acelleralivehtmd.builder.amber.TestAmberBuild(methodName='runTest')¶Bases: unittest.case.TestCase
addCleanup(function, *args, **kwargs)¶Add a function, with arguments, to be called when the test is completed. Functions added are called on a LIFO basis and are called after tearDown on test failure or success.
Cleanup items are called even if setUp fails (unlike tearDown).
addTypeEqualityFunc(typeobj, function)¶Add a type specific assertEqual style function to compare a type.
This method is for use by TestCase subclasses that need to register their own type equality functions to provide nicer error messages.
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assertAlmostEqual(first, second, places=None, msg=None, delta=None)¶Fail if the two objects are unequal as determined by their difference rounded to the given number of decimal places (default 7) and comparing to zero, or by comparing that the between the two objects is more than the given delta.
Note that decimal places (from zero) are usually not the same as significant digits (measured from the most significant digit).
If the two objects compare equal then they will automatically compare almost equal.
assertAlmostEquals(**kwargs)¶assertCountEqual(first, second, msg=None)¶An unordered sequence comparison asserting that the same elements, regardless of order. If the same element occurs more than once, it verifies that the elements occur the same number of times.
- self.assertEqual(Counter(list(first)),
- Counter(list(second)))
- Example:
- [0, 1, 1] and [1, 0, 1] compare equal.
- [0, 0, 1] and [0, 1] compare unequal.
assertDictContainsSubset(subset, dictionary, msg=None)¶Checks whether dictionary is a superset of subset.
assertDictEqual(d1, d2, msg=None)¶assertEqual(first, second, msg=None)¶Fail if the two objects are unequal as determined by the ‘==’ operator.
assertEquals(**kwargs)¶assertFalse(expr, msg=None)¶Check that the expression is false.
assertGreater(a, b, msg=None)¶Just like self.assertTrue(a > b), but with a nicer default message.
assertGreaterEqual(a, b, msg=None)¶Just like self.assertTrue(a >= b), but with a nicer default message.
assertIn(member, container, msg=None)¶Just like self.assertTrue(a in b), but with a nicer default message.
assertIs(expr1, expr2, msg=None)¶Just like self.assertTrue(a is b), but with a nicer default message.
assertIsInstance(obj, cls, msg=None)¶Same as self.assertTrue(isinstance(obj, cls)), with a nicer default message.
assertIsNone(obj, msg=None)¶Same as self.assertTrue(obj is None), with a nicer default message.
assertIsNot(expr1, expr2, msg=None)¶Just like self.assertTrue(a is not b), but with a nicer default message.
assertIsNotNone(obj, msg=None)¶Included for symmetry with assertIsNone.
assertLess(a, b, msg=None)¶Just like self.assertTrue(a < b), but with a nicer default message.
assertLessEqual(a, b, msg=None)¶Just like self.assertTrue(a <= b), but with a nicer default message.
assertListEqual(list1, list2, msg=None)¶A list-specific equality assertion.
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assertLogs(logger=None, level=None)¶Fail unless a log message of level level or higher is emitted on logger_name or its children. If omitted, level defaults to INFO and logger defaults to the root logger.
This method must be used as a context manager, and will yield a recording object with two attributes: output and records. At the end of the context manager, the output attribute will be a list of the matching formatted log messages and the records attribute will be a list of the corresponding LogRecord objects.
Example:
with self.assertLogs('foo', level='INFO') as cm:
logging.getLogger('foo').info('first message')
logging.getLogger('foo.bar').error('second message')
self.assertEqual(cm.output, ['INFO:foo:first message',
'ERROR:foo.bar:second message'])
assertMultiLineEqual(first, second, msg=None)¶Assert that two multi-line strings are equal.
assertNotAlmostEqual(first, second, places=None, msg=None, delta=None)¶Fail if the two objects are equal as determined by their difference rounded to the given number of decimal places (default 7) and comparing to zero, or by comparing that the between the two objects is less than the given delta.
Note that decimal places (from zero) are usually not the same as significant digits (measured from the most significant digit).
Objects that are equal automatically fail.
assertNotAlmostEquals(**kwargs)¶assertNotEqual(first, second, msg=None)¶Fail if the two objects are equal as determined by the ‘!=’ operator.
assertNotEquals(**kwargs)¶assertNotIn(member, container, msg=None)¶Just like self.assertTrue(a not in b), but with a nicer default message.
assertNotIsInstance(obj, cls, msg=None)¶Included for symmetry with assertIsInstance.
assertNotRegex(text, unexpected_regex, msg=None)¶Fail the test if the text matches the regular expression.
assertNotRegexpMatches(**kwargs)¶assertRaises(expected_exception, *args, **kwargs)¶Fail unless an exception of class expected_exception is raised by the callable when invoked with specified positional and keyword arguments. If a different type of exception is raised, it will not be caught, and the test case will be deemed to have suffered an error, exactly as for an unexpected exception.
If called with the callable and arguments omitted, will return a context object used like this:
with self.assertRaises(SomeException):
do_something()
An optional keyword argument ‘msg’ can be provided when assertRaises is used as a context object.
