Dear all, The Chemistry Development Kit(CDK) is very useful for my current work. However, I meet a problem: when I read and add hydrogens on the sybyl mol2 format 3D molecule by using CDK, it seems the added hydrogens have no coordinates. I use the code as below: "AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); CDKHydrogenAdder.getInstance(mol.getBuilder()).addImplicitHydrogens(mol); AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol); " The added hydrogens with coordinates is very important for my current project. I had checked the API of CDK, but I can not find the suitable way to solve this problem. So could anyone gives me some codes or suggestions on adding hydrogens with 3D coordinates on molecules? Thanks for your help. Sincerely, Qifeng
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