findRotamerNearest (
        atPos,
        idatmType,
        atom,
        neighbor,
        checkDist,
        )

guessTerminii ( mol )

bondWithHLength ( heavy,  idatmType )

findNearest (
        pos,
        atom,
        exclude,
        checkDist,
        )

terminiiFromSeqres ( mol,  sr )

hbondAddHydrogens (
        models,
        unknownsInfo={},
        hisScheme=None,
        )

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

Arguments are similar to simpleAddHydrogens() except that for histidines not in the hisScheme dictionary, the hydrogen-bond interactions determine the histidine protonation.

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

completeTerminalCarboxylate ( cter )

postAdd ( fakeN,  fakeC )

determineNamingSchemas ( molecule,  typeInfo )

Determine for each residue, method for naming hydrogens

The possible schemas are: 1) prepend -- put H in front of entire atom name 2) a set of hetero atoms that should be prepended (others will have the element symbol replaced with H)

In both cases, a number will be appended if more than one hydrogen is to be added. (Unless the base atom name ends in a prime ['] character, in which case additional primes will be added as long as the resulting name is 4 characters or less)

The "set" 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.

vdwRadius ( atom )

simpleAddHydrogens (
        models,
        unknownsInfo={},
        hisScheme=None,
        )

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.

The hisScheme keyword determines how histidines are handled. If it is None then the residue name is expected to be HIE, HID, HIP, or HIS indicating the protonation state is epsilon, delta, both, or unspecified respectively. Otherwise the value is a dictionary: the keys are histidine residues and the values are HIE/HID/HIP/HIS indication of the protonation state. Histindines not in the dictionary will be protonated based on the nitrogens' atom types.

the protonation is determined by the nitrogen atom type.

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,
        )

determineTerminii ( mols )

gatherUnknowns ( models,  prevUnknowns=[] )

Find atoms whose hydrogen-adding geometries are unknown

cmdAddH (
        molecules=None,
        hbond=True,
        useHisName=True,
        )

TerminiiError

IdatmTypeInfo

ChimeraExtension.py

gui.py

hbond.py

prefs.py

simple.py

unknownsGUI.py

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

helpdir