# Copyright 2017 by Bernhard Thiel. All rights reserved. # Revisions copyright 2024 James Krieger. # 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 PARTS of the parse_pdb_header module of Bio.PDB.""" import unittest try: import numpy as np # noqa F401 except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install NumPy if you want to use Bio.PDB." ) from None from Bio.PDB import PDBParser from Bio.PDB.parse_pdb_header import _parse_remark_465 from Bio.PDB.parse_pdb_header import parse_pdb_header class ParseReal(unittest.TestCase): """Testing with real PDB file(s).""" def test_1(self): """Parse the header of a known PDB file (1A8O).""" parser = PDBParser() struct = parser.get_structure("1A8O", "PDB/1A8O.pdb") self.assertAlmostEqual(struct.header["resolution"], 1.7) # Case-insensitive string comparisons known_strings = { "author": "T.R.Gamble,S.Yoo,F.F.Vajdos,U.K.Von Schwedler,D.K.Worthylake,H.Wang,J.P.Mccutcheon,W.I.Sundquist,C.P.Hill", "deposition_date": "1998-03-27", "head": "viral protein", "journal": "AUTH T.R.GAMBLE,S.YOO,F.F.VAJDOS,U.K.VON SCHWEDLER,AUTH 2 D.K.WORTHYLAKE,H.WANG,J.P.MCCUTCHEON,W.I.SUNDQUIST,AUTH 3 C.P.HILLTITL STRUCTURE OF THE CARBOXYL-TERMINAL DIMERIZATIONTITL 2 DOMAIN OF THE HIV-1 CAPSID PROTEIN.REF SCIENCE V. 278 849 1997REFN ISSN 0036-8075PMID 9346481DOI 10.1126/SCIENCE.278.5339.849", "journal_reference": "t.r.gamble,s.yoo,f.f.vajdos,u.k.von schwedler, d.k.worthylake,h.wang,j.p.mccutcheon,w.i.sundquist, c.p.hill structure of the carboxyl-terminal dimerization domain of the hiv-1 capsid protein. science v. 278 849 1997 issn 0036-8075 9346481 10.1126/science.278.5339.849 ", "keywords": "capsid, core protein, hiv, c-terminal domain, viral protein", "name": "hiv capsid c-terminal domain", "release_date": "1998-10-14", "structure_method": "x-ray diffraction", } for key, expect in known_strings.items(): self.assertEqual(struct.header[key].lower(), expect.lower()) def test_2(self): """Parse the header of another PDB file (2BEG).""" parser = PDBParser() struct = parser.get_structure("2BEG", "PDB/2BEG.pdb") known_strings = { "author": "T.Luhrs,C.Ritter,M.Adrian,D.Riek-Loher,B.Bohrmann,H.Dobeli,D.Schubert,R.Riek", "deposition_date": "2005-10-24", "head": "protein fibril", "journal": "AUTH T.LUHRS,C.RITTER,M.ADRIAN,D.RIEK-LOHER,B.BOHRMANN,AUTH 2 H.DOBELI,D.SCHUBERT,R.RIEKTITL 3D STRUCTURE OF ALZHEIMER'S AMYLOID-{BETA}(1-42)TITL 2 FIBRILS.REF PROC.NATL.ACAD.SCI.USA V. 102 17342 2005REFN ISSN 0027-8424PMID 16293696DOI 10.1073/PNAS.0506723102", "journal_reference": "t.luhrs,c.ritter,m.adrian,d.riek-loher,b.bohrmann, h.dobeli,d.schubert,r.riek 3d structure of alzheimer's amyloid-{beta}(1-42) fibrils. proc.natl.acad.sci.usa v. 102 17342 2005 issn 0027-8424 16293696 10.1073/pnas.0506723102 ", "keywords": "alzheimer's, fibril, protofilament, beta-sandwich, quenched hydrogen/deuterium exchange, pairwise mutagenesis, protein fibril", "name": "3d structure of alzheimer's abeta(1-42) fibrils", "release_date": "2005-11-22", "structure_method": "solution nmr", } for key, expect in known_strings.items(): self.assertEqual(struct.header[key].lower(), expect.lower()) def test_parse_pdb_with_remark_465(self): """Tests that