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Commit 01e5d92a authored by peastman's avatar peastman
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Merge pull request #90 from peastman/master 

Moved Python app layer tests into the main source tree
parents 52c444c5 d1d74008
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wrappers/python/tests/TestAmberPrmtopFile.py 0 → 100644
View file @ 01e5d92a
import unittest
from validateConstraints import *
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
class TestAmberPrmtopFile(unittest.TestCase):
"""Test the AmberPrmtopFile.createSystem() method."""
def setUp(self):
"""Set up the tests by loading the input files."""
# alanine dipeptide with explicit water
self.prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
# alanine dipeptide with implicit water
self.prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
def test_NonbondedMethod(self):
"""Test all five options for the nonbondedMethod parameter."""
methodMap = {NoCutoff:NonbondedForce.NoCutoff,
CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:NonbondedForce.CutoffPeriodic,
Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
for method in methodMap:
system = self.prmtop1.createSystem(nonbondedMethod=method)
forces = system.getForces()
self.assertTrue(any(isinstance(f, NonbondedForce) and
f.getNonbondedMethod()==methodMap[method]
for f in forces))
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
system = self.prmtop1.createSystem(nonbondedMethod=method,
nonbondedCutoff=2*nanometer,
constraints=HBonds)
cutoff_distance = 0.0*nanometer
cutoff_check = 2.0*nanometer
for force in system.getForces():
if isinstance(force, NonbondedForce):
cutoff_distance = force.getCutoffDistance()
self.assertEqual(cutoff_distance, cutoff_check)
def test_EwaldErrorTolerance(self):
"""Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
for method in [Ewald, PME]:
system = self.prmtop1.createSystem(nonbondedMethod=method,
ewaldErrorTolerance=1e-6,
constraints=HBonds)
tolerance = 0
tolerance_check = 1e-6
for force in system.getForces():
if isinstance(force, NonbondedForce):
tolerance = force.getEwaldErrorTolerance()
self.assertEqual(tolerance, tolerance_check)
def test_RemoveCMMotion(self):
"""Test both options (True and False) for the removeCMMotion parameter."""
for b in [True, False]:
system = self.prmtop1.createSystem(removeCMMotion=b)
forces = system.getForces()
self.assertEqual(any(isinstance(f, CMMotionRemover) for f in forces), b)
def test_RigidWaterAndConstraints(self):
"""Test all eight options for the constraints and rigidWater parameters."""
topology = self.prmtop1.topology
for constraints_value in [None, HBonds, AllBonds, HAngles]:
for rigidWater_value in [True, False]:
system = self.prmtop1.createSystem(constraints=constraints_value,
rigidWater=rigidWater_value)
validateConstraints(self, topology, system,
constraints_value, rigidWater_value)
def test_ImplicitSolvent(self):
"""Test the four types of implicit solvents using the implicitSolvent
parameter.
"""
for implicitSolvent_value in [HCT, OBC1, OBC2, GBn]:
system = self.prmtop2.createSystem(implicitSolvent=implicitSolvent_value)
forces = system.getForces()
if implicitSolvent_value in set([HCT, OBC1, GBn]):
force_type = CustomGBForce
else:
force_type = GBSAOBCForce
self.assertTrue(any(isinstance(f, force_type) for f in forces))
def test_ImplicitSolventParameters(self):
"""Test that solventDielectric and soluteDielectric are passed correctly
for the different types of implicit solvent.
"""
for implicitSolvent_value in [HCT, OBC1, OBC2, GBn]:
system = self.prmtop2.createSystem(implicitSolvent=implicitSolvent_value,
solventDielectric=50.0,
soluteDielectric = 0.9)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
if implicitSolvent_value in set([HCT, OBC1, GBn]):
for force in system.getForces():
if isinstance(force, CustomGBForce):
for j in range(force.getNumGlobalParameters()):
if (force.getGlobalParameterName(j) == 'solventDielectric' and
force.getGlobalParameterDefaultValue(j) == 50.0):
found_matching_solvent_dielectric = True
if (force.getGlobalParameterName(j) == 'soluteDielectric' and
force.getGlobalParameterDefaultValue(j) == 0.9):
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
else:
for force in system.getForces():
if isinstance(force, GBSAOBCForce):
if force.getSolventDielectric() == 50.0:
found_matching_solvent_dielectric = True
if force.getSoluteDielectric() == 0.9:
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestForceField.py 0 → 100644
View file @ 01e5d92a
import unittest
from validateConstraints import *
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
class TestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method."""
def setUp(self):
"""Set up the tests by loading the input pdb files and force field
xml files.
