|
Add hydrogens to structures
|
Imported modules
|
|
import chimera
from chimera import Element, Element_bondLength, idatm
from chimera.bondGeom import single
from chimera.idatm import geometry, substituents
import operator
import string
|
|
Functions
|
|
determineNamingSchemas
gatherUnknowns
hbondAddHydrogens
newHydrogen
simpleAddHydrogens
|
|
|
determineNamingSchemas
|
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
|
gatherUnknowns ( models, prevUnknowns=[] )
Find atoms whose hydrogen-adding geometries are unknown
|
|
|
hbondAddHydrogens
|
hbondAddHydrogens ( models, unknownsInfo={} )
Add hydrogens to given models, trying to preserve H-bonding
Otherwise similar to simpleAddHydrogens(); see comments there
|
|
|
newHydrogen
|
newHydrogen (
parentAtom,
Hnum,
totalHydrogens,
namingSchema,
)
|
|
|
simpleAddHydrogens
|
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.
|
|