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)