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# 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)
|
