BFEE2.postTreatment¶
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class
BFEE2.postTreatment.postTreatment(temperature, unit, jobType='geometric')[source]¶ Bases:
objectthe post-treatment of BFEE outputs
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alchemicalBindingFreeEnergy(filePathes, parameters)[source]¶ calculate binding free energy for geometric route
- Parameters
filePathes (list of strings, 8) – pathes of alchemical output files (step1-forward, step1-backward, step2-forward …)
parameters (np.array, floats, 9) – (eulerTheta, polarTheta, r, forceConstant1, FC2, FC3, FC4, FC5, FC6)
- Returns
np.array, float, 6: (contributions for step1, 2, 3, 4, bulk restraining contribution, free energy) np.array, float, 6: errors corresponding each contribution
- Return type
tuple
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geometricBindingFreeEnergy(filePathes, parameters)[source]¶ calculate binding free energy for geometric route
- Parameters
filePathes (list of strings, 8) – pathes of PMF files for step1 - step8
parameters (np.array, floats, 8) – (forceConstant1, FC2, FC3, FC4, FC5, FC6, r*, FC8)
- Returns
(contributions for step1, 2, 3, 4 … 8, bulk restraining contribution, free energy)
- Return type
np.array, float, 10
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