# Copyright 2017 by Francesco Gastaldello. All rights reserved. # Revisions copyright 2017 by Peter Cock. All rights reserved. # # Converted by Francesco Gastaldello from an older unit test copyright 2002 # by Thomas Hamelryck. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Unit tests for the Bio.PDB.MMCIF2Dict module.""" import unittest try: import numpy except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install NumPy if you want to use Bio.PDB." ) from None from Bio.PDB.MMCIF2Dict import MMCIF2Dict import io import textwrap class MMCIF2dictTests(unittest.TestCase): def test_MMCIF2dict(self): filename = "PDB/1A8O.cif" mmcif = MMCIF2Dict(filename) self.assertEqual(len(mmcif.keys()), 575) # Turn black code style off # fmt: off self.assertEqual( mmcif["_entity_poly_seq.mon_id"], [ "MSE", "ASP", "ILE", "ARG", "GLN", "GLY", "PRO", "LYS", "GLU", "PRO", "PHE", "ARG", "ASP", "TYR", "VAL", "ASP", "ARG", "PHE", "TYR", "LYS", "THR", "LEU", "ARG", "ALA", "GLU", "GLN", "ALA", "SER", "GLN", "GLU", "VAL", "LYS", "ASN", "TRP", "MSE", "THR", "GLU", "THR", "LEU", "LEU", "VAL", "GLN", "ASN", "ALA", "ASN", "PRO", "ASP", "CYS", "LYS", "THR", "ILE", "LEU", "LYS", "ALA", "LEU", "GLY", "PRO", "GLY", "ALA", "THR", "LEU", "GLU", "GLU", "MSE", "MSE", "THR", "ALA", "CYS", "GLN", "GLY", ] ) self.assertEqual( mmcif["_atom_site.Cartn_x"], [ "19.594", "20.255", "20.351", "19.362", "19.457", "20.022", "21.718", "21.424", "21.554", "21.835", "21.947", "21.678", "23.126", "23.098", "23.433", "22.749", "22.322", "22.498", "21.220", "20.214", "23.062", "24.282", "23.423", "25.429", "21.280", "20.173", "20.766", "21.804", "19.444", "18.724", "18.011", "17.416", "16.221", "15.459", "15.824", "20.116", "20.613", "20.546", "19.488", "19.837", "20.385", "19.526", "18.365", "20.090", "21.675", "21.698", "20.859", "20.729", "20.260", "19.435", "20.158", "19.512", "18.993", "20.056", "20.300", "21.486", "22.285", "23.286", "24.155", "23.025", "22.117", "21.236", "20.159", "19.231", "23.152", "24.037", "23.563", "22.398", "24.086", "25.003", "24.858", "23.861", "25.748", "24.459", "24.089", "23.580", "24.111", "25.415", "26.116", "25.852", "22.544", "21.960", "22.965", "22.928", "20.793", "19.999", "19.234", "20.019", "18.495", "19.286", "18.523", "23.861", "24.870", "25.788", "26.158", "25.684", "26.777", "26.215", "27.235", "28.136", "28.155", "29.030", "26.137", "26.994", "26.279", "26.880", "27.408", "28.345", "28.814", "28.620", "24.992", "24.151", "24.025", "24.139", "22.787", "21.629", "21.657", "20.489", "20.571", "19.408", "19.450", "18.365", "23.839", "23.720", "24.962", "24.853", "23.502", "23.661", "22.120", "26.137", "27.387", "27.511", "27.925", "28.595", "28.723", "28.016", "29.545", "27.136", "27.202", "26.238", "26.585", "26.850", "27.835", "27.667", "26.352", "25.494", "25.797", "24.325", "25.037", "23.984", "24.456", "24.305", "22.761", "21.538", "21.301", "20.586", "20.130", "19.415", "19.186", "25.033", "25.526", "26.755", "27.015", "25.771", "24.608", "23.508", "24.583", "22.406", "23.490", "22.406", "21.326", "27.508", "28.691", "28.183", "28.705", "29.455", "30.787", "31.428", "32.618", "33.153", "27.116", "26.508", "25.826", "25.827", "25.475", "26.150", "24.741", "25.264", "24.587", "25.587", "25.302", "23.789", "22.707", "21.787