"""
# alanine dipeptide with explicit water
self.pdb1 = PDBFile('systems/alanine-dipeptide-explicit.pdb')
self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
self.topology1 = self.pdb1.topology
self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
def test_NonbondedMethod(self):
"""Test all five options for the nonbondedMethod parameter."""
methodMap = {NoCutoff:NonbondedForce.NoCutoff,
CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:NonbondedForce.CutoffPeriodic,
Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
for method in methodMap:
system = self.forcefield1.createSystem(self.pdb1.topology,
nonbondedMethod=method)
forces = system.getForces()
self.assertTrue(any(isinstance(f, NonbondedForce) and
f.getNonbondedMethod()==methodMap[method]
for f in forces))
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
system = self.forcefield1.createSystem(self.pdb1.topology,
nonbondedMethod=method,
nonbondedCutoff=2*nanometer,
constraints=HBonds)
cutoff_distance = 0.0*nanometer
cutoff_check = 2.0*nanometer
for force in system.getForces():
if isinstance(force, NonbondedForce):
cutoff_distance = force.getCutoffDistance()
self.assertEqual(cutoff_distance, cutoff_check)
def test_RemoveCMMotion(self):
"""Test both options (True and False) for the removeCMMotion parameter."""
for b in [True, False]:
system = self.forcefield1.createSystem(self.pdb1.topology,removeCMMotion=b)
forces = system.getForces()
self.assertEqual(any(isinstance(f, CMMotionRemover) for f in forces), b)
def test_RigidWaterAndConstraints(self):
"""Test all eight options for the constraints and rigidWater parameters."""
topology = self.pdb1.topology
for constraints_value in [None, HBonds, AllBonds, HAngles]:
for rigidWater_value in [True, False]:
system = self.forcefield1.createSystem(topology,
constraints=constraints_value,
rigidWater=rigidWater_value)
validateConstraints(self, topology, system,
constraints_value, rigidWater_value)
def test_ImplicitSolvent(self):
"""Test the four types of implicit solvents using the implicitSolvent
parameter.
"""
topology = self.pdb2.topology
system = self.forcefield2.createSystem(topology)
forces = system.getForces()
self.assertTrue(any(isinstance(f, GBSAOBCForce) for f in forces))
def test_ImplicitSolventParameters(self):
"""Test that solventDielectric and soluteDielectric are passed correctly
for the different types of implicit solvent.
"""
topology = self.pdb2.topology
system = self.forcefield2.createSystem(topology, solventDielectric=50.0,
soluteDielectric=0.9)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
for force in system.getForces():
if isinstance(force, GBSAOBCForce):
if force.getSolventDielectric() == 50.0:
found_matching_solvent_dielectric = True
if force.getSoluteDielectric() == 0.9:
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestGromacsTopFile.py 0 → 100644
View file @ 01e5d92a
import unittest
from validateConstraints import *
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
class TestGromacsTopFile(unittest.TestCase):
"""Test the GromacsTopFile.createSystem() method."""
def setUp(self):
"""Set up the tests by loading the input files."""
