bondWithHLength ( heavy,  idatmType )

hbondAddHydrogens ( models,  unknownsInfo={} )

Add hydrogens to given models, trying to preserve H-bonding

determineNamingSchemas ( molecule,  typeInfo )

Determine for each residue, method for naming hydrogens

The two possible schemas are: replace -- put H in place of element name prepend -- put H in front of entire atom name

In both cases, a number will be appended if more than one hydrogen is to be added.

Replace is the preferred scheme and is used when the heavy atoms have been given reasonably distinctive names. Prepend is used mostly in small molecules where the atoms have names such as C1, C2, C3, N1, N2, etc. and replace would not work.

gatherUnknowns ( models,  prevUnknowns=[] )

Find atoms whose hydrogen-adding geometries are unknown

cmdAddH ( molecules=None,  hbond=False )

simpleAddHydrogens ( models,  unknownsInfo={} )

Add hydrogens to given models using simple geometric criteria

Geometric info for atoms whose IDATM types don't themselves provide sufficient information can be passed via the unknownsInfo dictionary. The keys are atoms and the values are dictionaries specifying the geometry and number of substituents (not only hydrogens) for the atom.

This routine adds hydrogens immediately even if some atoms have unknown geometries. To allow the user to intervene to specify geometries, use the initiateAddHyd function of the unknownsGUI module of this package.

roomiest (
        positions,
        attached,
        checkDist,
        )

newHydrogen (
        parentAtom,
        Hnum,
        totalHydrogens,
        namingSchema,
        pos,
        )

findNearest (
        pos,
        atom,
        exclude,
        checkDist,
        )

IdatmTypeInfo

ChimeraExtension.py

gui.py

hbond.py

simple.py

unknownsGUI.py

GUI to query user for hydrogen-addition info of non-IDATMed atoms

helpdir