", "21.910", "26.767", "27.806", "28.299", "28.656", "29.006", "28.944", "30.295", "30.744", "30.326", "29.441", "30.787", "28.332", "28.789", "27.943", "28.374", "28.803", "26.740", "25.833", "25.775", "24.998", "24.425", "24.354", "24.816", "24.535", "25.454", "26.601", "26.645", "25.240", "24.885", "27.391", "28.884", "29.200", "28.729", "29.998", "24.438", "23.066", "23.001", "23.824", "22.370", "22.035", "21.831", "21.174", "20.852", "20.917", "19.638", "20.949", "20.315", "18.908", "18.539", "20.262", "19.688", "20.414", "21.592", "19.714", "18.136", "16.775", "16.738", "15.875", "16.101", "15.478", "14.341", "13.247", "14.542", "17.668", "17.730", "18.064", "17.491", "18.754", "18.932", "18.279", "18.971", "19.343", "18.126", "17.905", "20.444", "21.777", "22.756", "24.069", "24.913", "17.344", "16.136", "15.146", "14.599", "15.468", "16.242", "17.164", "15.865", "14.932", "14.017", "14.495", "13.700", "13.904", "13.254", "12.332", "13.484", "11.975", "12.666", "14.303", "12.641", "14.280", "13.452", "15.793", "16.368", "16.285", "16.053", "17.815", "17.939", "17.221", "18.427", "16.438", "16.375", "14.950", "14.778", "16.869", "18.228", "16.791", "13.947", "12.529", "12.045", "11.151", "11.625", "11.950", "11.054", "11.086", "10.326", "12.589", "12.177", "13.076", "12.888", "11.978", "13.202", "10.883", "14.054", "14.963", "15.702", "15.846", "15.935", "15.286", "16.327", "14.580", "16.162", "16.876", "15.961", "16.391", "17.402", "18.238", "19.553", "18.506", "14.695", "13.703", "13.270", "13.262", "12.460", "11.372", "12.854", "12.954", "12.503", "13.541", "13.184", "12.008", "10.830", "10.505", "10.626", "10.093", "14.820", "15.887", "16.443", "17.416", "17.014", "16.627", "15.451", "17.619", "15.830", "16.248", "15.758", "14.809", "15.689", "16.404", "16.005", "14.639", "14.122", "17.109", "17.396", "16.559", "18.588", "14.018", "12.706", "12.516", "11.536", "12.617", "13.288", "14.522", "13.454", "13.383", "13.351", "12.406", "14.564", "14.482", "13.353", "15.552", "14.378", "14.488", "13.443", "12.968", "15.902", "16.144", "13.061", "12.087", "10.746", "10.157", "11.879", "11.014", "11.003", "10.171", "10.269", "10.273", "9.002", "9.101", "8.227", "8.612", "8.611", "7.224", "10.191", "10.458", "10.518", "9.916", "11.791", "11.677", "12.184", "12.967", "11.222", "11.377", "10.082", "9.885", "12.416", "13.824", "14.764", "14.287", "9.214", "7.937", "7.048", "6.294", "7.230", "7.828", "7.618", "8.090", "7.916", "7.189", "6.419", "6.871", "6.391", "6.449", "7.815", "8.305", "7.481", "7.371", "9.788", "10.832", "12.217", "10.789", "6.886", "6.080", "6.922", "8.149", "6.294", "7.024", "7.912", "7.680", "5.901", "4.734", "4.839", "8.952", "9.861", "10.886", "11.642", "10.910", "11.884", "13.285", "13.524", "11.599", "14.199", "15.563", "16.391", "16.022", "16.290", "16.498", "15.473", "17.509", "18.426", "18.875", "19.012", "19.645", "20.773", "20.264", "21.920", "19.082", "19.510", "18.471", "18.816", "19.784", "21.035", "20.954", "19.902", "21.955", "17.199", "16.109", "16.001", "15.690", "14.787", "14.776", "13.539", "13.220", "12.888", "16.301", "16.274", "17.413", "17.209", "16.429", "15.284", "15.332", "13.844", "18.606", "19.764", "19.548", "19.922", "21.047", "21.507", "23.105", "22.645", "18.915", "18.636", "17.640", "17.807", "18.050", "18.998", "17.730", "16.631", "15.593", "16.104", "15.685", "14.486", "17.033", "17.572", "18.985", "19.634", "17.525", "15.855", "19.451", "20.802", "21.001", "20.066", "21.152", "20.421", "20.725", "21.768", "19.817", "22.226", "22.536", "23.683", "24.328", "23.949", "15.165", "19.774", "22.152", "12.938", "23.499", "17.568", "13.544", "15.524", "31.249", "11.999", "14.511", "7.439", "19.303", "17.114", "21.867", "17.573", "26.151", "20.974", "20.796", "28.370", "29.565", "21.248", "25.744", "8.691", "30.789", "30.905", "28.623", "24.935", "23.462", "9.924", "28.729", "13.579", "23.652", "25.631", "17.799", "23.547", "16.363", "24.125", "33.063", "29.209", "10.391", "12.221", "18.997", "16.360", "27.915", "28.158", "21.975", "27.069", "30.148", "21.196", "8.864", "13.228", "18.577", "20.526", "25.758", "7.838", "20.569", "13.009", "19.229", "17.655", "30.445", "9.014", "3.398", "31.603", "16.543", "12.037", "7.261", "5.607", "23.532", "30.701", "32.300", "34.351", "9.450", "29.476", "13.681", "26.728", "10.004", "30.553", "23.569", "10.927", "17.983", "8.191", "32.095", "11.520", "13.249", "15.919", "11.187", "16.743", ] ) # Turn black code style on # fmt: on self.assertEqual( mmcif["_struct_ref.pdbx_seq_one_letter_code"], [ "GARASVLSGGELDKWEKIRLRPGGKKQYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTG" "SEELRSLYNT\n" "IAVLYCVHQRIDVKDTKEALDKIEEEQNKSKKKAQQAAADTGNNSQVSQNYPIVQNLQGQMVHQAISPRT" "LNAWVKVVEE\n" "KAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREP" "RGSDIAGTTS\n" "TLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQ" "EVKNWMTETL\n" "LVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVLAEAMSQVTNPATIMIQKGNFRNQRKTVK" "CFNCGKEGHI\n" "AKNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSHKGRPGNFLQSRPEPTAPPEESFRFGEETTT" "PSQKQEPIDK\n" "ELYPLASLRSLFGSDPSSQ" ], ) def test_underscores(self): # Test values starting with an underscore are not treated as keys filename = "PDB/4Q9R_min.cif" mmcif = MMCIF2Dict(filename) self.assertEqual(len(mmcif.keys()), 5) self.assertEqual( mmcif["_pdbx_audit_revision_item.item"], [ "_atom_site.B_iso_or_equiv", "_atom_site.Cartn_x", "_atom_site.Cartn_y", "_atom_site.Cartn_z", ], ) def test_quotefix(self): # Test quote characters parse correctly filename = "PDB/1MOM_min.cif" mmcif = MMCIF2Dict(filename) self.assertEqual(len(mmcif.keys()), 21) self.assertEqual( mmcif["_struct_conf.pdbx_PDB_helix_id"], [ "A", "A'", "B", "C", "B'", "D", "E", "C'", "F", "G", "H", "D'", "E'", "A'\"", "BC", "CD", "DE", ], ) def test_splitline(self): filename = "PDB/4Q9R_min.cif" mmcif = MMCIF2Dict(filename) self.assertEqual(list(mmcif._splitline("foo bar")), ["foo", "bar"]) self.assertEqual(list(mmcif._splitline(" foo bar ")), ["foo", "bar"]) self.assertEqual(list(mmcif._splitline("'foo' bar")), ["foo", "bar"]) self.assertEqual(list(mmcif._splitline('foo "bar"')), ["foo", "bar"]) self.assertEqual(list(mmcif._splitline("foo 'bar a' b")), ["foo", "bar a", "b"]) self.assertEqual(list(mmcif._splitline("foo 'bar'a' b")), ["foo", "bar'a", "b"]) self.assertEqual( list(mmcif._splitline('foo "bar\' a" b')), ["foo", "bar' a", "b"] ) self.assertEqual(list(mmcif._splitline("foo '' b")), ["foo", "", "b"]) self.assertEqual(list(mmcif._splitline("foo