|
|
registerLibrary
|
registerLibrary ( importName )
|
|
|
getRotamers
|
getRotamers (
res,
phi=None,
psi=None,
cisTrans="trans",
resType=None,
lib="Dunbrack",
log=False,
)
|
Exceptions
|
|
|
LimitationError( "N, CA, or C missing from %s:" " needed to position CB" % res )
|
|
|
|
processClashes
|
processClashes (
residue,
rotamers,
overlap,
hbondAllow,
scoreMethod,
makePBs,
pbColor,
pbWidth,
)
|
|
|
extractResInfo
|
extractResInfo ( res )
|
|
|
nukeGroup
|
nukeGroup ( groupName )
|
|
|
getRotamerParams
|
getRotamerParams (
res,
phi=None,
psi=None,
cisTrans="trans",
lib="Dunbrack",
)
return a list of RotamerParams (in descending probability order).
The return value is actually a boolean and a list of RotamerParams.
The boolean is True if the RotamerParams are backbone dependent. takes either a Residue instance, or a residue name (e.g. TRP) and
phi and psi angles. If phi or psi is None or the residue is
chain-terminal, then backbone-independent rotamers are returned.
raises NoResidueRotamersError if the residue isn't in the database
|
|
|
processVolume
|
processVolume (
rotamers,
columnName,
volume,
)
|
|
|
useRotamer
|
useRotamer (
oldRes,
rotRes,
log=False,
)
|
Exceptions
|
|
|
LimitationError( "N or CA missing from rotamer:" " cannot matchup with original residue" )
LimitationError( "N, CA, or C missing from %s:" " needed for side-chain pruning algorithm" % oldRes )
|
|
|
|
useBestRotamers
|
useBestRotamers (
resType,
targets,
criteria=defaultCriteria,
lib="Dunbrack",
overlapCutoff=options [ CLASH_THRESHOLD ],
hbondAllowance=options [ HBOND_ALLOWANCE ],
scoreMethod=options [ CLASH_METHOD ],
relax=True,
distSlop=recDistSlop,
angleSlop=recAngleSlop,
density=None,
)
|
Exceptions
|
|
|
MidasError( "No volume models in" " specified model numbers" )
MidasError( "No rotamer library named '%s'" % lib )
MidasError( "Density criteria requested" " but no density model specified" )
MidasError( "Multiple volume models in" " specified model numbers" )
|
|
|
|
processHbonds
|
processHbonds (
residue,
rotamers,
drawHbonds,
bondColor,
lineWidth,
relax,
distSlop,
angleSlop,
twoColors,
relaxColor,
groupName,
cacheDA=False,
)
|
|