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added value error if pka not provided for acidic or basic particles (#24
) * added value error if pka not provided for acidic or basic particles * remove acidity from peptide parameters, add marius as contributor, improve value error messages * added acidity test * adjusted the parameter files to not having acidity * removed all acididty in params * changed diameter to sigma * Add aditional unit tests, remove tests from samples instruction in Makefile * Add missing test to the CI --------- Co-authored-by: blancoapa <[email protected]> Co-authored-by: Pablo M. Blanco <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| # Import pyMBE and other libraries | ||
| import numpy as np | ||
| import pyMBE | ||
|
|
||
| # Create an instance of pyMBE library | ||
| pmb = pyMBE.pymbe_library() | ||
|
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||
| def check_acid_base_setup(input_parameters,acidity_setup): | ||
| """ | ||
| Checks if pyMBE stores in the pmb.df the input parameters for acid/base particles correctly. | ||
| Args: | ||
| input_parameters(`dict`): dictionary with the input parameters for define_particle. | ||
| acidity_setup(`dict`): dictionary with the expected setup that pyMBE should do in the pmb.df foor acid/base particles. | ||
| """ | ||
| pmb.define_particle(**input_parameters) | ||
| if input_parameters["acidity"] == "inert": | ||
| input_parameters.pop("q") | ||
| # Checks that the input parameters are stored properly | ||
| for parameter_key in input_parameters.keys(): | ||
| np.testing.assert_equal(actual=pmb.df[parameter_key].values[0], | ||
| desired=input_parameters[parameter_key], | ||
| verbose=True) | ||
| # Checks that the setup of the acid base properties is done correctly | ||
| for state in ["state_one","state_two"]: | ||
| for state_atribute in ["label","charge"]: | ||
| np.testing.assert_equal(actual=pmb.df[state][state_atribute].values[0], | ||
| desired=acidity_setup[state][state_atribute], | ||
| verbose=True) | ||
| # checks that pyMBE assigns different espresso type to each state | ||
| np.testing.assert_raises(AssertionError, np.testing.assert_equal, pmb.df["state_one"]["es_type"].values[0], pmb.df["state_two"]["es_type"].values[0]) | ||
|
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| print("*** Particle acidity unit tests ***") | ||
| print(f"*** Unit test: check that all acid/base input parameters in define_particle for an inert particle are correctly stored in pmb.df***") | ||
| # Clean pmb.df | ||
| pmb.setup_df() | ||
| input_parameters={"name":"I", | ||
| "acidity": "inert", | ||
| "pka": np.nan, | ||
| "q":2} | ||
| acidity_setup={"state_one":{"label":f"{input_parameters['name']}", | ||
| "charge":2}, | ||
| "state_two":{"label": np.nan, | ||
| "charge":np.nan},} | ||
|
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| check_acid_base_setup(input_parameters=input_parameters, | ||
| acidity_setup=acidity_setup) | ||
|
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| print(f"*** Unit test passed ***") | ||
| print(f"*** Unit test: check that all acid/base input parameters in define_particle for an acid are correctly stored in pmb.df***") | ||
| # Clean pmb.df | ||
| pmb.setup_df() | ||
| input_parameters={"name":"A", | ||
| "acidity": "acidic", | ||
| "pka":4} | ||
| acidity_setup={"state_one":{"label":f"{input_parameters['name']}H", | ||
| "charge":0}, | ||
| "state_two":{"label":f"{input_parameters['name']}", | ||
| "charge":-1},} | ||
|
|
||
| check_acid_base_setup(input_parameters=input_parameters, | ||
| acidity_setup=acidity_setup) | ||
| print(f"*** Unit test passed ***") | ||
| print(f"*** Unit test: check that all acid/base input parameters in define_particle for a base are correctly stored in pmb.df***") | ||
| # Clean pmb.df | ||
| pmb.setup_df() | ||
| input_parameters={"name":"B", | ||
| "acidity": "basic", | ||
| "pka":9} | ||
| acidity_setup={"state_one":{"label":f"{input_parameters['name']}H", | ||
| "charge":1}, | ||
| "state_two":{"label":f"{input_parameters['name']}", | ||
| "charge":0},} | ||
|
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||
| check_acid_base_setup(input_parameters=input_parameters, | ||
| acidity_setup=acidity_setup) | ||
| print(f"*** Unit test passed ***") | ||
| print(f"*** Unit test: check that set_particle_acidity raises a ValueError if pKa is not provided and pKa is acidic or basic ***") | ||
| input_parametersA={"name":"A", | ||
| "acidity": "acidic" } | ||
|
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||
| input_parametersB= {"name": "B", | ||
| "acidity": "basic"} | ||
| np.testing.assert_raises(ValueError, pmb.set_particle_acidity,**input_parametersA) | ||
| np.testing.assert_raises(ValueError, pmb.set_particle_acidity, **input_parametersB) | ||
| print(f"*** Unit test passed ***") | ||
| print(f"*** Unit test: check that set_particle_acidity raises a ValueError if a non-supported acidity is provided ***") | ||
| input_parametersA={"name":"A", | ||
| "acidity": "random" } | ||
| np.testing.assert_raises(ValueError, pmb.set_particle_acidity,**input_parametersA) | ||
| print(f"*** Unit test passed ***") | ||
| print(f"*** All unit tests passed ***") |