bar' b")), ["foo", "bar'", "b"]) self.assertEqual(list(mmcif._splitline("foo bar b'")), ["foo", "bar", "b'"]) # A hash (#) starts a comment iff it is preceded by whitespace or is at # the beginning of a line: # https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#lex self.assertEqual(list(mmcif._splitline("foo#bar")), ["foo#bar"]) self.assertEqual(list(mmcif._splitline("foo #bar")), ["foo"]) self.assertEqual(list(mmcif._splitline("foo# bar")), ["foo#", "bar"]) self.assertEqual(list(mmcif._splitline("#foo bar")), []) self.assertRaises(ValueError, list, mmcif._splitline("foo 'bar")) self.assertRaises(ValueError, list, mmcif._splitline("foo 'ba'r ")) self.assertRaises(ValueError, list, mmcif._splitline("foo \"bar'")) # quotes are allowed if not followed by whitespace self.assertEqual(list(mmcif._splitline("foo b'ar'")), ["foo", "b'ar'"]) self.assertEqual(list(mmcif._splitline("foo 'b'ar'")), ["foo", "b'ar"]) def test_verbatim_block(self): """Verbatim blocks parsed correctly. Verbatim blocks delimited by ";...;" should have the final newline stripped. Whitespace may be stripped from the end of the line but not the beginning. """ mmcif_dict = MMCIF2Dict( io.StringIO( "data_verbatim_test\n" "_test_value\n" ";First line\n" " Second line\n" "Third line\n" ";\n" ) ) self.assertEqual( mmcif_dict["_test_value"], ["First line\n Second line\nThird line"] ) def test_token_after_multiline(self): """Multi-line string followed by token on the same line.""" stream = io.StringIO("data_test _key1\n;foo bar\n; _key2 'value 2'\n") mmcif_dict = MMCIF2Dict(stream) self.assertEqual( mmcif_dict, {"data_": "test", "_key1": ["foo bar"], "_key2": ["value 2"]} ) stream = io.StringIO("data_test _key1\n;foo bar\n;# missing space here") with self.assertRaisesRegex(ValueError, "Missing whitespace"): mmcif_dict = MMCIF2Dict(stream) def test_truncated_multiline(self): stream = io.StringIO("data_test\n_key1\n;foo bar\n") with self.assertRaisesRegex(ValueError, "Missing closing semicolon"): mmcif_dict = MMCIF2Dict(stream) def test_inline_comments(self): """Comments may begin outside of column 1 if preceded by whitespace.""" mmcif_dict = MMCIF2Dict( io.StringIO( "data_verbatim_test\n" "_test_key_value_1 foo # Ignore this comment\n" "_test_key_value_2 foo#NotIgnored\n" "loop_\n" "_test_loop\n" "a b c d # Ignore this comment\n" "e f g\n" "\n" ) ) self.assertEqual(mmcif_dict["_test_key_value_1"], ["foo"]) self.assertEqual(mmcif_dict["_test_key_value_2"], ["foo#NotIgnored"]) self.assertEqual(mmcif_dict["_test_loop"], list("abcdefg")) def test_loop_keyword_case_insensitive(self): """Comments may begin outside of column 1.""" test_data = """\ data_verbatim_test _test_key_value foo # Ignore this comment loop_ _test_loop a b c d # Ignore this comment e f g """ mmcif_dict = MMCIF2Dict(io.StringIO(textwrap.dedent(test_data))) mmcif_dict2 = MMCIF2Dict( io.StringIO(textwrap.dedent(test_data.replace("loop_", "LOOP_"))) ) self.assertDictEqual(mmcif_dict, mmcif_dict2) mmcif_dict2 = MMCIF2Dict( io.StringIO(textwrap.dedent(test_data.replace("loop_", "looP_"))) ) self.assertDictEqual(mmcif_dict, mmcif_dict2) mmcif_dict2 = MMCIF2Dict( io.StringIO(textwrap.dedent(test_data.replace("_loop", "_LOOP"))) ) self.assertNotEqual(mmcif_dict, mmcif_dict2) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)