Package Biskit :: Module Prosa :: Class ProsaII

Class ProsaII

Instance Methods

__init__(self, executable='prosaII', temp_dir=T.tempDir())

setCleanup(self, value=1)

getCleanup(self)

setPairWindowSize(self, window=(1,600))
pair-interactions are calculated for residue pairs whose sequence separation lies in 'window'.

getPairWindowSize(self)

setSurfaceRange(self, interval=(0.,15.))
surface energy for a residue pair is calculated only, if their distance lies within the 'interval'.

getSurfaceRange(self)

setSurfaceFactor(self, factor=5.)
E_total = factor * E_surface + E_pair see manual for further recommendations

getSurfaceFactor(self)

run(self, command)

analyseEnergy(self, filename, object_name=None)
supports user-expansion

Method Details

[hide private]

init(self, executable='prosaII', temp_dir=T.tempDir())
(Constructor)

source code

setCleanup(self, value=1)

source code

getCleanup(self)

source code

setPairWindowSize(self, window=(1,600))

source code

pair-interactions are calculated for residue pairs whose sequence separation lies in 'window'. window must be a tuple. default values come from prosaII manual

getPairWindowSize(self)

source code

setSurfaceRange(self, interval=(0.,15.))

source code

surface energy for a residue pair is calculated only, if their distance lies within the 'interval'. otherwise energy is 0. interval must be tuple. default values come from prosaII manual