import unittest, os, sys
import ost
from ost import io, mol, settings, conop, seq
# check if we can import: fails if numpy or scipy not available
try:
from ost.mol.alg import stereochemistry
except ImportError:
print("Failed to import stereochemistry. Happens when numpy missing. " \
"Ignoring test_stereochemistry.py tests.")
sys.exit(0)
def _LoadFile(file_name):
"""Helper to avoid repeating input path over and over."""
return io.LoadPDB(os.path.join('testfiles', file_name))
class TestStereochemistry(unittest.TestCase):
def test_GetResidueType(self):
""" internal function in stereochemistry module, nevertheless crucial...
"""
ent = _LoadFile("10b2.pdb")
# get some residues
ile_a_199 = ent.FindResidue("A", mol.ResNum(199))
self.assertEqual(ile_a_199.GetName(), "ILE")
pro_a_200 = ent.FindResidue("A", mol.ResNum(200))
self.assertEqual(pro_a_200.GetName(), "PRO")
glu_a_201 = ent.FindResidue("A", mol.ResNum(201))
self.assertEqual(glu_a_201.GetName(), "GLU")
pro_a_202 = ent.FindResidue("A", mol.ResNum(202))
self.assertEqual(pro_a_202.GetName(), "PRO")
ser_a_221 = ent.FindResidue("A", mol.ResNum(221))
self.assertEqual(ser_a_221.GetName(), "SER")
gly_a_222 = ent.FindResidue("A", mol.ResNum(222))
self.assertEqual(gly_a_222.GetName(), "GLY")
arg_a_223 = ent.FindResidue("A", mol.ResNum(223))
self.assertEqual(arg_a_223.GetName(), "ARG")
c_b_75 = ent.FindResidue("B", mol.ResNum(75))
self.assertEqual(c_b_75.GetName(), "C")
a_b_76 = ent.FindResidue("B", mol.ResNum(76))
self.assertEqual(a_b_76.GetName(), "A")
# check PRO_CIS
res_type = stereochemistry._GetResidueType([ile_a_199.FindAtom("C"),
pro_a_200.FindAtom("N")])
self.assertEqual(res_type, "PRO_CIS")
res_type = stereochemistry._GetResidueType([pro_a_200.FindAtom("N"),
ile_a_199.FindAtom("C")])
self.assertEqual(res_type, "PRO_CIS")
res_type = stereochemistry._GetResidueType([ile_a_199.FindAtom("O"),
ile_a_199.FindAtom("C"),
pro_a_200.FindAtom("N")])
self.assertEqual(res_type, "PRO_CIS")
res_type = stereochemistry._GetResidueType([pro_a_200.FindAtom("N"),
ile_a_199.FindAtom("C"),
ile_a_199.FindAtom("O")])
self.assertEqual(res_type, "PRO_CIS")
# check PRO_TRANS
res_type = stereochemistry._GetResidueType([glu_a_201.FindAtom("C"),
pro_a_202.FindAtom("N")])
self.assertEqual(res_type, "PRO_TRANS")
res_type = stereochemistry._GetResidueType([pro_a_202.FindAtom("N"),
glu_a_201.FindAtom("C")])
self.assertEqual(res_type, "PRO_TRANS")
res_type = stereochemistry._GetResidueType([glu_a_201.FindAtom("O"),
glu_a_201.FindAtom("C"),
pro_a_202.FindAtom("N")])
self.assertEqual(res_type, "PRO_TRANS")
res_type = stereochemistry._GetResidueType([pro_a_202.FindAtom("N"),
glu_a_201.FindAtom("C"),
glu_a_201.FindAtom("O")])
self.assertEqual(res_type, "PRO_TRANS")
# check GLY
res_type = stereochemistry._GetResidueType([ser_a_221.FindAtom("C"),
gly_a_222.FindAtom("N")])
self.assertEqual(res_type, "GLY")
res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
ser_a_221.FindAtom("C")])
self.assertEqual(res_type, "GLY")
res_type = stereochemistry._GetResidueType([ser_a_221.FindAtom("O"),
ser_a_221.FindAtom("C"),
gly_a_222.FindAtom("N")])
self.assertEqual(res_type, "GLY")
res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
ser_a_221.FindAtom("C"),
ser_a_221.FindAtom("O")])
self.assertEqual(res_type, "GLY")
# check PEPTIDE
res_type = stereochemistry._GetResidueType([arg_a_223.FindAtom("C"),
gly_a_222.FindAtom("N")])
self.assertEqual(res_type, "PEPTIDE")
res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
arg_a_223.FindAtom("C")])
self.assertEqual(res_type, "PEPTIDE")
res_type = stereochemistry._GetResidueType([arg_a_223.FindAtom("O"),
arg_a_223.FindAtom("C"),
gly_a_222.FindAtom("N")])
