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More tests on read/write utils #120

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merged 5 commits into from
Aug 27, 2024
Merged

More tests on read/write utils #120

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c932964
add more read/write tests
daico007 Aug 25, 2024
09ebc81
errors on get_gaussian_log_file_data
daico007 Aug 25, 2024
43ffe48
add missing file, fix typo
daico007 Aug 25, 2024
94a5956
add remainder of the tests
daico007 Aug 26, 2024
fb992cc
fix bug
daico007 Aug 26, 2024
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13 changes: 13 additions & 0 deletions mosdef_dihedral_fit/tests/files/with_errors/dihedral_coords_position_with_errors_1.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
ERROR INVOKED
Row Highlight Display Tag Symbol X Y Z
1 No Show 1 C 0.038875 0.044324 -0.011413
2 No Show 2 C -1.465769 -0.032622 0.013366
3 No Show 3 C -2.132975 1.336603 0.000182
4 No Show 4 O 0.594959 -1.165924 0.000767
5 No Show 5 O 0.687419 1.039064 -0.038656
6 No Show 6 H -1.834701 1.923374 0.860427
7 No Show 7 H -1.861486 1.893480 -0.888336
8 No Show 8 H -1.773326 -0.632226 -0.838286
9 No Show 9 H -1.746313 -0.602379 0.894330
10 No Show 10 H -3.211788 1.226165 0.018599
11 No Show 11 H 1.541303 -1.055849 -0.015879
227 changes: 227 additions & 0 deletions mosdef_dihedral_fit/tests/test_file_read_write.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,10 +136,22 @@ def test_write_xyz_file_from_gaussian(self):
assert "dihedral_coords_position_1.xyz" in os.listdir()
assert "dihedral_coords_position_2.xyz" in os.listdir()

error_msg = "ERROR: The 'qm_coordinate_file_extension' variable extension is not listed or a an empty string."
with pytest.raises(ValueError, match=error_msg):
write_xyz_file_from_gaussian_coordinates(
atom_namesList, full_fn, "", "./", 2
)
write_restart_coor_from_xyz_file("./", 2)
assert "dihedral_coords_position_1.coor" in os.listdir()
assert "dihedral_coords_position_2.coor" in os.listdir()

error_fn = "with_errors/dihedral_coords_position_with_errors_"
full_error_fn = self.get_fn(error_fn)
with pytest.raises(TypeError):
write_xyz_file_from_gaussian_coordinates(
atom_namesList, full_error_fn, extension, "./", 1
)

def test_check_gaussian_angle_energy_file_correct(self):
full_path = self.get_fn(
"gaussian_style_output_files/CT_CT_C_OH/output/dihedral.txt"
Expand Down Expand Up @@ -185,6 +197,41 @@ def test_get_final_gaussian_output_file_data(self):
assert elements == ["C", "C", "H", "H", "H", "H", "H", "H"]
assert n_atoms == 8

# Wrong input types
with pytest.raises(TypeError):
get_final_gaussian_output_file_data(None, [3, 1, 2, 8])

# Dict value must be list of integers
with pytest.raises(TypeError):
get_final_gaussian_output_file_data(
{full_path: [0.1, 0.2, 0.3, -0.4]}, [3, 1, 2, 8]
)

# Dict key must be a string
with pytest.raises(TypeError):
get_final_gaussian_output_file_data(
{1: [0.1, 0.2, 0.3, 0.4]}, [3, 1, 2, 8]
)

# Dict value must be a list
with pytest.raises(TypeError):
get_final_gaussian_output_file_data(
{full_path: "ERROR"}, [3, 1, 2, 8]
)

# manual_dihedral_atom_numbers_list must be a list of len 4
with pytest.raises(TypeError):
get_final_gaussian_output_file_data(
{full_path: list(np.arange(32, dtype=int))}, None
)

# manual_dihedral_atom_numbers_list must be a list of integers
with pytest.raises(TypeError):
get_final_gaussian_output_file_data(
{full_path: list(np.arange(32, dtype=int))},
[0.1, 0.2, 0.3, 0.4],
)

def test_get_gaussian_log_file_data(self):
full_path = self.get_fn(
"gaussian/CT_CT_C_OH/output/CT_CT_C_OH_multiplicity_1.log"
Expand Down Expand Up @@ -265,6 +312,22 @@ def test_get_gaussian_log_file_data(self):
dihedral_atoms = out[5]
assert dihedral_atoms == [5, 1, 2, 3]

