def test_1KP8(self):
'''
test a dcd based on a large pdb complex (groel)
'''
#
pdbFileName = DataPath + '1KP8.pdb'
dcdFileName = moduleDataPath + 'test-results/1KP8-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 0
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = system.Molecule(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n', result_coor
self.assertEqual(len(result_coor[0]), 57085)
expected_sample_coor = numpy.array([104.484, 26.915, 12.538],
floattype)
sum_expected_coor = 6269170.260
self.assert_list_almost_equal(expected_sample_coor,
result_coor[0][100], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_1ATM_frame2(self):
'''
test a dcd with 2 frames based on a 1-atom pdb
write the 2nd frame
'''
#
pdbFileName = DataPath + '1ATM-1to2.pdb'
dcdFileName = moduleDataPath + 'test-results/1ATM-1to2-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 1
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = system.Molecule(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
expected_coor = numpy.array([[[73.944, 38.799, 41.652]]], floattype)
sum_expected_coor = 154.395
self.assert_list_almost_equal(expected_coor, result_coor, self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_rna_frame1to10_frame10(self):
'''
test a dcd based on a rna molecule of 10 frames
write the 10th frame
'''
#
# #
pdbFileName = DataPath + 'rna-1to10.pdb'
dcdFileName = moduleDataPath + 'test-results/rna-1to10-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 9
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = system.Molecule(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n', result_coor
self.assertEqual(len(result_coor[0]), 10632)
expected_sample_coor = numpy.array([-6.392, 14.348, 20.914], floattype)
sum_expected_coor = -42837.531
self.assert_list_almost_equal(expected_sample_coor,
result_coor[0][10631], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_1CRN(self):
'''
test a dcd based on a small protein (crambin)
'''
#
pdbFileName = DataPath + '1CRN.pdb'
dcdFileName = moduleDataPath + 'test-results/1CRN-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 0
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = system.Molecule(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n', result_coor
os.remove(dcdFileName)
self.assertEqual(len(result_coor[0]), 327)
expected_sample_coor = numpy.array([9.555, 2.856, 3.730], floattype)
sum_expected_coor = 8509.587
self.assert_list_almost_equal(expected_sample_coor,
result_coor[0][100], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
def test_1ATM_frame2(self):
'''
test a dcd with 2 frames based on a 1-atom pdb
write the 2nd frame
'''
#
pdbFileName = DataPath+'1ATM-1to2.pdb'
dcdFileName = moduleDataPath+'test-results/1ATM-1to2-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 1
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
expected_coor = numpy.array([[[73.944, 38.799, 41.652]]],floattype)
sum_expected_coor = 154.395
self.assert_list_almost_equal(expected_coor, result_coor, self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_rna_frame1to10_frame10(self):
'''
test a dcd based on a rna molecule of 10 frames
write the 10th frame
'''
#
# #
pdbFileName = DataPath+'rna-1to10.pdb'
dcdFileName = moduleDataPath+'test-results/rna-1to10-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 9
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n',result_coor
self.assertEqual(len(result_coor[0]),10632)
expected_sample_coor = numpy.array([-6.392, 14.348, 20.914],floattype)
sum_expected_coor = -42837.531
self.assert_list_almost_equal(expected_sample_coor,result_coor[0][10631], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_1KP8(self):
'''
test a dcd based on a large pdb complex (groel)
'''
#
pdbFileName = DataPath+'1KP8.pdb'
dcdFileName = moduleDataPath+'test-results/1KP8-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 0
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n',result_coor
self.assertEqual(len(result_coor[0]),57085)
expected_sample_coor = numpy.array([104.484, 26.915, 12.538],floattype)
sum_expected_coor = 6269170.260