parse_pdb_header now can identify some REMARK 465 entries.""" header = parse_pdb_header("PDB/2XHE.pdb") self.assertEqual(header["idcode"], "2XHE") self.assertTrue(header["has_missing_residues"]) self.assertEqual(len(header["missing_residues"]), 142) self.assertIn( { "model": None, "res_name": "GLN", "chain": "B", "ssseq": 267, "insertion": None, }, header["missing_residues"], ) header = parse_pdb_header("PDB/1A8O.pdb") self.assertFalse(header["has_missing_residues"]) self.assertEqual(header["missing_residues"], []) def test_parse_remark_465(self): """A UNIT-test for the private function _parse_remark_465.""" info = _parse_remark_465("GLU B 276") self.assertEqual( info, { "model": None, "res_name": "GLU", "chain": "B", "ssseq": 276, "insertion": None, }, ) info = _parse_remark_465("U R -9") # Based on PDB id: 7c7a self.assertEqual( info, { "model": None, "res_name": "U", "chain": "R", "ssseq": -9, "insertion": None, }, ) info = _parse_remark_465("2 GLU B 276B") self.assertEqual( info, { "model": 2, "res_name": "GLU", "chain": "B", "ssseq": 276, "insertion": "B", }, ) info = _parse_remark_465("A 2 11") self.assertEqual( info, { "model": None, "res_name": "A", "chain": "2", "ssseq": 11, "insertion": None, }, ) info = _parse_remark_465("1 DG B 9") self.assertEqual( info, {"model": 1, "res_name": "DG", "chain": "B", "ssseq": 9, "insertion": None}, ) def test_parse_header_line(self): """Unit test for parsing and converting fields in HEADER record.""" header = parse_pdb_header("PDB/header.pdb") self.assertEqual(header["head"], "structural genomics, unknown function") self.assertEqual(header["idcode"], "3EFG") self.assertEqual(header["deposition_date"], "2008-09-08") def test_parse_title_line(self): """Unit test for correct parsing of multiline title records.""" header = parse_pdb_header("PDB/1LCD.pdb") self.assertEqual( header["name"], "structure of the complex of lac repressor headpiece and an 11 " "base-pair half-operator determined by nuclear magnetic resonance " "spectroscopy and restrained molecular dynamics", ) def test_parse_no_title(self): """Unit test for sensible result with no TITLE line.""" header = parse_pdb_header("PDB/occupancy.pdb") self.assertEqual(header["name"], "") def test_parse_pdb_with_remark_99(self): """Tests that parse_pdb_header can identify REMARK 99 ASTRAL entries.""" header = parse_pdb_header("PDB/d256ba_.ent") self.assertIn("astral", header) self.assertEqual(header["astral"]["SCOP-sccs"], "a.24.3.1") self.assertEqual(header["astral"]["Source-PDB"], "256b") self.assertEqual(header["astral"]["Region"], "a:") self.assertEqual(header["astral"]["ASTRAL-SPACI"], "0.72") def test_parse_pdb_with_remark_350_biomoltrans(self): """Tests that parse_pdb_header now can identify some REMARK 350 entries.""" header = parse_pdb_header("PDB/2XHE.pdb") self.assertEqual( header["biomoltrans"], { "1": [ ["A", "B"], " 1.000000 0.000000 0.000000 0.00000 \n", " 0.000000 1.000000 0.000000 0.00000 \n", " 0.000000 0.000000 1.000000 0.00000 \n", ] }, ) def test_parse_pdb_without_remark_350_biomoltrans(self): header = parse_pdb_header("PDB/1LCD.pdb") self.assertEqual(header["biomoltrans"], {}) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)