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