# alanine dipeptide with explicit water
self.top1 = GromacsTopFile('systems/explicit.top', unitCellDimensions=Vec3(6.223, 6.223, 6.223)*nanometers)
# alanine dipeptide with implicit water
self.top2 = GromacsTopFile('systems/implicit.top')
def test_NonbondedMethod(self):
"""Test all five options for the nonbondedMethod parameter."""
methodMap = {NoCutoff:NonbondedForce.NoCutoff,
CutoffNonPeriodic:NonbondedForce.CutoffNonPeriodic,
CutoffPeriodic:NonbondedForce.CutoffPeriodic,
Ewald:NonbondedForce.Ewald, PME: NonbondedForce.PME}
for method in methodMap:
system = self.top1.createSystem(nonbondedMethod=method)
forces = system.getForces()
self.assertTrue(any(isinstance(f, NonbondedForce) and
f.getNonbondedMethod()==methodMap[method]
for f in forces))
def test_Cutoff(self):
"""Test to make sure the nonbondedCutoff parameter is passed correctly."""
for method in [CutoffNonPeriodic, CutoffPeriodic, Ewald, PME]:
system = self.top1.createSystem(nonbondedMethod=method,
nonbondedCutoff=2*nanometer,
constraints=HBonds)
cutoff_distance = 0.0*nanometer
cutoff_check = 2.0*nanometer
for force in system.getForces():
if isinstance(force, NonbondedForce):
cutoff_distance = force.getCutoffDistance()
self.assertEqual(cutoff_distance, cutoff_check)
def test_EwaldErrorTolerance(self):
"""Test to make sure the ewaldErrorTolerance parameter is passed correctly."""
for method in [Ewald, PME]:
system = self.top1.createSystem(nonbondedMethod=method,
ewaldErrorTolerance=1e-6,
constraints=HBonds)
tolerance = 0
tolerance_check = 1e-6
for force in system.getForces():
if isinstance(force, NonbondedForce):
tolerance = force.getEwaldErrorTolerance()
self.assertEqual(tolerance, tolerance_check)
def test_RemoveCMMotion(self):
"""Test both options (True and False) for the removeCMMotion parameter."""
for b in [True, False]:
system = self.top1.createSystem(removeCMMotion=b)
self.assertEqual(any(isinstance(f, CMMotionRemover) for f in system.getForces()), b)
def test_RigidWaterAndConstraints(self):
"""Test all eight options for the constraints and rigidWater parameters."""
topology = self.top1.topology
for constraints_value in [None, HBonds, AllBonds, HAngles]:
for rigidWater_value in [True, False]:
system = self.top1.createSystem(constraints=constraints_value,
rigidWater=rigidWater_value)
validateConstraints(self, topology, system,
constraints_value, rigidWater_value)
def test_ImplicitSolvent(self):
"""Test implicit solvent using the implicitSolvent parameter.
"""
system = self.top2.createSystem(implicitSolvent=OBC2)
self.assertTrue(any(isinstance(f, GBSAOBCForce) for f in system.getForces()))
def test_ImplicitSolventParameters(self):
"""Test that solventDielectric and soluteDielectric are passed correctly.
"""
system = self.top2.createSystem(implicitSolvent=OBC2,
solventDielectric=50.0,
soluteDielectric = 0.9)
found_matching_solvent_dielectric=False
found_matching_solute_dielectric=False
for force in system.getForces():
if isinstance(force, GBSAOBCForce):
if force.getSolventDielectric() == 50.0:
found_matching_solvent_dielectric = True
if force.getSoluteDielectric() == 0.9:
found_matching_solute_dielectric = True
if isinstance(force, NonbondedForce):
self.assertEqual(force.getReactionFieldDielectric(), 1.0)
self.assertTrue(found_matching_solvent_dielectric and
found_matching_solute_dielectric)
