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python-biopython  1.60
Public Member Functions
test_PDB.HeaderTests Class Reference

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Public Member Functions

def test_capsid
def test_fibril

Detailed Description

Tests for parse_pdb_header.

Definition at line 100 of file test_PDB.py.


Member Function Documentation

Parse the header of a known PDB file (1A8O).

Definition at line 103 of file test_PDB.py.

00103 
00104     def test_capsid(self):
00105         """Parse the header of a known PDB file (1A8O)."""
00106         parser = PDBParser()
00107         struct = parser.get_structure('1A8O', 'PDB/1A8O.pdb')
00108         self.assertAlmostEqual(struct.header['resolution'], 1.7)
00109         # Case-insensitive string comparisons
00110         known_strings = {
00111                 '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',
00112                 'deposition_date': '1998-03-27',
00113                 'head': 'viral protein',
00114                 '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',
00115                 '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 ',
00116                 'keywords': 'capsid, core protein, hiv, c-terminal domain, viral protein',
00117                 'name': ' hiv capsid c-terminal domain',
00118                 'release_date': '1998-10-14',
00119                 'structure_method': 'x-ray diffraction',
00120                 }
00121         for key, expect in known_strings.iteritems():
00122             self.assertEqual(struct.header[key].lower(), expect.lower())

Parse the header of another PDB file (2BEG).

Definition at line 123 of file test_PDB.py.

00123 
00124     def test_fibril(self):
00125         """Parse the header of another PDB file (2BEG)."""
00126         parser = PDBParser()
00127         struct = parser.get_structure('2BEG', 'PDB/2BEG.pdb')
00128         known_strings = {
00129                 'author': 'T.Luhrs,C.Ritter,M.Adrian,D.Riek-Loher,B.Bohrmann,H.Dobeli,D.Schubert,R.Riek',
00130                 'deposition_date': '2005-10-24',
00131                 'head': 'protein fibril',
00132                 '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",
00133                 '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 ",
00134                 'keywords': "alzheimer's, fibril, protofilament, beta-sandwich, quenched hydrogen/deuterium exchange, pairwise mutagenesis, protein fibril",
00135                 'name': " 3d structure of alzheimer's abeta(1-42) fibrils",
00136                 'release_date': '2005-11-22',
00137                 'structure_method': 'solution nmr',
00138                 }
00139         for key, expect in known_strings.iteritems():
00140             self.assertEqual(struct.header[key].lower(), expect.lower())
00141 


The documentation for this class was generated from the following file: