5.8 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:
5.8.1 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).
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.
5.8.2 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:
All hydrogens are removed in order to allow the correct atom type detection.
Atom type and valence attribution: the atom types are detected using the Meng convention (E. Meng and R. Lewis, J. Comp. Chem., 12, pp 891-898, 1991) updating it with the Nim atom type in order to detect the nitrogens in five member rings.
Atom type fixing if the molecule type is specified: to fix the incorrect atom types, VEGA uses two templates (NA.hyb for nucleic acids and PROTEIN.hyb for proteins) placed in the Data directory. They are text files witch format is explained in the header.
Placing and bonding of the required hydrogens.