alchemlyb.postprocessors.units¶
Unit conversion and constants¶
Some examples are given here to illustrate how to use the unit converter functions to convert units.
>>> import pandas as pd
>>> import alchemlyb
>>> from alchemtest.gmx import load_benzene
>>> from alchemlyb.parsing.gmx import extract_u_nk
>>> from alchemlyb.estimators import MBAR
>>> from alchemlyb.postprocessors.units import to_kcalmol, to_kJmol, to_kT
>>> bz = load_benzene().data
>>> u_nk_coul = alchemlyb.concat([extract_u_nk(xvg, T=300) for xvg in bz['Coulomb']])
>>> mbar_coul = MBAR().fit(u_nk_coul)
>>> mbar_coul.delta_f_
0.00 0.25 0.50 0.75 1.00
0.00 0.000000 1.619069 2.557990 2.986302 3.041156
0.25 -1.619069 0.000000 0.938921 1.367232 1.422086
0.50 -2.557990 -0.938921 0.000000 0.428311 0.483165
0.75 -2.986302 -1.367232 -0.428311 0.000000 0.054854
1.00 -3.041156 -1.422086 -0.483165 -0.054854 0.000000
>>> mbar_coul.delta_f_.attrs
{'temperature': 300, 'energy_unit': 'kT'}
The default unit is in \(kT\), which could be changed to \(kcal/mol\).
>>> delta_f_ = to_kcalmol(mbar_coul.delta_f_)
>>> delta_f_
0.00 0.25 0.50 0.75 1.00
0.00 0.000000 0.965228 1.524977 1.780319 1.813021
0.25 -0.965228 0.000000 0.559749 0.815092 0.847794
0.50 -1.524977 -0.559749 0.000000 0.255343 0.288045
0.75 -1.780319 -0.815092 -0.255343 0.000000 0.032702
1.00 -1.813021 -0.847794 -0.288045 -0.032702 0.000000
>>> delta_f_.attrs
{'temperature': 300, 'energy_unit': 'kcal/mol'}
- alchemlyb.postprocessors.units.to_kcalmol(df, T=None)¶
Convert the unit of a DataFrame to kcal/mol.
If temperature T is not provided, the DataFrame need to have attribute temperature and energy_unit. Otherwise, the temperature of the output dateframe will be set accordingly.
- Parameters
df (DataFrame) – DataFrame to convert unit.
T (float) – Temperature (default: None).
- Returns
df converted.
- Return type
DataFrame
The unit could also be changed to \(kJ/mol\).
>>> delta_f_ = to_kJmol(delta_f_)
>>> delta_f_
0.00 0.25 0.50 0.75 1.00
0.00 0.000000 4.038508 6.380495 7.448848 7.585673
0.25 -4.038508 0.000000 2.341987 3.410341 3.547165
0.50 -6.380495 -2.341987 0.000000 1.068354 1.205178
0.75 -7.448848 -3.410341 -1.068354 0.000000 0.136825
1.00 -7.585673 -3.547165 -1.205178 -0.136825 0.000000
>>> delta_f_.attrs
{'temperature': 300, 'energy_unit': 'kJ/mol'}
- alchemlyb.postprocessors.units.to_kJmol(df, T=None)¶
Convert the unit of a DataFrame to kJ/mol.
If temperature T is not provided, the DataFrame need to have attribute temperature and energy_unit. Otherwise, the temperature of the output dateframe will be set accordingly.
- Parameters
df (DataFrame) – DataFrame to convert unit.
T (float) – Temperature (default: None).
- Returns
df converted.
- Return type
DataFrame
And change back to \(kT\) again.
>>> delta_f_ = to_kT(delta_f_)
0.00 0.25 0.50 0.75 1.00
0.00 0.000000 1.619069 2.557990 2.986302 3.041156
0.25 -1.619069 0.000000 0.938921 1.367232 1.422086
0.50 -2.557990 -0.938921 0.000000 0.428311 0.483165
0.75 -2.986302 -1.367232 -0.428311 0.000000 0.054854
1.00 -3.041156 -1.422086 -0.483165 -0.054854 0.000000
>>> delta_f_.attrs
{'temperature': 300, 'energy_unit': 'kT'}
- alchemlyb.postprocessors.units.to_kT(df, T=None)¶
Convert the unit of a DataFrame to kT.
If temperature T is not provided, the DataFrame need to have attribute temperature and energy_unit. Otherwise, the temperature of the output dateframe will be set accordingly.
- Parameters
df (DataFrame) – DataFrame to convert unit.
T (float) – Temperature (default: None).
- Returns
df converted.
- Return type
DataFrame
A dispatch table approach is also provided to return the relevant converter for every units.
- alchemlyb.postprocessors.units.get_unit_converter(units)¶
Obtain the converter according to the unit string.
If units is ‘kT’, the to_kT converter is returned. If units is ‘kJ/mol’, the to_kJmol converter is returned. If units is ‘kcal/mol’, the to_kcalmol converter is returned.
- Parameters
units (str) – The unit that the function converts to.
- Returns
converter
- Return type
func
New in version 0.5.0.