def testReadGromos(self):
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad.trc')
traj = Trajectory(2, 0)
ok = False
try:
ReadGromosTrajectory(fName, traj)
except:
ok = True
self.assertTrue(ok)
traj = Trajectory(3, 3)
ok = False
try:
ReadGromosTrajectory(fName, traj)
except:
ok = True
self.assertTrue(ok)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad2.trc')
ok = False
try:
traj = Trajectory(3, 3)
ReadGromosTrajectory(fName, traj)
except:
ok = True
self.assertTrue(ok)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trc')
traj = Trajectory(3, 3)
ReadGromosTrajectory(fName, traj)
self.assertEqual(len(traj), 1)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trc')
traj = Trajectory(3, 3)
ReadGromosTrajectory(fName, traj)
self.assertEqual(len(traj), 2)
def testAddConformersFromGromosTrajectory(self):
mol = Chem.MolFromSmiles('CCC')
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trc')
traj = Trajectory(3, mol.GetNumAtoms())
ReadGromosTrajectory(fName, traj)
self.assertEqual(len(traj), 1)
for i in range(2):
traj.AddConformersToMol(mol)
self.assertEqual(mol.GetNumConformers(), i + 1)
self.assertEqual(mol.GetConformer(i).GetNumAtoms(), 3)
self.assertAlmostEqual(mol.GetConformer(i).GetAtomPosition(0).x, 1.941767)
self.assertAlmostEqual(mol.GetConformer(i).GetAtomPosition(2).z, -4.088006)
mol.RemoveAllConformers()
e = False
try:
traj.AddConformersToMol(mol, 1)
except:
e = True
self.assertTrue(e)
self.assertEqual(mol.GetNumConformers(), 0)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trc')
traj = Trajectory(3, mol.GetNumAtoms())
ReadGromosTrajectory(fName, traj)
self.assertEqual(len(traj), 2)
traj.AddConformersToMol(mol)
self.assertEqual(mol.GetNumConformers(), 2)
mol.RemoveAllConformers()
traj.AddConformersToMol(mol, 0, 0)
self.assertEqual(mol.GetNumConformers(), 1)
traj.AddConformersToMol(mol, 1)
self.assertEqual(mol.GetNumConformers(), 2)
def testTrajectory3D(self):
dim = 3
np = 10
ns = 5
traj = Trajectory(dim, np)
self.assertEqual(traj.Dimension(), dim)
self.assertEqual(traj.NumPoints(), np)
c = []
for i in range(np * dim):
c.append(float(i))
for i in range(ns):
traj.AddSnapshot(Snapshot(c, float(i)))
self.assertEqual(len(traj), ns)
e = False
try:
traj.GetSnapshot(ns)
except:
e = True
self.assertTrue(e)
e = False
try:
traj.GetSnapshot(0).GetPoint2D(np)
except:
e = True
self.assertTrue(e)
for i in range(np):
self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).x, float(i * dim))
self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).y, float(i * dim + 1))
self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).z, float(i * dim + 2))
if (not i):
e = False
try:
traj.GetSnapshot(0).GetPoint2D(i)
except:
e = True
self.assertTrue(e)
for i in range(ns):
self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i))
traj.RemoveSnapshot(0)
self.assertEqual(len(traj), ns - 1)
for i in range(ns - 1):
self.assertAlmostEqual(traj.GetSnapshot(i).GetEnergy(), float(i + 1))
traj.InsertSnapshot(0, Snapshot(c, 999.0))
self.assertEqual(len(traj), ns)
copySnapshot = Snapshot(traj.GetSnapshot(0))
traj.AddSnapshot(copySnapshot)
self.assertEqual(len(traj), ns + 1)
self.assertAlmostEqual(traj.GetSnapshot(0).GetEnergy(), 999.0)
self.assertAlmostEqual(traj.GetSnapshot(1).GetEnergy(), 1.0)
self.assertAlmostEqual(traj.GetSnapshot(len(traj) - 1).GetEnergy(), 999.0)
traj2 = Trajectory(traj)
self.assertEqual(len(traj), len(traj2))
def testAddConformersFromTrajectory(self):
molBlock = \
'\n' \
' RDKit 3D\n' \
'\n' \
' 71 74 0 0 0 0 0 0 0 0999 V2000\n' \
' 8.2543 3.1901 -0.3005 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 7.4558 1.9712 0.0938 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 7.3934 1.0441 -0.9483 O 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 6.6660 -0.0533 -0.4641 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 5.1928 0.2346 -0.4609 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 4.3713 -0.9410 -0.5770 N 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 3.1852 -1.0034 -1.2291 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.2914 0.1276 -1.6316 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.9308 -0.4468 -1.9908 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.1417 -0.7821 -0.7545 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -0.1848 0.3695 0.0456 N 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -1.5661 0.7686 -0.0745 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -2.4768 -0.0640 0.8206 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -3.8874 0.1143 0.3941 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -4.6333 -0.9984 0.0264 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -6.0127 -0.9516 -0.0400 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -6.7062 0.1599 0.3963 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.0408 0.4828 -0.1977 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -7.7914 1.1180 -1.5591 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.7622 1.4403 0.7265 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.8409 -0.7397 -0.4395 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.9121 -1.6637 0.4258 O 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -9.7414 -0.7636 -1.5059 O 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -5.9736 1.2357 0.8565 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -4.5843 1.2252 0.8530 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.6263 1.4884 -0.3942 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.0541 1.0258 -0.4230 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.9225 -2.3317 -1.2963 N 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 3.6061 -2.9745 -0.3180 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 3.3554 -4.1536 0.3735 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 3.7653 -4.2712 1.6948 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 4.8254 -3.4613 2.0796 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 5.1978 -2.3436 1.3419 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 4.5694 -2.0799 0.1305 C 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 9.3138 3.1372 0.0031 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 7.8117 4.0754 0.1798 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 8.2358 3.3535 -1.4074 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 6.4027 2.2146 0.3634 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 7.9270 1.5444 1.0040 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 7.0677 -0.2415 0.5615 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 6.9530 -0.9105 -1.1025 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 4.9578 0.7259 0.5137 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 4.9985 0.9430 -1.3033 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.7171 0.7264 -2.4494 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.3994 0.2339 -2.6810 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 1.1342 -1.4171 -2.5076 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -0.7632 -1.3370 -1.0391 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.7845 -1.4394 -0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.0125 0.1989 1.0673 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -1.6672 1.8215 0.2925 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -1.8705 0.7271 -1.1337 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -2.3045 0.3159 1.8590 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -2.1980 -1.1367 0.7635 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -4.1513 -1.9468 -0.2114 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -6.6138 -1.7460 -0.4718 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -7.0727 0.4399 -2.0858 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -7.3144 2.1076 -1.4482 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.7609 1.1720 -2.1135 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.3137 2.4504 0.5729 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -8.6170 1.0817 1.7580 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -9.8244 1.4444 0.4200 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -6.4629 2.0541 1.3719 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' -4.0445 2.0563 1.3058 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.3329 1.8224 -1.3991 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 0.4920 2.3164 0.3160 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.2025 0.3766 0.4766 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.7945 1.8369 -0.3969 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 2.4404 -4.6964 0.1303 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 3.3157 -5.0055 2.3587 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 5.4272 -3.7654 2.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 5.5668 -1.5069 1.9380 H 0 0 0 0 0 0 0 0 0 0 0 0\n' \
' 1 2 1 0\n' \
' 2 3 1 0\n' \
' 3 4 1 0\n' \
' 4 5 1 0\n' \
' 5 6 1 0\n' \
' 6 7 1 0\n' \
' 7 8 1 0\n' \
' 8 9 1 0\n' \
' 9 10 1 0\n' \
' 10 11 1 0\n' \
' 11 12 1 0\n' \
' 12 13 1 0\n' \
' 13 14 1 0\n' \
' 14 15 2 0\n' \
' 15 16 1 0\n' \
' 16 17 2 0\n' \
' 17 18 1 0\n' \
' 18 19 1 0\n' \
' 18 20 1 0\n' \
' 18 21 1 0\n' \
' 21 22 2 0\n' \
' 21 23 1 0\n' \
' 17 24 1 0\n' \
' 24 25 2 0\n' \
' 11 26 1 0\n' \
' 26 27 1 0\n' \
' 7 28 2 0\n' \
' 28 29 1 0\n' \
' 29 30 2 0\n' \
' 30 31 1 0\n' \
' 31 32 2 0\n' \
' 32 33 1 0\n' \
' 33 34 2 0\n' \
' 34 6 1 0\n' \
' 27 8 1 0\n' \
' 34 29 1 0\n' \
' 25 14 1 0\n' \
' 1 35 1 0\n' \
' 1 36 1 0\n' \
' 1 37 1 0\n' \
' 2 38 1 0\n' \
' 2 39 1 0\n' \
' 4 40 1 0\n' \
' 4 41 1 0\n' \
' 5 42 1 0\n' \
' 5 43 1 0\n' \
' 8 44 1 0\n' \
' 9 45 1 0\n' \
' 9 46 1 0\n' \
' 10 47 1 0\n' \
' 10 48 1 0\n' \
' 11 49 1 0\n' \
' 12 50 1 0\n' \
' 12 51 1 0\n' \
' 13 52 1 0\n' \
' 13 53 1 0\n' \
' 15 54 1 0\n' \
' 16 55 1 0\n' \
' 19 56 1 0\n' \
' 19 57 1 0\n' \
' 19 58 1 0\n' \
' 20 59 1 0\n' \
' 20 60 1 0\n' \
' 20 61 1 0\n' \
' 24 62 1 0\n' \
' 25 63 1 0\n' \
' 26 64 1 0\n' \
' 26 65 1 0\n' \
' 27 66 1 0\n' \
' 27 67 1 0\n' \
' 30 68 1 0\n' \
' 31 69 1 0\n' \
' 32 70 1 0\n' \
' 33 71 1 0\n' \
'M CHG 2 11 1 23 -1\n' \
'M END\n'
mol = Chem.MolFromMolBlock(molBlock, removeHs=False)
everySteps = 10
maxIts = 1000
gradTol = 0.01
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'Wrap', 'test_data',
'bilastine_trajectory.sdf')
w = Chem.SDWriter(fName)
field = ChemicalForceFields.MMFFGetMoleculeForceField(
mol, ChemicalForceFields.MMFFGetMoleculeProperties(mol))
(res, sv) = field.MinimizeTrajectory(everySteps, maxIts, gradTol)
self.assertEqual(res, 0)
traj = Trajectory(3, mol.GetNumAtoms(), sv)
mol.RemoveConformer(0)
traj.AddConformersToMol(mol)
for nConf in range(mol.GetNumConformers()):
mol.SetProp('ENERGY', '{0:.4f}'.format(traj.GetSnapshot(nConf).GetEnergy()))
w.write(mol, nConf)
w.close()
traj.Clear()
n1 = mol.GetNumConformers()
traj.AddConformersToMol(mol)
n2 = mol.GetNumConformers()
self.assertEqual(n1, n2)
# GetSnapshot should raise exception after Clear()
e = False
try:
traj.GetSnapshot(0)
except:
e = True
self.assertTrue(e)
def testReadAmberPython(self):
# reimplemented the Amber trajectory reader in Python
# let's check we get the same data as the C++ reader
# (test for building a trajectory out of Snapshots from Python)
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
traj = Trajectory(3, 3)
nCoords = traj.NumPoints() * 3
nSnapshots = 0
hnd = open(fName, 'r')
line = hnd.readline()
lineNum = 0
c = []
i = 0
while (line):
lineNum += 1
if (lineNum > 1):
tok = line.strip().split()
j = 0
while ((i < nCoords) and (j < len(tok))):
c.append(float(tok[j]))
j += 1
i += 1
if (i == nCoords):
nSnapshots += 1
traj.AddSnapshot(Snapshot(c))
c = []
i = 0
line = ' '.join(tok[j:]) + ' '
else:
line = ''
else:
line = ''
line += hnd.readline()
hnd.close()
self.assertEqual(i, 0)
self.assertEqual(nSnapshots, 2)
traj2 = Trajectory(3, 3)
ReadAmberTrajectory(fName, traj2)
self.assertEqual(len(traj), len(traj2))
self.assertEqual(traj.NumPoints(), traj2.NumPoints())
for snapshotNum in range(len(traj)):
for pointNum in range(traj.NumPoints()):
for i in range(3):
self.assertAlmostEqual(
traj.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i],
traj2.GetSnapshot(snapshotNum).GetPoint3D(pointNum)[i])