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import unittest
from ost import *
import subprocess
class TestPDB(unittest.TestCase):
def setUp(self):
pass
def test_compnd_parser(self):
e=io.LoadPDB('testfiles/pdb/compnd.pdb', restrict_chains="A")
self.assertEqual(e.GetChainCount(), 1)
ch = e.FindChain("A");
self.assertEqual(ch.GetIntProp("mol_id"), 1)
def test_properly_assigns_profile_properties(self):
io.profiles['TEST'] = io.IOProfile()
io.profiles['TEST'].fault_tolerant = False
self.assertFalse(io.profiles['TEST'].fault_tolerant)
self.assertFalse(io.profiles['TEST'].Copy().fault_tolerant)
io.profiles['TEST'].fault_tolerant = True
self.assertTrue(io.profiles['TEST'].fault_tolerant)
self.assertTrue(io.profiles['TEST'].Copy().fault_tolerant)
def test_no_bond_feasibility(self):
io.profiles['FEAS_CHECK']=io.IOProfile(processor=conop.HeuristicProcessor(check_bond_feasibility=True))
io.profiles['NO_FEAS_CHECK']=io.IOProfile(processor=conop.HeuristicProcessor(check_bond_feasibility=False))
e1=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A",profile='FEAS_CHECK')
e2=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A",profile='NO_FEAS_CHECK')
ed=io.LoadPDB('testfiles/pdb/simple_defective.pdb', restrict_chains="A")
res1=e1.FindResidue('A',3)
res2=e2.FindResidue('A',3)
resd=ed.FindResidue('A',3)
self.assertFalse(mol.BondExists(res1.FindAtom("CA"),res1.FindAtom("CB")))
self.assertTrue(mol.BondExists(res2.FindAtom("CA"),res2.FindAtom("CB")))
self.assertTrue(mol.BondExists(resd.FindAtom("CA"),resd.FindAtom("CB")))
@unittest.skip("not running tests requiring network access")
def test_remote_loading(self):
if subprocess.call(['ping google.com -c 1'], shell=True,
stdout=subprocess.PIPE, stderr=subprocess.PIPE) != 0:
print("No internet connection (or wrong OS) to test remote loading in "
"io.LoadPDB: ignoring unit test")
return
with self.assertRaises(IOError):
io.LoadPDB('1ake', remote=True, remote_repo="cheeseisgoodforyou")
# let's hope that crambin stays the same forever
crambin_pdb = io.LoadPDB('1crn', remote=True, remote_repo='pdb')
self.assertEqual(len(crambin_pdb.residues), 46)
self.assertEqual(len(crambin_pdb.atoms), 327)
def test_conect(self):
""" See whether read_conect has an effect on reading CONECT
"""
prot = io.LoadPDB("testfiles/pdb/conect.pdb")
res = prot.FindResidue("A", mol.ResNum(3))
a1 = res.FindAtom("N")
a2 = res.FindAtom("CA")
tmp = sorted([str(a1), str(a2)])
bond = None
for b in prot.bonds:
if sorted([str(b.GetFirst()), str(b.GetSecond())]) == tmp:
bond = b
break
self.assertTrue(bond is not None)
self.assertEqual(bond.bond_order, 1)
prot = io.LoadPDB("testfiles/pdb/conect.pdb", read_conect=True)
res = prot.FindResidue("A", mol.ResNum(3))
a1 = res.FindAtom("N")
a2 = res.FindAtom("CA")
tmp = sorted([str(a1), str(a2)])
bond = None
for b in prot.bonds:
if sorted([str(b.GetFirst()), str(b.GetSecond())]) == tmp:
bond = b
break
self.assertTrue(bond is not None)
self.assertEqual(bond.bond_order, 2) # now it should be two
if __name__== '__main__':
from ost import testutils
testutils.RunTests()
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