def amber_simplesolvated_charge_dHdl(): dataset = alchemtest.amber.load_simplesolvated() dHdl = alchemlyb.concat([amber.extract_dHdl(filename, T=300) for filename in dataset['data']['charge']]) return dHdl
def amber_simplesolvated_vdw_dHdl(): dataset = alchemtest.amber.load_simplesolvated() dHdl = pd.concat( [amber.extract_dHdl(filename) for filename in dataset['data']['vdw']]) return dHdl
def get_calculation_values(type_dic): ti = copy.deepcopy(type_dic) #mbar=copy.deepcopy(type_dic) ti_function = TI() #mbar_function = MBAR() for ef_key in type_dic.keys(): print(ef_key) ef_value = type_dic[ef_key] for ef_comp_sol_key in ef_value.keys(): ef_comp_sol_value = ef_value[ef_comp_sol_key] for ef_cal_type_key in ef_comp_sol_value.keys(): ef_cal_type_value = ef_comp_sol_value[ef_cal_type_key] ti_values = pd.concat( [amber.extract_dHdl(ti) for ti in ef_cal_type_value]) ti_function.fit(ti_values) ti[ef_key][ef_comp_sol_key][ ef_cal_type_key] = ti_function.delta_f_.loc[0.00, 0.50] #print (ef_key,ef_comp_sol_key,ef_cal_type_key,ti_function.delta_f_, ti_function.d_delta_f_) #mbar_values = pd.concat([amber.extract_u_nk(ti) for ti in ef_cal_type_value]) #print (mbar_values) #print (ti_values) #mbar_function.fit(mbar_values) #print (mbar_values) #print (mbar_function.delta_f_) #print (ef_key,ef_comp_sol_key,ef_cal_type_key,mbar_function.delta_f_.loc[0.00, 0.50]) #mbar[ef_key][ef_comp_sol_value][ef_cal_type_key] = mbar_function.delta_f_.loc[0.00, 0.50] return ti
def test_dHdl(filename, names=('time', 'lambdas'), shape=(500, 1)): """Test that dHdl has the correct form when extracted from files.""" dHdl = extract_dHdl(filename) assert dHdl.index.names == names assert dHdl.shape == shape
def test_dHdl_invalidfiles(invalid_file): assert extract_dHdl(invalid_file) is None