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Merge pull request #120 from daico007/more_read_write_testing
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More tests on read/write utils
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@bc118
bc118 authored Aug 27, 2024
2 parents 7d0384b + fb992cc commit 3efeca8
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Showing 3 changed files with 242 additions and 13 deletions.
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
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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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