self.assertEqual(res_type, "PEPTIDE")
res_type = stereochemistry._GetResidueType([gly_a_222.FindAtom("N"),
arg_a_223.FindAtom("C"),
arg_a_223.FindAtom("O")])
self.assertEqual(res_type, "PEPTIDE")
# check NA
res_type = stereochemistry._GetResidueType([a_b_76.FindAtom("P"),
c_b_75.FindAtom("O3'")])
self.assertEqual(res_type, "NA")
res_type = stereochemistry._GetResidueType([c_b_75.FindAtom("O3'"),
a_b_76.FindAtom("P")])
self.assertEqual(res_type, "NA")
res_type = stereochemistry._GetResidueType([a_b_76.FindAtom("O5'"),
a_b_76.FindAtom("P"),
c_b_75.FindAtom("O3'")])
self.assertEqual(res_type, "NA")
res_type = stereochemistry._GetResidueType([c_b_75.FindAtom("O3'"),
a_b_76.FindAtom("P"),
a_b_76.FindAtom("O5'")])
self.assertEqual(res_type, "NA")
def test_FullParameters(self):
""" Tests whether we get parameters for each bond/angle
"""
ent = _LoadFile("10b2.pdb")
data = stereochemistry.GetDefaultStereoData()
link_data = stereochemistry.GetDefaultStereoLinkData()
# do bonds
for b in ent.bonds:
param = stereochemistry.GetBondParam(b.first, b.second,
stereo_data=data,
stereo_link_data = link_data)
self.assertTrue(None not in param)
# do angles
angles = stereochemistry._GetAngles(ent.bonds)
for a in angles:
param = stereochemistry.GetAngleParam(a[0], a[1], a[2],
stereo_data=data,
stereo_link_data = link_data)
self.assertTrue(None not in param)
def test_StereoCheck(self):
""" Test StereoCheck
GetClashes, GetBadBonds and GetBadAngles get tested implicitely
"""
ent = _LoadFile("10b2.pdb")
sterochecked_ent, clashes, bad_bonds, bad_angles = \
stereochemistry.StereoCheck(ent)
self.assertEqual(len(clashes), 0)
self.assertEqual(len(bad_bonds), 0)
self.assertEqual(len(bad_angles), 0)
phe_A_218 = ent.FindResidue("A", mol.ResNum(218))
c_B_75 = ent.FindResidue("B", mol.ResNum(75))
phe_at = phe_A_218.FindAtom("CD2")
c_at = c_B_75.FindAtom("C4'")
ed = ent.EditXCS()
ed.SetAtomPos(phe_at, 0.5*(phe_at.GetPos() + c_at.GetPos()))
stereochecked_ent, clashes, bad_bonds, bad_angles = \
stereochemistry.StereoCheck(ent)
self.assertEqual(len(clashes), 2)
self.assertEqual(len(bad_bonds), 2)
self.assertEqual(len(bad_angles), 2)
# c_B_75 gets completely removed as two backbone atoms are involved
# in clashes. phe_A_218 has the sidechain removed
self.assertEqual(len(ent.residues)-1,
len(stereochecked_ent.residues))
c_B_75 = stereochecked_ent.FindResidue("B", mol.ResNum(75))
self.assertFalse(c_B_75.IsValid())
phe_A_218 = stereochecked_ent.FindResidue("A", mol.ResNum(218))
self.assertTrue(phe_A_218.IsValid())
phe_atoms = [a.GetName() for a in phe_A_218.atoms]
self.assertEqual(sorted(["N", "CA", "C", "O"]),
sorted(phe_atoms))
# reload and trigger the case where the nucleotide backbone remains
ent = _LoadFile("10b2.pdb")
c_B_75 = ent.FindResidue("B", mol.ResNum(75))
ser_A_219 = ent.FindResidue("A", mol.ResNum(219))
c_at = c_B_75.FindAtom("O2")
ser_at = ser_A_219.FindAtom("O")
ed = ent.EditXCS()
new_pos = ser_at.GetPos() + 0.6*(c_at.GetPos()-ser_at.GetPos())
ed.SetAtomPos(ser_at, new_pos)
stereochecked_ent, clashes, bad_bonds, bad_angles = \
stereochemistry.StereoCheck(ent)
self.assertEqual(len(clashes), 1)
self.assertEqual(len(bad_bonds), 1)
self.assertEqual(len(bad_angles), 1)
c_B_75 = stereochecked_ent.FindResidue("B", mol.ResNum(75))
self.assertTrue(c_B_75.IsValid())
ser_A_219 = stereochecked_ent.FindResidue("A", mol.ResNum(219))
self.assertFalse(ser_A_219.IsValid())
c_atoms = [a.GetName() for a in c_B_75.atoms]
exp_c_atoms = ["P", "OP1", "OP2", "O5'", "C5'", "C4'", "C3'",
"C2'", "C1'", "O4'", "O3'", "O2'"]
self.assertEqual(sorted(c_atoms), sorted(exp_c_atoms))
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound library available. Ignoring test_stereochemistry.py tests.')