print(line1, '!=', line2)
print(lineCount, matchCount, diffCount)
if args.rama:
if pdb_input:
pdb_structure.atom_to_internal_coordinates()
for r in pdb_structure.get_residues():
# print(r.internal_coord.get_dihedral('N:CA:C:O'))
if r.internal_coord:
print(r, r.internal_coord.get_angle('psi'), r.internal_coord.get_angle('phi'),
r.internal_coord.get_angle(
'omg'), r.internal_coord.get_angle('chi2'),
r.internal_coord.get_length('0C:1N'))
if args.ws:
if args.flex:
for r in pdb_structure.get_residues():
r.internal_coord.set_flexible()
if args.hb:
for r in pdb_structure.get_residues():
r.internal_coord.set_hbond()
write_SCAD(pdb_structure, outfile + '.scad', scale_val, pdbid=prot_id,
backboneOnly=args.backbone, includeCode=scadCode_val)
fileNo += 1
print('normal termination')
def test_write_SCAD(self):
"""Check SCAD output plus MaxPeptideBond and Gly CB.
SCAD tests: scaling, transform mtx, extra bond created (allBonds)
"""
sf = StringIO()
write_SCAD(
self.cif_4CUP2,
sf,
10.0,
pdbid="4cup",
backboneOnly=True,
includeCode=False,
)
sf.seek(0)
next_one = False
with as_handle(sf, mode="r") as handle:
for aline in handle.readlines():
if "// (1856_S_CB, 1856_S_CA, 1856_S_C)" in aline:
m = re.search(r"\[\s+(\d+\.\d+)\,", aline)
if m:
# test correctly scaled atom bond length
self.assertAlmostEqual(float(m.group(1)), 15.30582, places=3)
else:
self.fail("scaled atom bond length not found")
elif '[ 1, "1857M",' in aline:
next_one = True
elif next_one:
next_one = False
# test last residue transform looks roughly correct
# some differences due to sorting issues on different
# python versions
target = [-12.413, -3.303, 35.771, 1.0]
ms = re.findall( # last column of each row
r"\s+(-?\d+\.\d+)\s+\]", aline
)
if ms:
for i in range(0, 3):
self.assertAlmostEqual(float(ms[i]), target[i], places=0)
else:
self.fail("transform not found")
sf.seek(0)
IC_Residue.gly_Cbeta = True
IC_Chain.MaxPeptideBond = 100.0
chn = self.pdb_2XHE2[0]["A"]
chn.atom_to_internal_coordinates()
rt0 = chn.internal_coord.ordered_aa_ic_list[12]
rt1 = chn.internal_coord.ordered_aa_ic_list[16]
rt0.set_flexible()
rt1.set_hbond()
write_SCAD(
self.pdb_2XHE2[0]["A"],
sf,
10.0,
pdbid="2xhe",
# maxPeptideBond=100.0,
includeCode=False,
start=10,
fin=570,
)
sf.seek(0)
allBondsPass = False
maxPeptideBondPass = False
glyCbetaFound = False
startPass = True
finPass = True
flexPass = False
hbPass = False
with as_handle(sf, mode="r") as handle:
for aline in handle.readlines():
# test extra bond created in TRP (allBonds is True)
if '"Cres", 0, 0, 1, 0, StdBond, "W", 24, "CD2CE3CZ3"' in aline:
allBondsPass = True
# test 509_K-561_E long bond created
if "509_K" in aline and "561_E" in aline:
maxPeptideBondPass = True
if "(21_G_CB, 21_G_CA, 21_G_C)" in aline:
glyCbetaFound = True
target = [15.33630, 110.17513, 15.13861]
ms = re.findall(r"\s+(-?\d+\.\d+)", aline)
if ms:
for i in range(0, 3):
self.assertAlmostEqual(float(ms[i]), target[i], places=0)
else:
self.fail("Cbeta internal coords not found")
if "8_K_CA" in aline:
startPass = False
if "572_N_CA" in aline:
finPass = False
if 'FemaleJoinBond, FemaleJoinBond, "N", 13, "NCAC"' in aline:
flexPass = True
if 'HBond, "R", 16, "CACO"' in aline:
hbPass = True
self.assertTrue(allBondsPass, msg="missing extra ring close bonds")
self.assertTrue(glyCbetaFound, msg="gly CB not created")
self.assertTrue(maxPeptideBondPass, msg="ignored maxPeptideBond setting")
self.assertTrue(startPass, msg="writeSCAD wrote residue before start")
self.assertTrue(finPass, msg="writeSCAD wrote residue past fin")
self.assertTrue(flexPass, msg="writeSCAD residue 12 not flexible")
self.assertTrue(hbPass, msg="writeSCAD residue 16 no hbond")
def test_write_SCAD(self):
"""Check SCAD output plus MaxPeptideBond and Gly CB.
SCAD tests: scaling, transform mtx, extra bond created (allBonds)
"""
sf = StringIO()
write_SCAD(self.cif_4CUP,
sf,
10.0,
pdbid="4cup",
backboneOnly=True,
includeCode=False)
sf.seek(0)
next_one = False
with as_handle(sf, mode="r") as handle:
for aline in handle.readlines():
if "// (1856_S_CB, 1856_S_CA, 1856_S_C)" in aline:
m = re.search(r"\[\s+(\d+\.\d+)\,", aline)
if m:
# test correctly scaled atom bond length
self.assertAlmostEqual(float(m.group(1)),
15.30582,
places=3)
else:
self.fail("scaled atom bond length not found")
elif '[ 1, "1857M",' in aline:
next_one = True
elif next_one:
next_one = False
# test last residue transform looks roughly correct
# some differences due to sorting issues on different python
# versions
target = [-12.413, -3.303, 35.771, 1.0]
ms = re.findall( # last column of each row
r"\s+(-?\d+\.\d+)\s+\]", aline)
if ms:
for i in range(0, 3):
self.assertAlmostEqual(float(ms[i]),
target[i],
places=0)
else:
self.fail("transform not found")
sf.seek(0)
IC_Residue.gly_Cbeta = True
write_SCAD(
self.pdb_2XHE[0]["A"],
sf,
10.0,
pdbid="2xhe",
maxPeptideBond=100.0,
includeCode=False,
)
sf.seek(0)
allBondsPass = False
maxPeptideBondPass = False
glyCbetaFound = False
with as_handle(sf, mode="r") as handle:
for aline in handle.readlines():
# test extra bond created in TRP (allBonds is True)
if '"Cres", 0, 0, 1, 0, StdBond, "W", 24, "CD2CE3CZ3"' in aline:
allBondsPass = True
# test 509_K-561_E long bond created
if "509_K" in aline and "561_E" in aline:
maxPeptideBondPass = True
if "(21_G_CB, 21_G_CA, 21_G_C)" in aline:
glyCbetaFound = True
target = [15.33630, 110.17513, 15.13861]
ms = re.findall(r"\s+(-?\d+\.\d+)", aline)
if ms:
for i in range(0, 3):
self.assertAlmostEqual(float(ms[i]),
target[i],
places=0)
else:
self.fail("Cbeta internal coords not found")
self.assertTrue(allBondsPass)
self.assertTrue(glyCbetaFound)
self.assertTrue(maxPeptideBondPass)