The context manager keeps a reference to the exception as the ‘exception’ attribute. This allows you to inspect the exception after the assertion:
with self.assertRaises(SomeException) as cm:
do_something()
the_exception = cm.exception
self.assertEqual(the_exception.error_code, 3)
assertRaisesRegex(expected_exception, expected_regex, *args, **kwargs)¶Asserts that the message in a raised exception matches a regex.
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assertRaisesRegexp(**kwargs)¶assertRegex(text, expected_regex, msg=None)¶Fail the test unless the text matches the regular expression.
assertRegexpMatches(**kwargs)¶assertSequenceEqual(seq1, seq2, msg=None, seq_type=None)¶An equality assertion for ordered sequences (like lists and tuples).
For the purposes of this function, a valid ordered sequence type is one which can be indexed, has a length, and has an equality operator.
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assertSetEqual(set1, set2, msg=None)¶A set-specific equality assertion.
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assertSetEqual uses ducktyping to support different types of sets, and is optimized for sets specifically (parameters must support a difference method).
assertTrue(expr, msg=None)¶Check that the expression is true.
assertTupleEqual(tuple1, tuple2, msg=None)¶A tuple-specific equality assertion.
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assertWarns(expected_warning, *args, **kwargs)¶Fail unless a warning of class warnClass is triggered by the callable when invoked with specified positional and keyword arguments. If a different type of warning is triggered, it will not be handled: depending on the other warning filtering rules in effect, it might be silenced, printed out, or raised as an exception.
If called with the callable and arguments omitted, will return a context object used like this:
with self.assertWarns(SomeWarning):
do_something()
An optional keyword argument ‘msg’ can be provided when assertWarns is used as a context object.
The context manager keeps a reference to the first matching warning as the ‘warning’ attribute; similarly, the ‘filename’ and ‘lineno’ attributes give you information about the line of Python code from which the warning was triggered. This allows you to inspect the warning after the assertion:
with self.assertWarns(SomeWarning) as cm:
do_something()
the_warning = cm.warning
self.assertEqual(the_warning.some_attribute, 147)
assertWarnsRegex(expected_warning, expected_regex, *args, **kwargs)¶Asserts that the message in a triggered warning matches a regexp. Basic functioning is similar to assertWarns() with the addition that only warnings whose messages also match the regular expression are considered successful matches.
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assert_(**kwargs)¶countTestCases()¶currentResult = None¶debug()¶Run the test without collecting errors in a TestResult
defaultTestResult()¶doCleanups()¶Execute all cleanup functions. Normally called for you after tearDown.
fail(msg=None)¶Fail immediately, with the given message.
failIf(**kwargs)¶failIfAlmostEqual(**kwargs)¶failIfEqual(**kwargs)¶failUnless(**kwargs)¶failUnlessAlmostEqual(**kwargs)¶failUnlessEqual(**kwargs)¶failUnlessRaises(**kwargs)¶failureException¶alias of builtins.AssertionError
id()¶longMessage = True¶maxDiff = 640¶run(result=None)¶setUp()¶Hook method for setting up the test fixture before exercising it.
setUpClass()¶Hook method for setting up class fixture before running tests in the class.
shortDescription()¶Returns a one-line description of the test, or None if no description has been provided.
The default implementation of this method returns the first line of the specified test method’s docstring.
skipTest(reason)¶Skip this test.
subTest(msg=<object object>, **params)¶Return a context manager that will return the enclosed block of code in a subtest identified by the optional message and keyword parameters. A failure in the subtest marks the test case as failed but resumes execution at the end of the enclosed block, allowing further test code to be executed.
tearDown()¶Hook method for deconstructing the test fixture after testing it.
tearDownClass()¶Hook method for deconstructing the class fixture after running all tests in the class.
testProteinLigand()¶testWithProteinPrepare()¶testWithoutProteinPrepare()¶test_customDisulfideBonds()¶test_customTeLeapImports()¶htmd.builder.amber.build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0, saltanion=None, saltcation=None, disulfide=None, teleap=None, teleapimports=None, execute=True, atomtypes=None, offlibraries=None, gbsa=False, igb=2)¶Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
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| Returns: | molbuilt – The built system in a Molecule object |
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Example
>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build')
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu)
htmd.builder.amber.defaultAmberHome(teleap=None)¶Returns the default AMBERHOME as defined by the location of teLeap binary
htmd.builder.amber.defaultFf()¶Returns the default leaprc forcefield files used by amber.build
htmd.builder.amber.defaultParam()¶Returns the default parameter frcmod files used by amber.build
htmd.builder.amber.defaultTopo()¶Returns the default topology prepi files used by amber.build
htmd.builder.amber.htmdAmberHome()¶Returns the location of the AMBER files distributed with HTMD
htmd.builder.amber.listFiles()¶Lists all AMBER forcefield files available in HTMD
Example
>>> from htmd.builder import amber
>>> amber.listFiles()
---- Forcefield files list: ... ----
leaprc.constph
leaprc.DNA.bsc1
leaprc.DNA.OL15
leaprc.ff14SB.redq
...