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]