schrodinger.application.matsci.mstest module¶

Unit test related functions/classes.

schrodinger.application.matsci.mstest.assert_same_struct(struct1, struct2, target_rmsd=0.0, decimal=1, msg=None)¶

Assert that two structures are almost same.

Parameters:

struct1 (structure.Structure) – First structure
struct2 (structure.Structure) – Second structure
target_rmsd (float) – Target RMSD for two structures
decimal (int) – The number of decimal places used for comparing the two RMSD floats. In unittest needs to be set fairly loosely so that the tests pass on different OSs
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – when the two struct are not equal within given tolerance

schrodinger.application.matsci.mstest.mmexception_side_effect()¶

Get an MmException object that can be used as a side effect

Return type:: mm.MmException
Returns:: returns an mm.MmException object that can be used as a side effect for Mocks

class schrodinger.application.matsci.mstest.MSTestCase(*args, **kwargs)¶

Bases: TestCase

__init__(*args, **kwargs)¶: See parent for documentation. When using addTypeEqualityFunc for a new object, always add it to assertAlmostEqual.

numpy_equal(actual, desired, msg=None)¶: Call numpy equal

assertStructEqual(struct1, struct2, msg=None)¶

Assert that two structures are equivalent.

Parameters:

struct1 (structure.Structure) – First structure
struct2 (structure.Structure) – Second structure
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – when the two structures are not same.

assertStructAlmostEqual(struct1, struct2, target_rmsd=0.0, decimal=1, msg=None)¶

Assert that two structures are almost same.

Parameters:

struct1 (structure.Structure) – First structure
struct2 (structure.Structure) – Second structure
target_rmsd (float) – Target RMSD for two structures
decimal (int) – The number of decimal places used for comparing the two RMSD floats. In unittest needs to be set fairly loosely so that the tests pass on different OSs
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – when the two struct are not equal within given tolerance

assertAlmostEqual(actual, desired, decimal=6, msg=None, places=None)¶

Override assertAlmostEqual with numpy testing assert_almost_equal. Add functionality to test structure and dictionaries as well.

Parameters:

actual (array_like or dict or structure.Structure) – the object to check
desired (array_like or dict or structure.Structure) – the expected object
msg (str or None) – message shown if failure occurs
decimal (int) – desired precision
places (int) – Provided for compatibility with unittest API, which uses the places keyword rather than decimal. If given, will override the decimal value

typeTest(obj_type, actual, desired, msg)¶

Check if actual and desired are of given type.

Parameters:

obj_type (any class) – Object type to check actual and desired is of
actual (any class) – the actual object to check the type of
desired (any class) – the desired object to check the type of

Return bool:

True if type of actual and desired is obj_type else False

getCallResult(mocked_function, index=None, key=None, call_number=None, msg=None)¶

Get the value for the passed argument for the mocked function

Parameters:

mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – 0-based index of the argument to compare.
argument (str) – Name of the keyword argument
call_number (int) – Index of the call made to the function. None means the most recent call, calls are indexed starting at 1.
msg (str or None) – message shown if failure occurs

Return list or tuple or dict or set or frozenset or str:

value for the passed argument for the mocked function

Raises:

AssertionError – the mocked fuction was not called with input index or argument.

assertCallEqual(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is equal to value that the mocked fuction was called with.

Parameters:

actual – actual value of the mock call to compare to
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – index of the argument to compare
argument (str) – name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – If actual value is not equal to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallNotEqual(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is not equal to value that the mocked fuction was called with.

Parameters:

actual – actual value of the mock call to compare to
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – If actual value is equal to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallIn(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is in the container that the mocked fuction was called with.

Parameters:

actual – value to check if it was in the call argument
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – If actual value is not in to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallNotIn(actual, mocked_function, index=None, argument=None, call_number=None, msg=None)¶

Check if the actual value is not in the container that the mocked fuction was called with.

Parameters:

actual – value to check if it was not in the call argument
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call

Raises:

AssertionError – If actual value is not in to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCallAlmostEqual(actual, mocked_function, index=None, argument=None, call_number=None, msg=None, decimal=6)¶

Check if the actual value is equal to value that the mocked fuction was called with.

