pub_soft/rdkit
3
0
Fork 0
mirror of https://github.com/rdkit/rdkit.git synced 2026-06-03 21:44:30 +08:00
Code Issues Packages Projects Releases Wiki Activity
Files
master
rdkit/Code/GraphMol/Wrap/testTrajectory.py
Ric 880a8e5725 Reformat Python code for 2023.03 release (#6294) 
* run yapf

* run isort

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
2023-04-28 06:53:56 +02:00

511 lines
19 KiB
Python
Raw Permalink Blame History

import os
import sys
import unittest
from rdkit import Chem, RDConfig
from rdkit.Chem import ChemicalForceFields, rdtrajectory
from rdkit.Chem.rdtrajectory import (ReadAmberTrajectory, ReadGromosTrajectory,
Snapshot, Trajectory)
def feq(v1, v2, tol=1.0e-4):
return abs(v1 - v2) < tol
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testSnapshot(self):
s = Snapshot([])
e = False
try:
s.GetPoint2D(12)
except Exception:
e = True
self.assertTrue(e)
s = Snapshot([0.0, 0.0, 0.0])
e = False
try:
s.GetPoint2D(0)
except Exception:
e = True
self.assertTrue(e)
def testTrajectory2D(self):
dim = 2
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 Exception:
e = True
self.assertTrue(e)
e = False
try:
traj.GetSnapshot(0).GetPoint2D(np)
except Exception:
e = True
self.assertTrue(e)
for i in range(np):
self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint2D(i).x, float(i * dim))
self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint2D(i).y, float(i * dim + 1))
e = False
try:
self.assertAlmostEqual(traj.GetSnapshot(0).GetPoint3D(i).z, 0.0)
except Exception:
e = True
self.assertFalse(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 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 Exception:
e = True
self.assertTrue(e)
e = False
try:
traj.GetSnapshot(0).GetPoint2D(np)
except Exception:
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 Exception:
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 testReadAmber(self):
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad.trx')
traj = Trajectory(2, 0)
ok = False
try:
ReadAmberTrajectory(fName, traj)
except Exception:
ok = True
self.assertTrue(ok)
traj = Trajectory(3, 3)
ok = False
try:
ReadAmberTrajectory(fName, traj)
except Exception:
ok = True
self.assertTrue(ok)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords_bad2.trx')
ok = False
try:
traj = Trajectory(3, 3)
ReadAmberTrajectory(fName, traj)
except Exception:
ok = True
self.assertTrue(ok)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trx')
traj = Trajectory(3, 3)
ReadAmberTrajectory(fName, traj)
self.assertEqual(len(traj), 1)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
traj = Trajectory(3, 3)
ReadAmberTrajectory(fName, traj)
self.assertEqual(len(traj), 2)
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])
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 Exception:
ok = True
self.assertTrue(ok)
traj = Trajectory(3, 3)
ok = False
try:
ReadGromosTrajectory(fName, traj)
except Exception:
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 Exception:
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 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 Exception:
e = True
self.assertTrue(e)
def testAddConformersFromAmberTrajectory(self):
mol = Chem.MolFromSmiles('CCC')
rdbase = os.environ['RDBASE']
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords.trx')
traj = Trajectory(3, mol.GetNumAtoms())
ReadAmberTrajectory(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, 0.1941767)
self.assertAlmostEqual(mol.GetConformer(i).GetAtomPosition(2).z, -0.4088006)
mol.RemoveAllConformers()
e = False
try:
traj.AddConformersToMol(mol, 1)
except Exception:
e = True
self.assertTrue(e)
self.assertEqual(mol.GetNumConformers(), 0)
fName = os.path.join(rdbase, 'Code', 'GraphMol', 'test_data', 'water_coords2.trx')
traj = Trajectory(3, mol.GetNumAtoms())
ReadAmberTrajectory(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 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 Exception:
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)
if __name__ == '__main__':
print("Testing Trajectory wrapper")
unittest.main()
Reference in New Issue View Git Blame Copy Permalink