# Input must be a dict
with pytest.raises(TypeError):
get_gaussian_log_file_data(None)

# Dict key must be a string
with pytest.raises(TypeError):
get_gaussian_log_file_data({1: out_indices})

# Dict value must be a list of integers
with pytest.raises(TypeError):
get_gaussian_log_file_data({full_path: [0.1, 0.2, 0.3, -0.4]})

# Dict value must be a list
with pytest.raises(TypeError):
get_gaussian_log_file_data({full_path: "ERROR"})

def test_write_qm_data_files(self):
full_path = self.get_fn(
"gaussian/CT_CT_C_OH/output/CT_CT_C_OH_multiplicity_1.log"
Expand All @@ -273,6 +336,19 @@ def test_write_qm_data_files(self):
write_qm_data_files({full_path: out_indices})
assert os.path.exists("extracted_gaussian_data/dihedral.txt")

# qm_engine not in list
with pytest.raises(ValueError):
write_qm_data_files(None, qm_engine="None")

# when qm_engine="gaussian_style_final_files"
# manual_dihedral_atom_numbers_list must be a list of len 4
with pytest.raises(TypeError):
write_qm_data_files(
{full_path: out_indices},
None,
qm_engine="gaussian_style_final_files",
)

def test_get_matching_dihedral_info_and_opls_fitting_data(self):
out = get_matching_dihedral_info_and_opls_fitting_data(
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
Expand Down Expand Up @@ -351,6 +427,102 @@ def test_get_matching_dihedral_info_and_opls_fitting_data(self):
]
assert np.allclose(opls_paramsList[0], expected_opls_params)

# fit_dihedral_atom_types must be a list of length 4
with pytest.raises(TypeError):
out = get_matching_dihedral_info_and_opls_fitting_data(
fit_dihedral_atom_types=["HC", "CT", "CT"],
psf_path_and_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files.psf"
),
qm_log_file_dict={
self.get_fn(
"gaussian/HC_CT_CT_HC/output/HC_CT_CT_HC_multiplicity_1.log"
): []
},
mol2_file=self.get_fn(
"gaussian/HC_CT_CT_HC/input/starting_coords/ethane_aa.mol2"
),
qm_engine="gaussian",
manual_dihedral_atom_numbers_list=None,
)

# Each element of fit_dihedral_atom_types must be a string
with pytest.raises(TypeError):
out = get_matching_dihedral_info_and_opls_fitting_data(
fit_dihedral_atom_types=[1, 2, 3, 4],
psf_path_and_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files.psf"
),
qm_log_file_dict={
self.get_fn(
"gaussian/HC_CT_CT_HC/output/HC_CT_CT_HC_multiplicity_1.log"
): []
},
mol2_file=self.get_fn(
"gaussian/HC_CT_CT_HC/input/starting_coords/ethane_aa.mol2"
),
qm_engine="gaussian",
manual_dihedral_atom_numbers_list=None,
)

# fit_dihedral_atom_types must be a list
with pytest.raises(TypeError):
out = get_matching_dihedral_info_and_opls_fitting_data(
fit_dihedral_atom_types=None,
psf_path_and_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files.psf"
),
qm_log_file_dict={
self.get_fn(
"gaussian/HC_CT_CT_HC/output/HC_CT_CT_HC_multiplicity_1.log"
): []
},
mol2_file=self.get_fn(
"gaussian/HC_CT_CT_HC/input/starting_coords/ethane_aa.mol2"
),
qm_engine="gaussian",
manual_dihedral_atom_numbers_list=None,
)

# When qm_engine="gaussian_style_final_files"
# manual_dihedral_atom_numbers_list must be a list of len 4
with pytest.raises(TypeError):
out = get_matching_dihedral_info_and_opls_fitting_data(
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
psf_path_and_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files.psf"
),
qm_log_file_dict={
self.get_fn(
"gaussian/HC_CT_CT_HC/output/HC_CT_CT_HC_multiplicity_1.log"
): []
},
mol2_file=self.get_fn(
"gaussian/HC_CT_CT_HC/input/starting_coords/ethane_aa.mol2"
),
qm_engine="gaussian_style_final_files",
manual_dihedral_atom_numbers_list=None,
)

