Package schrodinger :: Package application :: Package desmond :: Module replica_dE :: Class replica_container

Class replica_container

object --+
         |
        replica_container

Instance Methods

[hide private]

__init__(self, basename=None, run_bennett=True)
x.__init__(...) initializes x; see help(type(x)) for signature

_addReplica(self, replica)

read_dE_Replicas(self, basename, nreplicas=12)

getReplica(self, number)

get_nrep(self)

printInfo(self)

_getFMin(self)

_getRMin(self)

_getFMax(self)

_getRMax(self)

set_globalMin(self)

set_globalMax(self)

getOverlap(self, irepA, irepB)

export(self)

run_bennett(self, directory, n_win, temperature=300.0, begin_time=100.0, end_time=-1.0, random_seed=2111839, result_fname='result', description='Desmond bennett analysis', n_block=5)
Calculate Bennett Acceptance Ratio (BAR)

setup_freeenergy_calc(self, directory='.', begin_time=100.0, end_time=-1.0, delta_time=30.0)
Setup free energy calculation using BAR.

calc_freeenergy_Stime(self, directory, n_win, last_time, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, window=500.0, random_seed=2111839, descrip='Bennett Sliding')

calc_freeenergy_Rtime(self, directory, n_win, last_time, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, random_seed=2111839, descrip='Bennett Reverse')

calc_freeenergy_Ftime(self, directory, n_win, time, temperature=300.0, begin_time=100.0, end_time=-1.0, delta_time=30.0, random_seed=2111839, descrip='Bennett Forward')

process_bennett_log(self, fname='bennett.log')

export_dE_data(self, data, bennett_dG, bennett_per_replica)

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, basename=None, run_bennett=True)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

Class replica_container

__init__(self, basename=None, run_bennett=True) (Constructor)

init(self, basename=None, run_bennett=True)
(Constructor)