|
|
estimateNetCharge
|
estimateNetCharge ( atoms )
|
|
|
addNonstandardResCharges
|
addNonstandardResCharges (
residues,
netCharge,
method=None,
gaffType=None,
status=None,
)
|
|
|
cmdAddNonstdCharge
|
cmdAddNonstdCharge (
residues,
netCharge,
method=None,
gaffType=None,
)
|
Exceptions
|
|
|
MidasError("Residues not all the same type" " (%s != %s)" %( resName, r.type ) )
MidasError( "No such residues" )
MidasError(str( v ) )
MidasError("Residues have differing number of" " atoms (%d != %d)" %(numAtom, len( r.atoms ) ) )
|
|
|
|
initiateAddCharges
|
initiateAddCharges (
models=None,
method=None,
gaffType=None,
status=None,
cb=None,
nogui=None,
amberNucleicPhosphorylation=None,
)
|
|
|
addStandardCharges
|
addStandardCharges (
models=None,
status=None,
phosphorylation=None,
nogui=None,
)
|
|
|
cmdAddAllCharge
|
cmdAddAllCharge (
molecules=None,
method=None,
gaffType=None,
)
|
Exceptions
|
|
|
MidasError( "Atom specifier does not select any models" )
|
|
|
|
cmdAddStdCharge
|
cmdAddStdCharge ( molecules=None )
|
|