6.9 Add hydrogens

In order to add hydrogens to a molecule, you can use a specific dialog that can be shown by Edit Add Hydrogens main menu item:

 

Add hydrogens

 

6.9.1 Dialog options

In this dialog, you can select the molecule type (Generic organic, Protein, Nucleic acid), the nomenclature type (normal progressive number or IUPAC nomenclature), the possibility to process 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.
Finally, you user must click Add to add the hydrogens.

 

6.9.2 About the method

To add hydrogens, the recognition of atom types and 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 in 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. You must remember that this check is disabled selecting Generic organic molecule type.
The method can be summarized in the following steps: