def testPDB_sel_type_hetero(self): # preparation pdb = atomset.PDB() # function to test pdb.initialise("tests/data/pdb_test_ligand.pdb", type="HETERO") # assertion pdbContent = "MODEL 1\n\ ATOM 1717 H ASN A 119 25.915 9.925 -7.236 1.00 31.61 H \n\ ATOM 1718 CA ASN A 119 27.159 10.509 -6.736 1.00 33.83 C \n\ TER\n\ HETATM 1733 O1 AIN L 1 13.907 16.130 0.624 0.50 28.52 O \n\ TER\n\ HETATM 1753 CA CA B 1 16.636 15.477 0.293 1.00 3.39 Ca2+\n\ TER\n\ ENDMDL\n\ END \n" atom1 = atomset.Atom( "HETATM 1733 O1 AIN L 1 13.907 16.130 0.624 0.50 28.52 O " ) atom2 = atomset.Atom( "HETATM 1753 CA CA B 1 16.636 15.477 0.293 1.00 3.39 Ca2+" ) goldenAtomsDict = {atom1.id: atom1, atom2.id: atom2} self.assertEqual(pdb.pdb, pdbContent) self.assertEqual(pdb.atoms, goldenAtomsDict)
def testPDB_from_str(self): # preparation with open("tests/data/pdb_test.pdb", "rt") as pdbfile: pdbstring = pdbfile.read() pdb = atomset.PDB() # function to test pdb.initialise(pdbstring) # assertion pdbContent = "ATOM 1 N ASN A 1 7.920 22.268 9.257 1.00 15.18 N1+\n\ ATOM 2 CA CYS A 1 8.394 20.916 9.575 1.00 16.24 C \n\ ATOM 3 CA ASN A 1 7.870 19.937 8.524 1.00 16.63 C \n\ ATOM 4 O ASN A 1 7.030 20.308 7.700 1.00 16.13 O \n\ ATOM 5 CB CYS A 1 8.108 20.445 11.030 1.00 16.53 C \n" atom1 = atomset.Atom( "ATOM 1 N ASN A 1 7.920 22.268 9.257 1.00 15.18 N1+" ) atom2 = atomset.Atom( "ATOM 2 CA CYS A 1 8.394 20.916 9.575 1.00 16.24 C " ) atom3 = atomset.Atom( "ATOM 3 CA ASN A 1 7.870 19.937 8.524 1.00 16.63 C " ) atom4 = atomset.Atom( "ATOM 4 O ASN A 1 7.030 20.308 7.700 1.00 16.13 O " ) atom5 = atomset.Atom( "ATOM 5 CB CYS A 1 8.108 20.445 11.030 1.00 16.53 C " ) goldenAtomsDict = { atom1.id: atom1, atom2.id: atom2, atom3.id: atom3, atom4.id: atom4, atom5.id: atom5 } self.assertEqual(pdb.pdb, pdbContent) self.assertEqual(pdb.atoms, goldenAtomsDict)
def testPDB_sel_chain(self): # preparation pdb = atomset.PDB() # function to test pdb.initialise("tests/data/pdb_test2.pdb", chain="B") # assertion pdbContent = "ATOM 1 N ASN A 1 7.920 22.268 9.257 1.00 15.18 N1+\n\ ATOM 2 CA CYS B 1 8.394 20.916 9.575 1.00 16.24 C \n\ ATOM 3 CA ASN B 1 7.870 19.937 8.524 1.00 16.63 C \n\ ATOM 4 O ASN A 2 7.030 20.308 7.700 1.00 16.13 O \n\ ATOM 5 CB CYS A 2 8.108 20.445 11.030 1.00 16.53 C \n" atom2 = atomset.Atom( "ATOM 2 CA CYS B 1 8.394 20.916 9.575 1.00 16.24 C " ) atom3 = atomset.Atom( "ATOM 3 CA ASN B 1 7.870 19.937 8.524 1.00 16.63 C " ) goldenAtomsDict = {atom2.id: atom2, atom3.id: atom3} self.assertEqual(pdb.pdb, pdbContent) self.assertEqual(pdb.atoms, goldenAtomsDict)