self.assert_list_almost_equal(expected_sample_coor,result_coor[0][100], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_1CRN(self):
'''
test a dcd based on a small protein (crambin)
'''
#
pdbFileName = DataPath+'1CRN.pdb'
dcdFileName = moduleDataPath+'test-results/1CRN-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 0
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
print '\nresult_coor \n',result_coor
os.remove(dcdFileName)
self.assertEqual(len(result_coor[0]),327)
expected_sample_coor = numpy.array([9.555, 2.856, 3.730],floattype)
sum_expected_coor = 8509.587
self.assert_list_almost_equal(expected_sample_coor,result_coor[0][100], self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
def test_2AAD_frame3(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
write the 3rd frame
'''
#
pdbFileName = DataPath+'2AAD-1to3.pdb'
dcdFileName = moduleDataPath+'test-results/2AAD-1to3-writedcd_step-test.dcd'
#
nnatoms = 1
frame = 2
step = 1
self.o.read_pdb(pdbFileName)
#fp=dcdio.open_dcd_write(dcdFileName)
#self.o.write_dcd_header(fp, nnatoms)
fp = self.o.open_dcd_write(dcdFileName)
self.o.write_dcd_step(fp, frame, step)
dcdio.close_dcd_write(fp)
#
otest = sasmol.SasMol(0)
otest.read_dcd(dcdFileName)
result_coor = otest.coor()
sum_result_coor = sum(sum(sum(result_coor)))
expected_coor = numpy.array([[[ 73.944, -41.799, 41.652], [ 74.229, -42.563, 40.456], [ 75.667, -43.093, 40.463], [ 76.264, -43.279, 39.401], [ 73.210, -43.734, 40.336], [ 71.856, -43.168, 39.926], [ 73.677, -44.782, 39.354], [ 70.721, -44.177, 39.946], [ 76.231, -43.330, 41.647], [ 77.592, -43.852, 41.730], [ 78.617, -42.820, 42.184], [ 79.712, -43.169, 42.656], [ 77.671, -45.097, 42.648], [ 77.054, -44.816, 43.910], [ 76.970, -46.273, 42.000]]],floattype)
sum_expected_coor = 1095.772
self.assert_list_almost_equal(expected_coor, result_coor, self.prcsn)
self.assertAlmostEqual(sum_result_coor, sum_expected_coor, self.prcsn)
os.remove(dcdFileName)
def test_rna_1to10frames(self):
'''
test a dcd of 10 frames based on a rna molecule
'''
#
pdbFileName = DataPath+'rna.pdb'
self.o.read_pdb(pdbFileName)
nset = 10
#
dcdFileName = moduleDataPath+'test-results/rna-1to10-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_1KP8(self):
'''
test a dcd from a large protein complex (groel)
'''
#
pdbFileName = DataPath+'1KP8.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath+'test-results/1KP8-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_2AAD(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
'''
#
pdbFileName = DataPath + '2AAD.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath + 'test-results/2AAD-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_rna_1to10frames(self):
'''
test a dcd of 10 frames based on a rna molecule
'''
#
pdbFileName = DataPath + 'rna.pdb'
self.o.read_pdb(pdbFileName)
nset = 10
#
dcdFileName = moduleDataPath + 'test-results/rna-1to10-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_1KP8(self):
'''
test a dcd from a large protein complex (groel)
'''
#
pdbFileName = DataPath + '1KP8.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath + 'test-results/1KP8-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
def test_2AAD(self):
'''
test a dcd with 3 frames based on a 2-aa pdb
'''
#
pdbFileName = DataPath+'2AAD.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath+'test-results/2AAD-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_1CRN(self):
'''
test a dcd from a small protein (crambin)
'''
#
pdbFileName = DataPath+'1CRN.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath+'test-results/1CRN-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize>0)
os.remove(dcdFileName)
def test_1CRN(self):
'''
test a dcd from a small protein (crambin)
'''
#
pdbFileName = DataPath + '1CRN.pdb'
self.o.read_pdb(pdbFileName)
nset = 3
#
dcdFileName = moduleDataPath + 'test-results/1CRN-writedcd_header-test.dcd'
fp = dcdio.open_dcd_write(dcdFileName)
self.o.write_dcd_header(fp, nset)
dcdio.close_dcd_write(fp)
fsize = os.path.getsize(dcdFileName)
print fsize
self.assertTrue(fsize > 0)
os.remove(dcdFileName)
