htmd.builder.charmm module¶

class htmd.builder.charmm.TestCharmmBuild(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.

Parameters: typeobj – The data type to call this function on when both values are of the same type in assertEqual(). function – The callable taking two arguments and an optional msg= argument that raises self.failureException with a useful error message when the two arguments are not equal.
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.

Parameters: list1 – The first list to compare. list2 – The second list to compare. msg – Optional message to use on failure instead of a list of differences.
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.

Parameters: expected_exception – Exception class expected to be raised. expected_regex – Regex (re pattern object or string) expected to be found in error message. args – Function to be called and extra positional args. kwargs – Extra kwargs. msg – Optional message used in case of failure. Can only be used when assertRaisesRegex is used as a context manager.
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.

Parameters: seq1 – The first sequence to compare. seq2 – The second sequence to compare. seq_type – The expected datatype of the sequences, or None if no datatype should be enforced. msg – Optional message to use on failure instead of a list of differences.
assertSetEqual(set1, set2, msg=None)

A set-specific equality assertion.

Parameters: set1 – The first set to compare. set2 – The second set to compare. msg – Optional message to use on failure instead of a list of differences.

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.

Parameters: tuple1 – The first tuple to compare. tuple2 – The second tuple to compare. msg – Optional message to use on failure instead of a list of differences.
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.

Parameters: expected_warning – Warning class expected to be triggered. expected_regex – Regex (re pattern object or string) expected to be found in error message. args – Function to be called and extra positional args. kwargs – Extra kwargs. msg – Optional message used in case of failure. Can only be used when assertWarnsRegex is used as a context manager.
assert_(**kwargs)
countTestCases()
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.

classmethod 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.

classmethod tearDownClass()

Hook method for deconstructing the class fixture after running all tests in the class.

test_build()
test_customDisulfideBonds()
test_disulfideWithInsertion()
htmd.builder.charmm.build(mol, topo=None, param=None, stream=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0, saltanion=None, saltcation=None, disulfide=None, patches=None, noregen=None, aliasresidues=None, psfgen=None, execute=True, _clean=True)

Builds a system for CHARMM

Uses VMD and psfgen to build a system for CHARMM. Additionally it allows for ionization and adding of disulfide bridges.

Parameters: mol (Molecule object) – The Molecule object containing the system topo (list of str) – A list of topology rtf files. Use charmm.listFiles to get a list of available topology files. Default: [‘top/top_all36_prot.rtf’, ‘top/top_all36_lipid.rtf’, ‘top/top_water_ions.rtf’] param (list of str) – A list of parameter prm files. Use charmm.listFiles to get a list of available parameter files. Default: [‘par/par_all36_prot.prm’, ‘par/par_all36_lipid.prm’, ‘par/par_water_ions.prm’] stream (list of str) – A list of stream str files containing topologies and parameters. Use charmm.listFiles to get a list of available stream files. Default: [‘str/prot/toppar_all36_prot_arg0.str’] prefix (str) – The prefix for the generated pdb and psf files outdir (str) – The path to the output directory Default: ‘./build’ caps (dict) – A dictionary with keys segids and values lists of strings describing the caps of that segment. e.g. caps[‘P’] = [‘first ACE’, ‘last CT3’] or caps[‘P’] = [‘first none’, ‘last none’]. Default: will apply ACE and CT3 caps to proteins and none caps to the rest. ionize (bool) – Enable or disable ionization saltconc (float) – Salt concentration (in Molar) to add to the system after neutralization. saltanion ({'CLA'}) – The anion type. Please use only CHARMM ion atom names. saltcation ({'SOD', 'MG', 'POT', 'CES', 'CAL', 'ZN2'}) – The cation type. Please use only CHARMM ion atom names. disulfide (list of pairs of atomselection strings) – If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of residues forming the disulfide bridge. patches (list of str) – Any further patches the user wants to apply noregen (list of str) – A list of patches that must not be regenerated (angles and dihedrals) Default: [‘FHEM’, ‘PHEM’, ‘PLOH’, ‘PLO2’, ‘PLIG’, ‘PSUL’] aliasresidues (dict of aliases) – A dictionary of key: value pairs of residue names we want to alias psfgen (str) – Path to psfgen executable used to build for CHARMM execute (bool) – Disable building. Will only write out the input script needed by psfgen. Does not include ionization. molbuilt – The built system in a Molecule object Molecule object

Example

>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> mol.filter("not resname BEN")
>>> molbuilt = charmm.build(mol, outdir='/tmp/build', ionize=False)
Bond between A: [serial 185 resid 42 resname CYS chain A segid 0]
B: [serial 298 resid 58 resname CYS chain A segid 0]...
>>> # More complex example
>>> topos  = ['top/top_all36_prot.rtf', './benzamidine.rtf', 'top/top_water_ions.rtf']
>>> params = ['par/par_all36_prot.prm', './benzamidine.prm', 'par/par_water_ions.prm']
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> ar = {'SAPI24': 'SP24'}  # Alias large resnames to a short-hand version
>>> molbuilt = charmm.build(mol, topo=topos, param=params, outdir='/tmp/build', saltconc=0.15, disulfide=disu, aliasresidues=ar)

htmd.builder.charmm.combine(prmlist, outfile)

Combines CHARMM parameter files Take a list of parameters files and combine them into a single file (useful for acemd)

Parameters: prmlist (list) – List of parameter files to combine outfile (str) – Output filename of combined parameter files
htmd.builder.charmm.defaultParam()

Returns the default parameters used by charmm.build

htmd.builder.charmm.defaultStream()

Returns the default stream files used by charmm.build

htmd.builder.charmm.defaultTopo()

Returns the default topologies used by charmm.build

htmd.builder.charmm.htmdCharmmHome()

Returns the location of the CHARMM files distributed with HTMD

htmd.builder.charmm.listFiles()

Lists all available Charmm topologies and parameter files

Examples

>>> from htmd.builder import charmm
>>> charmm.listFiles()
---- Topologies files list...

htmd.builder.charmm.search(key, name)

Searches for CHARMM files containing a given definition.

Parameters: key (str) – A key name (str) – The corresponding name

Examples

>>> charmm.search(key='RESI', name = 'CHL1')

htmd.builder.charmm.split(filename, outdir)

Splits a stream file into an rtf and prm file.

Parameters: filename (str) – Stream file name