Parameters:

actual (list or tuple or dict or set or frozenset or str) – actual value of the mock call to compare to
mocked_function (unittest.mock.MagicMock) – mocked function which was called
index (int) – Index of the argument to compare
argument (str) – Name of the keyword argument
call_number (int or None) – Number of the call made to the function. If none the last call will be taken and 1 will be oldest (first) call
msg (str or None) – message shown if failure occurs
decimal (int) – desired precision

Raises:

AssertionError – If actual value is not equal (within the decimal places) to value that the mocked fuction was called with or the fuction was not called with input index/argument.

assertCalledTimes(times, mocked_function, msg=None)¶

Check if the mocked fuction was called passed number of times

Parameters:

times (int) – number of times mocked_function was called
mocked_function (unittest.mock.MagicMock) – mocked function which was called
msg (str or None) – message shown if failure occurs

Raises:

AssertionError – If the mocked fuction was not called the passed amount of time

assertFlag(cmd, flag, value=None, is_in=True)¶

Check that an expected flag is in (or not in) the command line list and also check the value of that flag. Note that the language used here is for the command line, but this function works for any sequence where one might want to simultaneously check the ith and i+1th values together.

Examples:: self.assertFlag(cmd, ‘-gpu’) self.assertFlag(cmd, ‘-HOST’, value=’bolt_personal:5’) self.assertFlag(cmd, ‘-nosystem’, is_in=False)

Parameters:

cmd (list) – The list to check
flag – The item to check if it is in cmd (may be any type)
value – If given, the item following flag will be checked to see if it is equal to value.
is_in (bool) – If true, checks if flag is in cmd. If False, checks that flag is not in cmd, and value is ignored.

Raises:

AssertionError – If flag violates the is_in setting, or if value is given and does not match the item after flag.

assertTableContentsEqual(table, expected_contents, expected_column_headers=None)¶

Assert that the actual table contents match the expected ones. Optionally checks table headers too.

Parameters:

table (QtWidgets.QTableWidget) – The table to get actual contents from
expected_contents (list) – List of lists containing the desired data in the table. Each inner list has the contents of a row.
expected_column_headers (list) – If not None, the column headers in the table will be compared with this list

Raises:

AssertionError – If the contents are not equal

assertStageEqual(stage1, stage2)¶

Assert that the two desmond stages are equal.

Parameters:

stage1 (sea.Map) – first stage
stage2 (sea.Map) – Second stage

Raises:

AssertionError – If the contents are not equal

schrodinger.application.matsci.mstest.matsci_scripts_testfile(path)¶

Get the full path to the test file at mmshare/python/test/matsci/path

Parameters:: path (str) – Relative path of file
Return type:: str
Returns:: Full path to file

schrodinger.application.matsci.mstest.matsci_application_testfile(path)¶

Get the full path to the test file at mmshare/python/test/application/matsci/path

Parameters:: path (str) – Relative path of file
Return type:: str
Returns:: Full path to file

schrodinger.application.matsci.mstest.load_structure(filename)¶

Load the first structure from the given file in the testfile directory where structures are stored

Parameters:: filename (str) – The name of the structure file
Return type:: structure.Structure
Returns:: The first structure in filename

schrodinger.application.matsci.mstest.mock_json_load_from_fh(module, contents_dict)¶

Context manager to mock json.load on a file handle in the given module and return the given contents dictionary.

Parameters:

module (module) – the module using open and json
contents_dict (dict) – the contents dictionary

schrodinger.application.matsci.mstest.set_wa_dont_show_on_screen(widget)¶

Sets WA_DontShowOnScreen attribute to True for the given widget

Parameters:: widget (QWidget) – The widget whose WA_DontShowOnScreen attribute is to be set.

schrodinger.application.matsci.mstest.set_feature_flag(flag, state)¶

Set feature flag to a requested state and yield.

Parameters:

flag (str or int) – mmutil constant for the feature flag or name
state (bool) – Whether feature flag should be enabled or disabled

schrodinger.application.matsci.mstest.ms_use_rdkit_ff_helper(state)¶

Yield with MS_USE_RDKIT feature flag set to state.

Parameters:: state (bool) – Whether feature flag should be enabled or disabled

schrodinger.application.matsci.mstest.cycle_feature_flag(flag)¶

Loop over a feature flag being turned on and off (On first, Off second)

Parameters:: flag (int or str) – mmutil constant for the feature flag (int) or name (str)
Ytype:: bool
Yields:: The current flag state