: 0 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 4 arom?: 0 chi: 0 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: 4 arom?: 0 chi: 1 2 9 F chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0 3 17 Cl chg: 0 deg: 1 exp: 1 imp: 0 hyb: 4 arom?: 0 chi: 0 4 8 O chg: 0 deg: 1 exp: 1 imp: 1 hyb: 4 arom?: 0 chi: 0 Bonds: 0 0->1 order: 1 conj?: 0 aromatic?: 0 1 1->2 order: 1 conj?: 0 aromatic?: 0 2 1->3 order: 1 conj?: 0 aromatic?: 0 3 1->4 order: 1 conj?: 0 aromatic?: 0
There is logic in the mol block parser to assign stereochemistry to 3D conformers: https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/MolFileParser.cpp#L3153 but this ends up not being called if there are no wedged bonds. That doesn't make sense... we shouldn't require wedged bonds in the case of a 3D conformer.
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Fixes rdkit#5328
d1278f3
Fixes rdkit#5327 probably a good idea to add a bit more testing here
d640eb9
[WIP] Fixes #5327 and #5328 (#5330)
21639a6
* Fixes #5328 Fixes #5327 probably a good idea to add a bit more testing here * more tests!
greglandrum
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Describe the bug
Here's a demo:
if we call
AssignStereochemistryFrom3D()
then the chiral center is recognized:There is logic in the mol block parser to assign stereochemistry to 3D conformers: https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/MolFileParser.cpp#L3153
but this ends up not being called if there are no wedged bonds. That doesn't make sense... we shouldn't require wedged bonds in the case of a 3D conformer.
Configuration (please complete the following information):
The text was updated successfully, but these errors were encountered: