schrodinger.application.canvas.r_group_dee module
R-Group Analysis Dead End elimination
-
class
schrodinger.application.canvas.r_group_dee.
SimulatedAnnealing
(energy_matrix, sa_seed=None, t_factor=None, tmax_mult=None)[source]
Bases: object
-
static
getChoiceSpectrum
(choices)[source]
-
__init__
(energy_matrix, sa_seed=None, t_factor=None, tmax_mult=None)[source]
Initializer for simulated annealing class.
- Parameters
energy_matrix (DEE_EnergyMatrix
) – precalculated pairwise matrix used by SA.
sa_seed (float) – SA random number generator seed
t_fac – Factor (<1) by which T will be multiplied at each T change
tmax_mult (float) – Factor by which no. of st. will be multiplied to get starting T
-
run
()[source]
-
is_another_best_config
(solution)[source]
-
new_best
(energy, solution)[source]
-
report_t
(t, start_E, end_E, tsteps, totalCnt, acceptCnt)[source]
-
getNewSolution
(solution_old)[source]
-
neighbor
(solution)[source]
-
new_temperature
(old_t)[source]
-
boltzmann_probability
(e_old, e_new, t)[source]
-
getBestMatch
()[source]
-
class
schrodinger.application.canvas.r_group_dee.
DEE_Backtracking
(energy_matrix)[source]
Bases: object
-
__init__
(energy_matrix)[source]
Initialize self. See help(type(self)) for accurate signature.
-
minimize
()[source]
-
backtrack
(solution)[source]
-
reject
(solution)[source]
-
accept
(solution)[source]
-
first
(solution)[source]
-
next
(solution)[source]
-
output
(solution)[source]
-
getBestMatch
()[source]
-
class
schrodinger.application.canvas.r_group_dee.
DEE_EnergyMatrix
(choices, uij)[source]
Bases: object
-
__init__
(choices, uij)[source]
Initialize self. See help(type(self)) for accurate signature.
-
numPos
()[source]
-
numChoices
()[source]
-
calculateEnergy
(solution)[source]
-
calculateEnergyDifference
(solution_old, e_old, istruct, solution_new)[source]
-
initialSolution
()[source]
-
checkSolution
(solution)[source]
-
convertSolution
(solution)[source]
-
applyEnergyFilter
(solution, current_energy)[source]
-
eliminateSingles
()[source]
-
eliminatePairs
()[source]
-
applyGoldsteinSingles
(k, a, b)[source]
-
schrodinger.application.canvas.r_group_dee.
main
()[source]