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)¶ Bases:
object
-
static
getChoiceSpectrum
(choices)¶
-
__init__
(energy_matrix, sa_seed=None, t_factor=None, tmax_mult=None)¶ 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
()¶
-
is_another_best_config
(solution)¶
-
new_best
(energy, solution)¶
-
report_t
(t, start_E, end_E, tsteps, totalCnt, acceptCnt)¶
-
getNewSolution
(solution_old)¶
-
neighbor
(solution)¶
-
new_temperature
(old_t)¶
-
boltzmann_probability
(e_old, e_new, t)¶
-
getBestMatch
()¶
-
static
-
class
schrodinger.application.canvas.r_group_dee.
DEE_Backtracking
(energy_matrix)¶ Bases:
object
-
__init__
(energy_matrix)¶ Initialize self. See help(type(self)) for accurate signature.
-
minimize
()¶
-
backtrack
(solution)¶
-
reject
(solution)¶
-
accept
(solution)¶
-
first
(solution)¶
-
next
(solution)¶
-
output
(solution)¶
-
getBestMatch
()¶
-
-
class
schrodinger.application.canvas.r_group_dee.
DEE_EnergyMatrix
(choices, uij)¶ Bases:
object
-
__init__
(choices, uij)¶ Initialize self. See help(type(self)) for accurate signature.
-
numPos
()¶
-
numChoices
()¶
-
calculateEnergy
(solution)¶
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calculateEnergyDifference
(solution_old, e_old, istruct, solution_new)¶
-
initialSolution
()¶
-
checkSolution
(solution)¶
-
convertSolution
(solution)¶
-
applyEnergyFilter
(solution, current_energy)¶
-
eliminateSingles
()¶
-
eliminatePairs
()¶
-
applyGoldsteinSingles
(k, a, b)¶
-
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schrodinger.application.canvas.r_group_dee.
main
()¶