Hi all,
I have an issue handling stereochemistry with CDK. I am using CDK-1.5.13. I
have the following molecule:
Mol 1: [H][C@@]1(O)[C@@H](CO)O[C@@]([H])(OC2CCC3CCC(=O)OC3C2)[C@
]([H])(O)[C@H]1O
I am using the following code to add implicit hydrogens and further convert
them into explicit ones. The resulting structure serves as input for
another function.
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
CDKHydrogenAdder.getInstance(molecule
.getBuilder()).addImplicitHydrogens(molecule);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
Unfortunately, the stereochemistry in structure that results from this code
is messed up. This is what I get in return:
Mol2: [H][C@@]1(O[H])[C@@](C(O[H])([H])[H])(O[C@
@]([H])(OC2(C(C(C3(C(C(C(=O)OC3(C2([H])[H])[H])([H])[H])([H])[H])[H])([H])[H])([H])[H])[H])[C@
]([H])(O[H])[C@]1(O[H])[H])[H]
But what I think should be returned is
Mol3: [H]OC([H])([H])[C@@]1([H])O[C@
@]([H])(OC2([H])C([H])([H])C([H])([H])C3([H])C([H])([H])C([H])([H])C(=O)OC3([H])C2([H])[H])[C@
]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]
Is there a reason for the change of stereochemical information? How to fix
the code in order to obtain the Mol3 structure?
Thank you so much for your help.
Best,
Yannick
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