# qm_engine must be "gaussian" or "gaussian_style_final_files"
with pytest.raises(ValueError):
out = get_matching_dihedral_info_and_opls_fitting_data(
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
psf_path_and_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files.psf"
),
qm_log_file_dict={
self.get_fn(
"gaussian/HC_CT_CT_HC/output/HC_CT_CT_HC_multiplicity_1.log"
): []
},
mol2_file=self.get_fn(
"gaussian/HC_CT_CT_HC/input/starting_coords/ethane_aa.mol2"
),
qm_engine="None",
manual_dihedral_atom_numbers_list=None,
)

def test_change_gomc_ff_file_dihedral_values(self):
new_file = self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_zeroed.inp"
Expand All @@ -375,3 +547,58 @@ def test_change_gomc_ff_file_dihedral_values(self):
break

assert checkFile

with pytest.raises(TypeError):
change_gomc_ff_file_dihedral_values(
read_gomc_ff_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_per_xml.inp"
),
new_gomc_ff_filename=new_file,
fit_dihedral_atom_types=[],
fit_dihedral_opls_k_0_1_2_3_4_values=[1, 0, 0, 0],
)

# zero_dihedral_atom_types must be a list or None
with pytest.raises(TypeError):
change_gomc_ff_file_dihedral_values(
read_gomc_ff_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_per_xml.inp"
),
new_gomc_ff_filename=new_file,
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
fit_dihedral_opls_k_0_1_2_3_4_values=[1, 0, 0, 0, 0],
zero_dihedral_atom_types="INVALID",
)

with pytest.raises(TypeError):
change_gomc_ff_file_dihedral_values(
read_gomc_ff_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_per_xml.inp"
),
new_gomc_ff_filename=new_file,
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
fit_dihedral_opls_k_0_1_2_3_4_values=[1, 0, 0, 0, 0],
zero_dihedral_atom_types=["CT"],
)

with pytest.raises(TypeError):
change_gomc_ff_file_dihedral_values(
read_gomc_ff_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_per_xml.inp"
),
new_gomc_ff_filename=new_file,
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
fit_dihedral_opls_k_0_1_2_3_4_values=[1, 0, 0, 0, 0],
zero_dihedral_atom_types=[1, 2, 3, 4],
)

with pytest.raises(ValueError):
change_gomc_ff_file_dihedral_values(
read_gomc_ff_filename=self.get_fn(
"gaussian/HC_CT_CT_HC/output/GOMC_pdb_psf_ff_files_dihedrals_per_xml.inp"
),
new_gomc_ff_filename=new_file,
fit_dihedral_atom_types=["HC", "CT", "CT", "HC"],
fit_dihedral_opls_k_0_1_2_3_4_values=[1, 0, 0, 0, 0],
zero_dihedral_atom_types=["HC", "CT", "CT", "HC"],
)
15 changes: 2 additions & 13 deletions mosdef_dihedral_fit/utils/file_read_and_write.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -171,10 +171,8 @@ def write_xyz_file_from_gaussian_coordinates(
and qm_coordinate_file_extension[0] == "."
):
qm_coordinate_file_extension = qm_coordinate_file_extension[1:]

elif len(qm_coordinate_file_extension) > 0:
qm_coordinate_file_extension = qm_coordinate_file_extension

else:
raise ValueError(
"ERROR: The 'qm_coordinate_file_extension' variable extension is not listed or a an empty string."
Expand Down Expand Up @@ -519,7 +517,7 @@ def get_final_gaussian_output_file_data(
else:
for key_j, value_j in qm_log_file_dict.items():
if not isinstance(key_j, str):
raise ValueError(
raise TypeError(
f"ERROR: In the 'get_final_gaussian_output_file_data' function, "
f"the 'qm_log_file_dict' key "
f"'{key_j}' is a {type(key_j)} not a string."
Expand Down Expand Up @@ -804,7 +802,7 @@ def get_gaussian_log_file_data(
else:
for key_j, value_j in qm_log_file_dict.items():
if not isinstance(key_j, str):
raise ValueError(
raise TypeError(
f"ERROR: In the 'get_gaussian_log_file_data' function, "
f"the 'qm_log_file_dict' key "
f"'{key_j}' is a {type(key_j)} not a string."
Expand Down Expand Up @@ -1948,15 +1946,6 @@ def change_gomc_ff_file_dihedral_values(
for list_i in zero_dihedral_atom_types:
if not len(list_i) == 4:
raise TypeError(zero_dihedral_atom_types_error)

if (
isinstance(list_i[0], str)
and isinstance(list_i[1], str)
and isinstance(list_i[2], str)
and isinstance(list_i[3], str)
):
raise TypeError(zero_dihedral_atom_types_error)

elif not isinstance(zero_dihedral_atom_types, type(None)):
raise TypeError(zero_dihedral_atom_types_error)

Expand Down
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