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/TestModeller.py 0 → 100755
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wrappers/python/tests/TestNumpyCompatibility.py 0 → 100644
View file @ 01e5d92a
import unittest
import numpy as np
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
class TestNumpyCompatibility(unittest.TestCase):
def setUp(self):
prmtop = app.AmberPrmtopFile('systems/water-box-216.prmtop')
system = prmtop.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=0.9*unit.nanometers,
constraints=app.HBonds, rigidWater=True,
ewaldErrorTolerance=0.0005)
integrator = mm.LangevinIntegrator(300*unit.kelvin, 1.0/unit.picoseconds,
2.0*unit.femtoseconds)
self.simulation = app.Simulation(prmtop.topology, system, integrator,
mm.Platform.getPlatformByName('Reference'))
def test_setPositions(self):
n_particles = self.simulation.context.getSystem().getNumParticles()
input = np.random.randn(n_particles, 3)
self.simulation.context.setPositions(input)
output = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)
np.testing.assert_array_almost_equal(input, output)
def test_setPositions_units(self):
n_particles = self.simulation.context.getSystem().getNumParticles()
input = unit.Quantity(np.random.randn(n_particles, 3), unit.angstroms)
self.simulation.context.setPositions(input)
output = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)
np.testing.assert_array_almost_equal(input.value_in_unit(unit.nanometers), output.value_in_unit(unit.nanometers))
def test_setVelocities(self):
n_particles = self.simulation.context.getSystem().getNumParticles()
input = np.random.randn(n_particles, 3)
self.simulation.context.setVelocities(input)
output = self.simulation.context.getState(getVelocities=True).getVelocities(asNumpy=True)
np.testing.assert_array_almost_equal(input, output)
def test_setVelocities_units(self):
n_particles = self.simulation.context.getSystem().getNumParticles()
input = unit.Quantity(np.random.randn(n_particles, 3), unit.angstroms / unit.femtoseconds)
self.simulation.context.setVelocities(input)
output = self.simulation.context.getState(getVelocities=True).getVelocities(asNumpy=True)
np.testing.assert_array_almost_equal(input.value_in_unit(unit.angstroms / unit.femtoseconds),
output.value_in_unit(unit.angstroms / unit.femtoseconds))
def test_tabulatedFunction(self):
f = mm.CustomNonbondedForce('g(r)')
r = np.linspace(0,10)
g_of_r = np.sin(r)
indx = f.addFunction('g', g_of_r, np.min(r), np.max(r))
name, g_of_r_out, min_r_out, max_r_out = f.getFunctionParameters(indx)
np.testing.assert_array_almost_equal(g_of_r, np.asarray(g_of_r_out))
assert min_r_out == np.min(r)
assert max_r_out == np.max(r)
def test_CMAP(self):
f = mm.CMAPTorsionForce()
energy = np.random.randn(10*10)
f.addMap(10, energy)
size, energy_out = f.getMapParameters(0)
assert size == 10
np.testing.assert_array_almost_equal(energy, np.asarray(energy_out))
if __name__ == '__main__':
unittest.main()
wrappers/python/tests/systems/1T2Y.pdb 0 → 100644
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wrappers/python/tests/systems/alanine-dipeptide-explicit.pdb 0 → 100644
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wrappers/python/tests/systems/alanine-dipeptide-implicit.pdb 0 → 100644
View file @ 01e5d92a
REMARK ACE
ATOM 1 1HH3 ACE 1 2.000 1.000 -0.000
ATOM 2 CH3 ACE 1 2.000 2.090 0.000
ATOM 3 2HH3 ACE 1 1.486 2.454 0.890
ATOM 4 3HH3 ACE 1 1.486 2.454 -0.890
ATOM 5 C ACE 1 3.427 2.641 -0.000
ATOM 6 O ACE 1 4.391 1.877 -0.000
ATOM 7 N ALA 2 3.555 3.970 -0.000
ATOM 8 H ALA 2 2.733 4.556 -0.000
ATOM 9 CA ALA 2 4.853 4.614 -0.000
ATOM 10 HA ALA 2 5.408 4.316 0.890
ATOM 11 CB ALA 2 5.661 4.221 -1.232
ATOM 12 1HB ALA 2 5.123 4.521 -2.131
ATOM 13 2HB ALA 2 6.630 4.719 -1.206
ATOM 14 3HB ALA 2 5.809 3.141 -1.241
ATOM 15 C ALA 2 4.713 6.129 0.000
ATOM 16 O ALA 2 3.601 6.653 0.000
ATOM 17 N NME 3 5.846 6.835 0.000
ATOM 18 H NME 3 6.737 6.359 -0.000
ATOM 19 CH3 NME 3 5.846 8.284 0.000
ATOM 20 1HH3 NME 3 4.819 8.648 0.000
ATOM 21 2HH3 NME 3 6.360 8.648 0.890
ATOM 22 3HH3 NME 3 6.360 8.648 -0.890
TER
END
wrappers/python/tests/systems/alanine-dipeptide-implicit.prmtop 0 → 100644
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%VERSION VERSION_STAMP = V0001.000 DATE = 12/02/09 14:15:18
%FLAG TITLE
%FORMAT(20a4)
ACE
%FLAG POINTERS
%FORMAT(10I8)
22 7 12 9 25 11 35 17 0 0
99 3 9 11 17 8 16 13 7 0
0 0 0 0 0 0 0 0 10 0
0
%FLAG ATOM_NAME
%FORMAT(20a4)
HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
HH32HH33
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
-3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
-1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
1.77849648E+00 1.77849648E+00
%FLAG MASS
%FORMAT(5E16.8)
1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
1.00800000E+00 1.00800000E+00
%FLAG ATOM_TYPE_INDEX
%FORMAT(10I8)
1 2 1 1 3 4 5 6 2 7
2 1 1 1 3 4 5 6 2 7
7 7
%FLAG NUMBER_EXCLUDED_ATOMS
%FORMAT(10I8)
6 7 4 3 7 3 10 4 10 7
6 3 2 1 7 3 5 4 3 2
1 1
%FLAG NONBONDED_PARM_INDEX
%FORMAT(10I8)
1 2 4 7 11 16 22 2 3 5
8 12 17 23 4 5 6 9 13 18
24 7 8 9 10 14 19 25 11 12
13 14 15 20 26 16 17 18 19 20
21 27 22 23 24 25 26 27 28
%FLAG RESIDUE_LABEL
%FORMAT(20a4)
ACE ALA NME
%FLAG RESIDUE_POINTER
%FORMAT(10I8)
1 7 17
%FLAG BOND_FORCE_CONSTANT
%FORMAT(5E16.8)
5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
3.10000000E+02 4.34000000E+02 3.37000000E+02
%FLAG BOND_EQUIL_VALUE
%FORMAT(5E16.8)
1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
1.52600000E+00 1.01000000E+00 1.44900000E+00
%FLAG ANGLE_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E+01 3.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
5.00000000E+01 3.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
3.50000000E+01
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
1.91113635E+00
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 0.00000000E+00 5.30000000E-01 1.50000000E-01
5.00000000E-01 8.50000000E-01 3.00000000E-01 1.55555556E-01 7.00000000E-02
1.00000000E-01 1.05000000E+01 1.00000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00
4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 2.00000000E+00
4.00000000E+00 2.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 3.14159400E+00 3.14159400E+00
%FLAG SOLTY
%FORMAT(5E16.8)
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00
%FLAG LENNARD_JONES_ACOEF
%FORMAT(5E16.8)
7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
6.20665997E+04 5.94667300E+01 3.25969625E+03
%FLAG LENNARD_JONES_BCOEF
%FORMAT(5E16.8)
2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
1.13252061E+02 1.93248820E+00 1.43076527E+01
%FLAG BONDS_INC_HYDROGEN
%FORMAT(10I8)
3 6 3 3 9 3 0 3 3 30
33 3 30 36 3 30 39 3 24 27
5 18 21 7 54 57 5 54 60 5
54 63 5 48 51 7
%FLAG BONDS_WITHOUT_HYDROGEN
