|
|
findRotamerNearest
|
findRotamerNearest (
atPos,
idatmType,
atom,
neighbor,
checkDist,
)
|
|
|
guessTerminii
|
guessTerminii ( mol )
|
|
|
bondWithHLength
|
bondWithHLength ( heavy, idatmType )
|
|
|
findNearest
|
findNearest (
pos,
atom,
exclude,
checkDist,
)
|
|
|
terminiiFromSeqres
|
terminiiFromSeqres ( mol, sr )
|
Exceptions
|
|
|
TerminiiError( "Can't get mol seqs" )
TerminiiError( "No SEQRES for chain %s" % chainID )
TerminiiError( "Sequence longer than SEQRES!" " (chain %s)" % chainID )
|
|
|
|
hbondAddHydrogens
|
hbondAddHydrogens (
models,
unknownsInfo=None,
hisScheme=None,
)
|
|
|
newHydrogen
|
newHydrogen (
parentAtom,
Hnum,
totalHydrogens,
namingSchema,
pos,
)
|
|
|
completeTerminalCarboxylate
|
completeTerminalCarboxylate ( cter )
|
|
|
postAdd
|
postAdd ( fakeN, fakeC )
|
|
|
determineNamingSchemas
|
determineNamingSchemas ( molecule, typeInfo )
|
|
|
vdwRadius
|
vdwRadius ( atom )
|
|
|
simpleAddHydrogens
|
simpleAddHydrogens (
models,
unknownsInfo=None,
hisScheme=None,
)
|
|
|
roomiest
|
roomiest (
positions,
attached,
checkDist,
)
|
|
|
determineTerminii
|
determineTerminii ( mols )
|
|
|
gatherUnknowns
|
gatherUnknowns ( models, prevUnknowns=None )
|
|
|
cmdAddH
|
cmdAddH (
molecules=None,
hbond=None,
useHisName=None,
)
|
|