Useful manipulations on PDB files
Test(methodName=’runTest’)[source]¶Bases: unittest.case.TestCase
Methods
addCleanup(function, *args, **kwargs) |
Add a function, with arguments, to be called when the test is completed. |
addTypeEqualityFunc(typeobj, function) |
Add a type specific assertEqual style function to compare a type. |
assertAlmostEqual(first, second[, places, …]) |
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. |
assertAlmostEquals(first, second[, places, …]) |
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. |
assertDictContainsSubset(expected, actual[, msg]) |
Checks whether actual is a superset of expected. |
assertEqual(first, second[, msg]) |
Fail if the two objects are unequal as determined by the ‘==’ operator. |
assertEquals(first, second[, msg]) |
Fail if the two objects are unequal as determined by the ‘==’ operator. |
assertFalse(expr[, msg]) |
Check that the expression is false. |
assertGreater(a, b[, msg]) |
Just like self.assertTrue(a > b), but with a nicer default message. |
assertGreaterEqual(a, b[, msg]) |
Just like self.assertTrue(a >= b), but with a nicer default message. |
assertIn(member, container[, msg]) |
Just like self.assertTrue(a in b), but with a nicer default message. |
assertIs(expr1, expr2[, msg]) |
Just like self.assertTrue(a is b), but with a nicer default message. |
assertIsInstance(obj, cls[, msg]) |
Same as self.assertTrue(isinstance(obj, cls)), with a nicer default message. |
assertIsNone(obj[, msg]) |
Same as self.assertTrue(obj is None), with a nicer default message. |
assertIsNot(expr1, expr2[, msg]) |
Just like self.assertTrue(a is not b), but with a nicer default message. |
assertIsNotNone(obj[, msg]) |
Included for symmetry with assertIsNone. |
assertItemsEqual(expected_seq, actual_seq[, msg]) |
An unordered sequence specific comparison. |
assertLess(a, b[, msg]) |
Just like self.assertTrue(a < b), but with a nicer default message. |
assertLessEqual(a, b[, msg]) |
Just like self.assertTrue(a <= b), but with a nicer default message. |
assertListEqual(list1, list2[, msg]) |
A list-specific equality assertion. |
assertMultiLineEqual(first, second[, msg]) |
Assert that two multi-line strings are equal. |
assertNotAlmostEqual(first, second[, …]) |
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. |
assertNotAlmostEquals(first, second[, …]) |
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. |
assertNotEqual(first, second[, msg]) |
Fail if the two objects are equal as determined by the ‘!=’ operator. |
assertNotEquals(first, second[, msg]) |
Fail if the two objects are equal as determined by the ‘!=’ operator. |
assertNotIn(member, container[, msg]) |
Just like self.assertTrue(a not in b), but with a nicer default message. |
assertNotIsInstance(obj, cls[, msg]) |
Included for symmetry with assertIsInstance. |
assertNotRegexpMatches(text, unexpected_regexp) |
Fail the test if the text matches the regular expression. |
assertRaises(excClass[, callableObj]) |
Fail unless an exception of class excClass is raised by callableObj when invoked with arguments args and keyword arguments kwargs. |
assertRaisesRegexp(expected_exception, …) |
Asserts that the message in a raised exception matches a regexp. |
assertRegexpMatches(text, expected_regexp[, msg]) |
Fail the test unless the text matches the regular expression. |
assertSequenceEqual(seq1, seq2[, msg, seq_type]) |
An equality assertion for ordered sequences (like lists and tuples). |
assertSetEqual(set1, set2[, msg]) |
A set-specific equality assertion. |
assertTrue(expr[, msg]) |
Check that the expression is true. |
assertTupleEqual(tuple1, tuple2[, msg]) |
A tuple-specific equality assertion. |
assert_(expr[, msg]) |
Check that the expression is true. |
debug() |
Run the test without collecting errors in a TestResult |
doCleanups() |
Execute all cleanup functions. |
fail([msg]) |
Fail immediately, with the given message. |
failureException |
alias of AssertionError |
setUp() |
Hook method for setting up the test fixture before exercising it. |
setUpClass() |
Set up paths. |
shortDescription() |
Returns a one-line description of the test, or None if no description has been provided. |
skipTest(reason) |
Skip this test. |
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. |
| XtestSplit | |
| __call__ | |
| assertDictEqual | |
| countTestCases | |
| defaultTestResult | |
| failIf | |
| failIfAlmostEqual | |
| failIfEqual | |
| failUnless | |
| failUnlessAlmostEqual | |
| failUnlessEqual | |
| failUnlessRaises | |
| id | |
| run | |
| testCheckPdbs | |
| testGetInfo1 | |
| testGetInfo2 | |
| testReliableSidechains | |
| testSelectResidues | |
| testSelectResiduesKeepIdxs | |
| testSequence1 | |
| testStdResidues | |
| testStdResiduesCctbx | |
| testStripAtomTypes | |
| testStripHetatm | |
| testStripHydrogen | |
| testXyzCbCoordinates | |
| testXyzCoordinates |
Xselect_residues(inpath=None, outpath=None, residues=None)[source]¶Create a new pdb by selecting only the numbered residues from the list. This only keeps ATOM lines - everything else gets discarded.
Args: infile: path to input pdb outfile: path to output pdb residues: list of integers of the residues to keep
Return: Number of residues written
Xstd_residues(pdbin, pdbout)[source]¶Switch any non-standard AA’s to their standard names. We also remove any ANISOU lines.
extract_chain(inpdb, outpdb, chainID=None, newChainID=None, cAlphaOnly=False, renumber=True)[source]¶Extract chainID from inpdb and renumner. If cAlphaOnly is set, strip down to c-alpha atoms
get_info(inpath)[source]¶Read a PDB and extract as much information as possible into a PdbInfo object
keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None)[source]¶Only keep those atoms in targetpdb that are in refpdb and write the result to outpdb. We also take care of renaming any chains.
num_atoms_and_residues(pdbin, first=False)[source]¶“Return number of atoms and residues in a pdb file. If all is True, return all atoms and residues, else just for the first chain in the first model’
prepare_nmr_model(nmr_model_in, models_dir)[source]¶Split an nmr pdb into its constituent parts and standardise the lengths
reliable_sidechains(inpath=None, outpath=None)[source]¶Only output non-backbone atoms for residues in the res_names list.
reliable_sidechains_cctbx(pdbin=None, pdbout=None)[source]¶Only output non-backbone atoms for residues in the res_names list.
renumber_residues_gaps(pdbin, pdbout, gaps, start=1)[source]¶Renumber the residues in the chain based on specified gaps
| Parameters: |
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split_into_chains(pdbin, chain=None, directory=None)[source]¶Split a pdb file into its separate chains
standardise(pdbin, pdbout, chain=None, del_hetatm=False)[source]¶Rename any non-standard AA, remove solvent and only keep most probably conformation.
std_residues_cctbx(pdbin, pdbout, del_hetatm=False)[source]¶Map all residues in MODRES section to their standard counterparts optionally delete all other HETATMS
to_single_chain(inpath, outpath)[source]¶Condense a single-model multi-chain pdb to a single-chain pdb