%FORMAT(10I8)
12 15 1 12 18 2 3 12 4 42
45 1 42 48 2 24 30 6 24 42
4 18 24 8 48 54 8
%FLAG ANGLES_INC_HYDROGEN
%FORMAT(10I8)
12 18 21 2 9 3 12 4 6 3
9 5 6 3 12 4 0 3 6 5
0 3 9 5 0 3 12 4 42 48
51 2 36 30 39 5 33 30 36 5
33 30 39 5 27 24 30 9 27 24
42 10 24 30 33 11 24 30 36 11
24 30 39 11 21 18 24 12 18 24
27 13 60 54 63 16 57 54 60 16
57 54 63 16 51 48 54 12 48 54
57 13 48 54 60 13 48 54 63 13
%FLAG ANGLES_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 1 12 18 24 3 3 12
15 6 3 12 18 7 45 42 48 1
42 48 54 3 30 24 42 8 24 42
45 6 24 42 48 7 18 24 30 14
18 24 42 15
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
15 12 18 21 1 15 12 -18 21 2
12 18 24 27 3 9 3 12 15 3
9 3 12 18 3 6 3 12 15 3
6 3 12 18 3 3 12 18 21 2
0 3 12 15 3 0 3 12 18 3
45 42 48 51 1 45 42 -48 51 2
42 48 54 57 3 42 48 54 60 3
42 48 54 63 3 39 30 24 42 9
36 30 24 42 9 33 30 24 42 9
27 24 30 33 9 27 24 30 36 9
27 24 30 39 9 27 24 42 45 3
27 24 42 48 3 24 42 48 51 2
21 18 24 27 3 21 18 24 30 3
21 18 24 42 3 18 24 30 33 9
18 24 30 36 9 18 24 30 39 9
51 48 54 57 3 51 48 54 60 3
51 48 54 63 3 12 24 -18 -21 13
42 54 -48 -51 13
%FLAG DIHEDRALS_WITHOUT_HYDROGEN
%FORMAT(10I8)
15 12 18 24 2 12 18 24 30 4
12 18 -24 30 5 12 18 -24 30 6
12 18 24 42 7 12 18 -24 42 8
3 12 18 24 2 45 42 48 54 2
30 24 42 45 3 30 24 42 48 10
30 24 -42 48 11 24 42 48 54 2
18 24 42 45 3 18 24 42 48 7
18 24 -42 48 8 3 18 -12 -15 12
24 48 -42 -45 12
%FLAG EXCLUDED_ATOMS_LIST
%FORMAT(10I8)
2 3 4 5 6 7 3 4 5 6
7 8 9 4 5 6 7 5 6 7
6 7 8 9 10 11 15 7 8 9
8 9 10 11 12 13 14 15 16 17
9 10 11 15 10 11 12 13 14 15
16 17 18 19 11 12 13 14 15 16
17 12 13 14 15 16 17 13 14 15
14 15 15 16 17 18 19 20 21 22
17 18 19 18 19 20 21 22 19 20
21 22 20 21 22 21 22 22 0
%FLAG HBOND_ACOEF
%FORMAT(5E16.8)
%FLAG HBOND_BCOEF
%FORMAT(5E16.8)
%FLAG HBCUT
%FORMAT(5E16.8)
%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
H1 H1
%FLAG TREE_CHAIN_CLASSIFICATION
%FORMAT(20a4)
M M E E M E M E M E 3 E E E M E M E M E
E E
%FLAG JOIN_ARRAY
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG IROTAT
%FORMAT(10I8)
0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0
0 0
%FLAG RADIUS_SET
%FORMAT(1a80)
H(N)-modified Bondi radii (mbondi2)
%FLAG RADII
%FORMAT(5E16.8)
1.20000000E+00 1.70000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.20000000E+00
1.70000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.70000000E+00
1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.20000000E+00
1.20000000E+00 1.20000000E+00
%FLAG SCREEN
%FORMAT(5E16.8)
8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
8.50000000E-01 8.50000000E-01
wrappers/python/tests/systems/explicit.top 0 → 100644
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wrappers/python/tests/systems/implicit.top 0 → 100644
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wrappers/python/tests/systems/lysozyme-implicit.pdb 0 → 100644
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wrappers/python/tests/systems/methanol-box.pdb 0 → 100644
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wrappers/python/tests/systems/water-box-216.prmtop 0 → 100644
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wrappers/python/tests/validateConstraints.py 0 → 100644
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wrappers/python/tests/validateModeller.py 0 → 100644
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