6.8 Add hydrogens

In order to add the hydrogens to a molecule, a specific dialog box was developed that is accessible trough the Edit -> Add -> Hydrogens main menu item:

Add hydrogens

 

6.8.1 The dialog functions

In this dialog it's possible to select the molecule type (Generic organic, Protein, Nucleic acid), the nomenclature type (normal progressive number or IUPAC nomenclature), the processing of the selected atoms only (Consider selected atoms only) and where the hydrogens are placed in the molecule file (After each heavy atom or at Residue end). Check Use the bond order to assign the atom types if the molecule has uncertain geometry (e.g. 2D instead of 3D structure) and the bond order is correctly assigned. That's useful to add the hydrogens to the molecules in some 2D SDF databases.
After the choose of the options, the user must click the Add button to add the hydrogens. The Close button closes the window without adding the hydrogens.

 

6.8.2 About the method

To add the hydrogens, the recognition of the atom types and the valences is needed. The powerful ATDL geometry-independent engine can't be used because the atom valences are incomplete due to the missing hydrogens and so the implemented method is based on the original code included into Babel 1.6 (© 1992-96, W. Patrick Walters, Matthew T. Stahl) that detects the atom valences considering the atomic distances and the bond angles. Unluckily, this is the method limit because some structures don't have a canonical geometry and so the valence detection can be wrong. VEGA introduces an algorithm that fixes the atom type and the valence detection when the user specify the type of the molecule. Please remember that this procedure is disabled selecting Generic organic molecule type.
The method can be summarized in the following steps: