def testJACPMESwitch(self):
""" Tests the DHFR Gromacs system nrg and force (PME w/ switch) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('10.DHFR-PME-Switch'), 'topol.top'))
gro = load_file(os.path.join(get_fn('10.DHFR-PME-Switch'), 'conf.gro'))
top.box = gro.box[:]
# Create the system and context, then calculate the energy decomposition
system = top.createSystem(nonbondedMethod=app.PME,
constraints=app.HBonds,
nonbondedCutoff=0.9*u.nanometers,
ewaldErrorTolerance=1.0e-5)
context = mm.Context(system, mm.VerletIntegrator(0.001), mm.Platform.getPlatformByName('CPU'))
context.setPositions(gro.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 1628.54739, places=3)
self.assertAlmostEqual(energies['angle'], 3604.58751, places=3)
self.assertAlmostEqual(energies['dihedral'], 6490.00844, delta=0.002)
self.assertRelativeEqual(energies['nonbonded'], 23616.457584, places=3)
gmxfrc = get_forces_from_xvg(
os.path.join(get_fn('10.DHFR-PME-Switch'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 5)
def testWriteCharmm27Top(self):
""" Tests writing a Gromacs topology file with CHARMM 27 FF """
top = load_file(get_fn('1aki.charmm27.top'))
GromacsTopologyFile.write(top,
get_fn('1aki.charmm27.top', written=True))
top2 = load_file(get_fn('1aki.charmm27.top', written=True))
self._charmm27_checks(top)
def testJAC(self):
""" Tests the JAC benchmark Gromacs system nrg and force (no PBC) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('07.DHFR-Liquid-NoPBC'), 'topol.top'))
gro = load_file(os.path.join(get_fn('07.DHFR-Liquid-NoPBC'), 'conf.gro'))
# Create the system and context, then calculate the energy decomposition
system = top.createSystem()
context = mm.Context(system, mm.VerletIntegrator(0.001), mm.Platform.getPlatformByName('CPU'))
context.setPositions(gro.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 35.142565, places=3)
self.assertAlmostEqual(energies['angle'], 3735.514669, places=3)
self.assertAlmostEqual(energies['dihedral'], 7277.741635, delta=0.002)
self.assertRelativeEqual(energies['nonbonded'], -288718.981405, places=4)
gmxfrc = get_forces_from_xvg(
os.path.join(get_fn('07.DHFR-Liquid-NoPBC'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 0.5)
def testDuplicateSystemNames(self):
""" Tests that Gromacs topologies never have duplicate moleculetypes """
parm = load_file(get_fn('phenol.prmtop'))
parm = parm * 20 + load_file(get_fn('biphenyl.prmtop')) * 20
top = GromacsTopologyFile.from_structure(parm)
top.write(get_fn('phenol_biphenyl.top', written=True))
top2 = GromacsTopologyFile(get_fn('phenol_biphenyl.top', written=True))
self.assertEqual(len(top.residues), 40)
def testWriteAmber99SBILDN(self):
""" Tests writing a Gromacs topology with multiple molecules """
top = load_file(get_fn('1aki.ff99sbildn.top'))
GromacsTopologyFile.write(top,
get_fn('1aki.ff99sbildn.top', written=True),
combine=None)
top2 = load_file(get_fn('1aki.ff99sbildn.top', written=True))
self._check_ff99sbildn(top2)
self._check_equal_structures(top, top2)
def main():
""" The main function """
global excepthook, debug
# Launch the root window
root = tk.Tk()
root.resizable(True, True)
# Replace the default excepthook with mine
sys.excepthook = excepthook
# See if we were provided a topology file on the command-line
parser = OptionParser(usage='%prog [<prmtop>]')
parser.add_option('-d',
'--debug',
dest='debug',
default=False,
action='store_true',
help='Show detailed tracebacks ' +
'when an error is detected.')
opt, args = parser.parse_args()
debug = opt.debug
# If the user provided a CL argument, that is the prmtop_name. Otherwise,
# open up a file choosing dialog box to get the input from the user
if len(args) == 0:
prmtop_name = file_chooser('Topology')
elif len(args) == 1:
prmtop_name = args[0]
else:
sys.stderr.write('Unknown command-line options. Ignoring\n')
prmtop_name = file_chooser('Topology')
# If we chose no prmtop file,
if not prmtop_name: raise ParmError('No prmtop chosen!')
# Load the amber prmtop and check for errors
amber_prmtop = ParmList()
parm = load_file(prmtop_name)
amber_prmtop.add_parm(parm)
# Make this overwritable -- the all of the file save boxes will ask the user
# for verification before saving over an existing file. There's no need for
# the AmberParm security layer.
Action.overwrite = True
fname = split(prmtop_name)[1]
root.title('xParmED: Editing/viewing [%s] Choose an operation' % fname)
# Now build the action list on root
app = ParmedApp(root, amber_prmtop)
app.pack(fill=tk.BOTH, expand=1)
root.mainloop()
print('Thank you for using xParmEd!\n%s' % Logo())
def testTiny(self):
""" Test tiny Gromacs system nrg and frc (no PBC) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('01.1water'), 'topol.top'))
gro = load_file(os.path.join(get_fn('01.1water'), 'conf.gro'))
# create the system and context, then calculate the energy decomposition
system = top.createSystem(constraints=app.HBonds, rigidWater=True)
context = mm.Context(system, mm.VerletIntegrator(0.001), mm.Platform.getPlatformByName('CPU'))
context.setPositions(gro.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Make sure they match Lee-Ping's answers (both energies and forces)
self.assertAlmostEqual(energies['bond'], 1.63805, places=4)
self.assertAlmostEqual(energies['angle'], 0.014803, places=4)
gmxfrc = get_forces_from_xvg(os.path.join(get_fn('01.1water'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 0.01)
def randomize_mol2_residue_names(mol2_filenames):
"""Find unique residue names for a list of MOL2 files. Then
re-write the MOL2 files using ParmEd with the unique identifiers.
"""
import chemistry
names = get_unique_names(len(mol2_filenames))
for k, filename in enumerate(mol2_filenames):
struct = chemistry.load_file(filename)
struct.name = names[k]
mol2file = chemistry.formats.Mol2File
mol2file.write(struct, filename)
def main():
""" The main function """
global excepthook, debug
# Launch the root window
root = tk.Tk()
root.resizable(True, True)
# Replace the default excepthook with mine
sys.excepthook = excepthook
# See if we were provided a topology file on the command-line
parser = OptionParser(usage = '%prog [<prmtop>]')
parser.add_option('-d', '--debug', dest='debug', default=False,
action='store_true', help='Show detailed tracebacks ' +
'when an error is detected.')
opt, args = parser.parse_args()
debug = opt.debug
# If the user provided a CL argument, that is the prmtop_name. Otherwise,
# open up a file choosing dialog box to get the input from the user
if len(args) == 0:
prmtop_name = file_chooser('Topology')
elif len(args) == 1:
prmtop_name = args[0]
else:
sys.stderr.write('Unknown command-line options. Ignoring\n')
prmtop_name = file_chooser('Topology')
# If we chose no prmtop file,
if not prmtop_name: raise ParmError('No prmtop chosen!')
# Load the amber prmtop and check for errors
amber_prmtop = ParmList()
parm = load_file(prmtop_name)
amber_prmtop.add_parm(parm)
# Make this overwritable -- the all of the file save boxes will ask the user
# for verification before saving over an existing file. There's no need for
# the AmberParm security layer.
Action.overwrite = True
fname = split(prmtop_name)[1]
root.title('xParmED: Editing/viewing [%s] Choose an operation' % fname)
# Now build the action list on root
app = ParmedApp(root, amber_prmtop)
app.pack(fill=tk.BOTH, expand=1)
root.mainloop()
print('Thank you for using xParmEd!\n%s' % Logo())
def testVerySmall(self):
""" Test very small Gromacs system nrg and frc (no PBC) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('02.6water'), 'topol.top'))
gro = load_file(os.path.join(get_fn('02.6water'), 'conf.gro'))
# create the system and context, then calculate the energy decomposition
system = top.createSystem(constraints=app.HBonds, rigidWater=True,
flexibleConstraints=True)
context = mm.Context(system, mm.VerletIntegrator(0.001), mm.Platform.getPlatformByName('CPU'))
context.setPositions(gro.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 0, places=4)
self.assertAlmostEqual(energies['nonbonded'], -108.277803, places=3)
gmxfrc = get_forces_from_xvg(os.path.join(get_fn('02.6water'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 0.05)
def testSmallDoublePeptide(self):
""" Test interacting peptides Gromacs system nrg and frc (no PBC) """
# Load the top and gro files
top = load_file(os.path.join(get_fn('03.AlaGlu'), 'topol.top'))
gro = load_file(os.path.join(get_fn('03.AlaGlu'), 'conf.gro'))
# create the system and context, then calculate the energy decomposition
system = top.createSystem()
context = mm.Context(system, mm.VerletIntegrator(0.001), mm.Platform.getPlatformByName('CPU'))
context.setPositions(gro.positions)
energies = energy_decomposition(top, context, nrg=u.kilojoules_per_mole)
# Compare with Lee-Ping's answers. Make sure we zero-out forces for
# virtual sites, since OMM doesn't do this and Gromacs does.
self.assertAlmostEqual(energies['bond'], 1.5307999, places=4)
self.assertAlmostEqual(energies['angle'], 6.5804488, places=4)
self.assertAlmostEqual(energies['dihedral'], 80.379714, places=4)
self.assertAlmostEqual(energies['nonbonded'], -275.142487, places=3)
gmxfrc = get_forces_from_xvg(os.path.join(get_fn('03.AlaGlu'), 'force.xvg'))
ommfrc = context.getState(getForces=True).getForces().value_in_unit(
u.kilojoules_per_mole/u.nanometer)
zero_ep_frc(ommfrc, top)
max_diff = get_max_diff(gmxfrc, ommfrc)
self.assertLess(max_diff, 0.05)
def testDistanceBasedMaskPDB(self):
""" Test distance-based mask selections on a PDB file """
parm = load_file(get_fn('4lzt.pdb'))
# All atoms within 5 A of residue 8
mask1 = mask.AmberMask(parm, ':8<@5')
sel = mask1.Selection()
self.assertGreater(sum(sel), 0)
for i, atom in enumerate(parm.atoms):
for j, a2 in enumerate(parm.residues[7]):
dx = atom.xx - a2.xx
dy = atom.xy - a2.xy
dz = atom.xz - a2.xz
if dx*dx + dy*dy + dz*dz < 25:
self.assertTrue(sel[i])
break
else:
self.assertFalse(sel[i])
def testAmoebaParmPandas(self):
""" Tests creating a pandas DataFrame from an AmoebaParm """
parm = load_file(get_fn('nma.parm7'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], parm.ptr('natom'))
multipoles = [
'multipole_111', 'multipole_211', 'multipole_212', 'multipole_222',
'multipole_411', 'multipole_412', 'multipole_422', 'multipole_413',
'multipole_423', 'multipole_433'
]
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.type_idx, parm.atoms[i].type_idx)
self.assertEqual(r1.class_idx, parm.atoms[i].class_idx)
self.assertTrue(
np.all(r1[multipoles] == np.array(parm.atoms[i].multipoles)))
self.assertEqual(r1.polarizability, parm.atoms[i].polarizability)
self.assertEqual(r1.vdw_parent, parm.atoms[i].vdw_parent.idx)
self.assertNotIn('xx', df)
self.assertNotIn('xy', df)
self.assertNotIn('xz', df)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('segid', df)
def testAmoebaParmPandas(self):
""" Tests creating a pandas DataFrame from an AmoebaParm """
parm = load_file(get_fn('nma.parm7'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], parm.ptr('natom'))
multipoles = ['multipole_111', 'multipole_211', 'multipole_212',
'multipole_222', 'multipole_411', 'multipole_412',
'multipole_422', 'multipole_413', 'multipole_423',
'multipole_433']
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.type_idx, parm.atoms[i].type_idx)
self.assertEqual(r1.class_idx, parm.atoms[i].class_idx)
self.assertTrue(np.all(r1[multipoles] ==
np.array(parm.atoms[i].multipoles)))
self.assertEqual(r1.polarizability, parm.atoms[i].polarizability)
self.assertEqual(r1.vdw_parent, parm.atoms[i].vdw_parent.idx)
self.assertNotIn('xx', df)
self.assertNotIn('xy', df)
self.assertNotIn('xz', df)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('segid', df)
def testWriteGroFile(self):
""" Tests writing GRO file """
gro = GromacsGroFile.parse(get_fn('1aki.ff99sbildn.gro'))
GromacsGroFile.write(gro, get_fn('1aki.ff99sbildn.gro', written=True))
gro = load_file(get_fn('1aki.ff99sbildn.gro', written=True))
self.assertIsInstance(gro, Structure)
self.assertEqual(len(gro.atoms), 1960)
self.assertEqual(len(gro.residues), 129)
self.assertAlmostEqual(gro.atoms[0].xx, 44.6)
self.assertAlmostEqual(gro.atoms[0].xy, 49.86)
self.assertAlmostEqual(gro.atoms[0].xz, 18.10)
self.assertAlmostEqual(gro.atoms[1959].xx, 50.97)
self.assertAlmostEqual(gro.atoms[1959].xy, 39.80)
self.assertAlmostEqual(gro.atoms[1959].xz, 38.64)
self.assertAlmostEqual(gro.box[0], 74.1008)
self.assertAlmostEqual(gro.box[1], 74.10080712)
self.assertAlmostEqual(gro.box[2], 74.10074585)
self.assertAlmostEqual(gro.box[3], 70.52882666)
self.assertAlmostEqual(gro.box[4], 109.47126278)
self.assertAlmostEqual(gro.box[5], 70.52875398)
def add_parm(self, parm):
""" Add a parm to the list """
# Make sure this parm is not part of the list already
if isinstance(parm, string_types):
if parm in self._parm_names:
raise DuplicateParm('%s already in ParmList' % parm)
try:
parm = load_file(parm)
except FormatNotFound:
raise ParmError('Could not determine file type of %s' % parm)
if not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
elif not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
if str(parm) in self._parm_names:
raise DuplicateParm('%s already in ParmList' % parm)
# Otherwise, add in the new parm's name
self._parm_names.append(str(parm))
self._parm_instances.append(parm)
# A newly added topology file is the currently active parm
self.current_index = len(self._parm_instances) - 1
self.parm = parm
def testAmberParmPandas(self):
""" Tests creating a pandas DataFrame from an AmberParm """
parm = load_file(get_fn('tip4p.parm7'))
parm.load_rst7(get_fn('tip4p.rst7'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], len(parm.atoms))
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.xx, parm.atoms[i].xx)
self.assertEqual(r1.xy, parm.atoms[i].xy)
self.assertEqual(r1.xz, parm.atoms[i].xz)
self.assertEqual(r1.vx, parm.atoms[i].vx)
self.assertEqual(r1.vy, parm.atoms[i].vy)
self.assertEqual(r1.vz, parm.atoms[i].vz)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
self.assertNotIn('segid', df)
def testAmberParmPandas(self):
""" Tests creating a pandas DataFrame from an AmberParm """
parm = load_file(get_fn('tip4p.parm7'))
parm.load_rst7(get_fn('tip4p.rst7'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], len(parm.atoms))
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.xx, parm.atoms[i].xx)
self.assertEqual(r1.xy, parm.atoms[i].xy)
self.assertEqual(r1.xz, parm.atoms[i].xz)
self.assertEqual(r1.vx, parm.atoms[i].vx)
self.assertEqual(r1.vy, parm.atoms[i].vy)
self.assertEqual(r1.vz, parm.atoms[i].vz)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
self.assertNotIn('segid', df)
def add_parm(self, parm):
""" Add a parm to the list """
# Make sure this parm is not part of the list already
if isinstance(parm, basestring):
if parm in self._parm_names:
raise DuplicateParm('%s already in ParmList' % parm)
try:
parm = load_file(parm)
except FormatNotFound:
raise ParmError('Could not determine file type of %s' % parm)
if not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
elif not isinstance(parm, Structure):
raise ParmError('Added parm must be Structure or a subclass')
if str(parm) in self._parm_names:
raise DuplicateParm('%s already in ParmList' % parm)
# Otherwise, add in the new parm's name
self._parm_names.append(str(parm))
self._parm_instances.append(parm)
# A newly added topology file is the currently active parm
self.current_index = len(self._parm_instances) - 1
self.parm = parm
def testCharmmPSFPandas(self):
""" Tests creating a pandas DataFrame from a CharmmPsfFile """
parm = load_file(get_fn('ala_ala_ala.psf'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], len(parm.atoms))
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.segid, parm.atoms[i].segid)
self.assertNotIn('xx', df)
self.assertNotIn('xy', df)
self.assertNotIn('xz', df)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
def testCharmmPSFPandas(self):
""" Tests creating a pandas DataFrame from a CharmmPsfFile """
parm = load_file(get_fn('ala_ala_ala.psf'))
df = parm.to_dataframe()
self.assertEqual(df.shape[0], len(parm.atoms))
for i, r1 in df.iterrows():
self.assertEqual(r1.charge, parm.atoms[i].charge)
self.assertEqual(r1['name'], parm.atoms[i].name)
self.assertEqual(r1.radii, parm.atoms[i].radii)
self.assertEqual(r1.screen, parm.atoms[i].screen)
self.assertEqual(r1.type, parm.atoms[i].type)
self.assertEqual(r1.occupancy, parm.atoms[i].occupancy)
self.assertEqual(r1.bfactor, parm.atoms[i].bfactor)
self.assertEqual(r1.altloc, parm.atoms[i].altloc)
self.assertEqual(r1.rmin, parm.atoms[i].rmin)
self.assertEqual(r1.epsilon, parm.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, parm.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, parm.atoms[i].epsilon_14)
self.assertEqual(r1.resname, parm.atoms[i].residue.name)
self.assertEqual(r1.resid, parm.atoms[i].residue.idx)
self.assertEqual(r1.resnum, parm.atoms[i].residue.number)
self.assertEqual(r1.chain, parm.atoms[i].residue.chain)
self.assertEqual(r1.join, parm.atoms[i].join)
self.assertEqual(r1.nb_idx, parm.atoms[i].nb_idx)
self.assertEqual(r1.segid, parm.atoms[i].segid)
self.assertNotIn('xx', df)
self.assertNotIn('xy', df)
self.assertNotIn('xz', df)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
def testPDBPandas(self):
""" Test 4lzt.pdb conversion to DataFrame (w/ anisou and positions) """
pdb = load_file(get_fn('4lzt.pdb'))
df = pdb.to_dataframe()
self.assertIn('U11', df)
self.assertIn('U22', df)
self.assertIn('U33', df)
self.assertIn('U12', df)
self.assertIn('U13', df)
self.assertIn('U23', df)
# Make sure that when one of the anisotropic B-factors is not set, the
# NaN gets properly put in its place
pdb.atoms[0].anisou = None
df2 = pdb.to_dataframe()
self.assertIn('U11', df)
self.assertIn('U22', df)
self.assertIn('U33', df)
self.assertIn('U12', df)
self.assertIn('U13', df)
self.assertIn('U23', df)
# Now make sure they are all equal except for the first atom, and that
# the data matches the PDB information
anisou = ['U11', 'U22', 'U33', 'U12', 'U13', 'U23']
for (i, r1), (j, r2) in zip(df.iterrows(), df2.iterrows()):
if i == 0:
# Easy NaN check
self.assertNotEqual(r2.U11, r2.U11)
self.assertNotEqual(r2.U22, r2.U22)
self.assertNotEqual(r2.U33, r2.U33)
self.assertNotEqual(r2.U12, r2.U12)
self.assertNotEqual(r2.U13, r2.U13)
self.assertNotEqual(r2.U23, r2.U23)
# Check against df1
self.assertNotEqual(r1.U11, r2.U11)
self.assertNotEqual(r1.U22, r2.U22)
self.assertNotEqual(r1.U33, r2.U33)
self.assertNotEqual(r1.U12, r2.U12)
self.assertNotEqual(r1.U13, r2.U13)
self.assertNotEqual(r1.U23, r2.U23)
else:
self.assertEqual(r1.U11, r2.U11)
self.assertEqual(r1.U22, r2.U22)
self.assertEqual(r1.U33, r2.U33)
self.assertEqual(r1.U12, r2.U12)
self.assertEqual(r1.U13, r2.U13)
self.assertEqual(r1.U23, r2.U23)
self.assertTrue(np.all(np.abs(r1[anisou] - pdb.atoms[i].anisou) < 1e-4))
self.assertEqual(r1.charge, 0)
self.assertEqual(r1.charge, pdb.atoms[i].charge)
self.assertEqual(r1['name'], pdb.atoms[i].name)
self.assertEqual(r1.radii, pdb.atoms[i].radii)
self.assertEqual(r1.screen, pdb.atoms[i].screen)
self.assertEqual(r1.type, pdb.atoms[i].type)
self.assertEqual(r1.occupancy, pdb.atoms[i].occupancy)
self.assertEqual(r1.bfactor, pdb.atoms[i].bfactor)
self.assertEqual(r1.altloc, pdb.atoms[i].altloc)
self.assertEqual(r1.rmin, pdb.atoms[i].rmin)
self.assertEqual(r1.epsilon, pdb.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, pdb.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, pdb.atoms[i].epsilon_14)
self.assertEqual(r1.resname, pdb.atoms[i].residue.name)
self.assertEqual(r1.resid, pdb.atoms[i].residue.idx)
self.assertEqual(r1.resnum, pdb.atoms[i].residue.number)
self.assertEqual(r1.chain, pdb.atoms[i].residue.chain)
self.assertEqual(r1.join, pdb.atoms[i].join)
self.assertEqual(r1.nb_idx, pdb.atoms[i].nb_idx)
self.assertEqual(r1.xx, pdb.atoms[i].xx)
self.assertEqual(r1.xy, pdb.atoms[i].xy)
self.assertEqual(r1.xz, pdb.atoms[i].xz)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
self.assertNotIn('segid', df)
from __future__ import division, print_function
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry import load_file
from chemistry.openmm.reporters import NetCDFReporter
from chemistry import unit as u
# Load the Gromacs files
print('Loading Gromacs files...')
top = load_file('dhfr_gas.top')
gro = load_file('dhfr_gas.gro')
# Create the OpenMM system
print('Creating OpenMM System')
system = top.createSystem(nonbondedMethod=app.NoCutoff,
constraints=app.HBonds, implicitSolvent=app.GBn2,
implicitSolventSaltConc=0.1*u.moles/u.liter,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
1.0/u.picoseconds, # Friction coefficient
2.0*u.femtoseconds, # Time step
)
from __future__ import division, print_function
import sys
# OpenMM Imports
import simtk.openmm as mm
import simtk.openmm.app as app
# ParmEd Imports
from chemistry import load_file
from chemistry.openmm.reporters import NetCDFReporter
from chemistry import unit as u
# Load the Gromacs files
print('Loading Gromacs files...')
top = load_file('dhfr_pme.top')
gro = load_file('dhfr_pme.gro')
# Transfer the unit cell information from the GRO file to the top object
top.box = gro.box[:]
# Create the OpenMM system
print('Creating OpenMM System')
system = top.createSystem(nonbondedMethod=app.PME,
nonbondedCutoff=8.0*u.angstroms,
constraints=app.HBonds,
)
# Create the integrator to do Langevin dynamics
integrator = mm.LangevinIntegrator(
300*u.kelvin, # Temperature of heat bath
import glob, os, chemistry
import networkx
import mdtraj as md
filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/*.prmtop")
#filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/57-55-6_1000_313.2*.prmtop")
filenames = glob.glob(
"/home/kyleb/lb_benchmark_openmoltools/tleap/121182*.prmtop")
#filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/126492-54-4_1000_315*.prmtop")
for filename in filenames:
base = os.path.splitext(os.path.split(filename)[-1])[0]
prmtop_filename = "/home/kyleb/lb_benchmark_openmoltools/tleap/" + base + ".prmtop"
inpcrd_filename = "/home/kyleb/lb_benchmark_openmoltools/tleap/" + base + ".inpcrd"
print(prmtop_filename, inpcrd_filename)
prmtop0 = chemistry.load_file(prmtop_filename)
t0 = md.load(inpcrd_filename, top=prmtop_filename)
t0 = t0.atom_slice(t0.top.select("resSeq 0"))
prmtop_filename = "/home/kyleb/liquid_benchmark_3_14//tleap/" + base + ".prmtop"
inpcrd_filename = "/home/kyleb/liquid_benchmark_3_14//tleap/" + base + ".inpcrd"
prmtop1 = chemistry.load_file(prmtop_filename)
t1 = md.load(inpcrd_filename, top=prmtop_filename)
t1 = t1.atom_slice(t1.top.select("resSeq 0"))
top0 = prmtop0.to_dataframe()
top0 = top0[top0.resid == 0]
top1 = prmtop1.to_dataframe()
top1 = top1[top1.resid == 0]
b0 = t0.top.to_dataframe()[1]
b1 = t1.top.to_dataframe()[1]
g0 = networkx.from_edgelist(b0)
g1 = networkx.from_edgelist(b1)
def testPDBPandas(self):
""" Test 4lzt.pdb conversion to DataFrame (w/ anisou and positions) """
pdb = load_file(get_fn('4lzt.pdb'))
df = pdb.to_dataframe()
self.assertIn('U11', df)
self.assertIn('U22', df)
self.assertIn('U33', df)
self.assertIn('U12', df)
self.assertIn('U13', df)
self.assertIn('U23', df)
# Make sure that when one of the anisotropic B-factors is not set, the
# NaN gets properly put in its place
pdb.atoms[0].anisou = None
df2 = pdb.to_dataframe()
self.assertIn('U11', df)
self.assertIn('U22', df)
self.assertIn('U33', df)
self.assertIn('U12', df)
self.assertIn('U13', df)
self.assertIn('U23', df)
# Now make sure they are all equal except for the first atom, and that
# the data matches the PDB information
anisou = ['U11', 'U22', 'U33', 'U12', 'U13', 'U23']
for (i, r1), (j, r2) in zip(df.iterrows(), df2.iterrows()):
if i == 0:
# Easy NaN check
self.assertNotEqual(r2.U11, r2.U11)
self.assertNotEqual(r2.U22, r2.U22)
self.assertNotEqual(r2.U33, r2.U33)
self.assertNotEqual(r2.U12, r2.U12)
self.assertNotEqual(r2.U13, r2.U13)
self.assertNotEqual(r2.U23, r2.U23)
# Check against df1
self.assertNotEqual(r1.U11, r2.U11)
self.assertNotEqual(r1.U22, r2.U22)
self.assertNotEqual(r1.U33, r2.U33)
self.assertNotEqual(r1.U12, r2.U12)
self.assertNotEqual(r1.U13, r2.U13)
self.assertNotEqual(r1.U23, r2.U23)
else:
self.assertEqual(r1.U11, r2.U11)
self.assertEqual(r1.U22, r2.U22)
self.assertEqual(r1.U33, r2.U33)
self.assertEqual(r1.U12, r2.U12)
self.assertEqual(r1.U13, r2.U13)
self.assertEqual(r1.U23, r2.U23)
self.assertTrue(
np.all(np.abs(r1[anisou] - pdb.atoms[i].anisou) < 1e-4))
self.assertEqual(r1.charge, 0)
self.assertEqual(r1.charge, pdb.atoms[i].charge)
self.assertEqual(r1['name'], pdb.atoms[i].name)
self.assertEqual(r1.radii, pdb.atoms[i].radii)
self.assertEqual(r1.screen, pdb.atoms[i].screen)
self.assertEqual(r1.type, pdb.atoms[i].type)
self.assertEqual(r1.occupancy, pdb.atoms[i].occupancy)
self.assertEqual(r1.bfactor, pdb.atoms[i].bfactor)
self.assertEqual(r1.altloc, pdb.atoms[i].altloc)
self.assertEqual(r1.rmin, pdb.atoms[i].rmin)
self.assertEqual(r1.epsilon, pdb.atoms[i].epsilon)
self.assertEqual(r1.rmin_14, pdb.atoms[i].rmin_14)
self.assertEqual(r1.epsilon_14, pdb.atoms[i].epsilon_14)
self.assertEqual(r1.resname, pdb.atoms[i].residue.name)
self.assertEqual(r1.resid, pdb.atoms[i].residue.idx)
self.assertEqual(r1.resnum, pdb.atoms[i].residue.number)
self.assertEqual(r1.chain, pdb.atoms[i].residue.chain)
self.assertEqual(r1.join, pdb.atoms[i].join)
self.assertEqual(r1.nb_idx, pdb.atoms[i].nb_idx)
self.assertEqual(r1.xx, pdb.atoms[i].xx)
self.assertEqual(r1.xy, pdb.atoms[i].xy)
self.assertEqual(r1.xz, pdb.atoms[i].xz)
self.assertNotIn('vx', df)
self.assertNotIn('vy', df)
self.assertNotIn('vz', df)
self.assertNotIn('type_idx', df)
self.assertNotIn('class_idx', df)
for key in df.keys():
self.assertFalse(key.startswith('multipole'))
self.assertNotIn('polarizability', df)
self.assertNotIn('vdw_parent', df)
self.assertNotIn('segid', df)
"""
Tests the fancy indexing and slicing capabilities of Structure
"""
import chemistry as chem
import random
import unittest
import utils
parm = chem.load_file(utils.get_fn('trx.prmtop'))
pdb1 = chem.load_file(utils.get_fn('4lzt.pdb'))
pdb2 = chem.load_file(utils.get_fn('1kip.cif'))
class TestStructureSlicing(unittest.TestCase):
""" Tests the fancy slicing/indexing of Structure """
def testIntIndex(self):
""" Tests simple Structure indexing (integer) """
for i, atom in enumerate(parm.atoms):
self.assertIs(atom, parm[i])
for i, atom in enumerate(pdb1.atoms):
self.assertIs(atom, pdb1[i])
for i, atom in enumerate(pdb2.atoms):
self.assertIs(atom, pdb2[i])
def testSimpleSlice(self):
""" Tests simple atom slicing """
sl11 = parm[:10]
sl21 = pdb1[:10]
sl31 = pdb2[:10]
sl12 = parm[10:20]
cas, n_molecules, temperature = filename_munger(prmtop_filename)
print(cas, temperature)
dcd_filename = DATA_PATH + "/production/%s_%s_%s_production.dcd" % (cas, n_molecules, temperature)
csv_filename = DATA_PATH + "/production/%s_%s_%s_production.csv" % (cas, n_molecules, temperature)
try:
traj = md.load(dcd_filename, top=prmtop_filename)
except IOError:
continue
if traj.unitcell_lengths is None: continue
rho = pd.read_csv(csv_filename)["Density (g/mL)"].values * 1000. # g / mL -> kg /m3
initial_traj_length = len(traj)
initial_density_length = len(rho)
[t0, g, Neff] = pymbar.timeseries.detectEquilibration(rho)
mu = rho[t0:].mean()
sigma = rho[t0:].std() * Neff ** -0.5
prmtop = chemistry.load_file(prmtop_filename)
charges = prmtop.to_dataframe().charge.values
temperature = float(temperature)
traj = traj[t0 * len(traj) / len(rho):]
dielectric = md.geometry.static_dielectric(traj, charges, temperature)
dielectric_sigma_fixedblock = dipole_errorbars.bootstrap_old(traj, charges, temperature, fixed_block_length)[1]
block_length = dipole_errorbars.find_block_size(traj, charges, temperature)
dielectric_sigma = dipole_errorbars.bootstrap(traj, charges, temperature, block_length, num_bootstrap)
formula = cirpy.resolve(cas, "formula")
data.append(dict(cas=cas, temperature=temperature, n_trimmed=t0, inefficiency=g, initial_traj_length=initial_traj_length, initial_density_length=initial_density_length, density=mu, density_sigma=sigma, Neff=Neff, n_frames=traj.n_frames, dielectric=dielectric, dielectric_sigma=dielectric_sigma, dielectric_sigma_fixedblock=dielectric_sigma_fixedblock, block_length=block_length, formula=formula))
print(data[-1])
data = pd.DataFrame(data)
data.to_csv("./tables/predictions.csv")
"""
Tests the fancy indexing and slicing capabilities of Structure
"""
import chemistry as chem
from chemistry.utils.six.moves import range, zip
import random
import unittest
import utils
parm = chem.load_file(utils.get_fn('trx.prmtop'))
pdb1 = chem.load_file(utils.get_fn('4lzt.pdb'))
pdb2 = chem.load_file(utils.get_fn('1kip.cif'))
class TestStructureSlicing(unittest.TestCase):
""" Tests the fancy slicing/indexing of Structure """
def testIntIndex(self):
""" Tests simple Structure indexing (integer) """
for i, atom in enumerate(parm.atoms):
self.assertIs(atom, parm[i])
for i, atom in enumerate(pdb1.atoms):
self.assertIs(atom, pdb1[i])
for i, atom in enumerate(pdb2.atoms):
self.assertIs(atom, pdb2[i])
def testSimpleSlice(self):
""" Tests simple atom slicing """
sl11 = parm[:10]
sl21 = pdb1[:10]
sl31 = pdb2[:10]
sl12 = parm[10:20]
#!/usr/bin/env python import openmoltools.utils import chemistry in_prmtop = 'toluene_cyclohexane_10_500.prmtop' in_crd = 'toluene_cyclohexane_10_500.inpcrd' #Convert AMBER to GROMACS via acpype openmoltools.utils.convert_via_acpype( 'mixture', in_prmtop, in_crd, out_top = 'toluene_cyclohexane_10_500_acpype.top', out_gro = 'toluene_cyclohexane_10_500_acpype.gro' ) #Convert AMBER to GROMACS via ParmEd structure = chemistry.amber.AmberParm( in_prmtop, in_crd ) #Gromacs topology gromacs_topology = chemistry.gromacs.GromacsTopologyFile.from_structure( structure ) #Write gromacs_topology.write( 'toluene_cyclohexane_10_500_parmed.top' ) chemistry.gromacs.GromacsGroFile.write( gromacs_topology, 'toluene_cyclohexane_10_500_parmed.gro') #Create a second AMBER coordinate file so it will have the same precision as the gro file gromacs_topology2 = chemistry.load_file( 'toluene_cyclohexane_10_500_parmed.top' ) gro = chemistry.gromacs.GromacsGroFile.parse( 'toluene_cyclohexane_10_500_parmed.gro' ) gromacs_topology2.box = gro.box gromacs_topology2.positions = gro.positions amberparm = chemistry.amber.AmberParm.from_structure( gromacs_topology2 ) amberparm.write_parm( 'toluene_cyclohexane_10_500_parmed.prmtop' ) amberparm.write_rst7( 'toluene_cyclohexane_10_500_parmed.crd' )
def testReadAmber99SBILDN(self):
""" Tests parsing a Gromacs topology with Amber99SBILDN and water """
top = load_file(get_fn('1aki.ff99sbildn.top'))
self._check_ff99sbildn(top)
import glob, os, chemistry
import networkx
import mdtraj as md
filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/*.prmtop")
#filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/57-55-6_1000_313.2*.prmtop")
filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/121182*.prmtop")
#filenames = glob.glob("/home/kyleb/lb_benchmark_openmoltools/tleap/126492-54-4_1000_315*.prmtop")
for filename in filenames:
base = os.path.splitext(os.path.split(filename)[-1])[0]
prmtop_filename = "/home/kyleb/lb_benchmark_openmoltools/tleap/" + base + ".prmtop"
inpcrd_filename = "/home/kyleb/lb_benchmark_openmoltools/tleap/" + base + ".inpcrd"
print(prmtop_filename, inpcrd_filename)
prmtop0 = chemistry.load_file(prmtop_filename)
t0 = md.load(inpcrd_filename, top=prmtop_filename)
t0 = t0.atom_slice(t0.top.select("resSeq 0"))
prmtop_filename = "/home/kyleb/liquid_benchmark_3_14//tleap/" + base + ".prmtop"
inpcrd_filename = "/home/kyleb/liquid_benchmark_3_14//tleap/" + base + ".inpcrd"
prmtop1 = chemistry.load_file(prmtop_filename)
t1 = md.load(inpcrd_filename, top=prmtop_filename)
t1 = t1.atom_slice(t1.top.select("resSeq 0"))
top0 = prmtop0.to_dataframe()
top0 = top0[top0.resid == 0]
top1 = prmtop1.to_dataframe()
top1 = top1[top1.resid == 0]
b0 = t0.top.to_dataframe()[1]
b1 = t1.top.to_dataframe()[1]
g0 = networkx.from_edgelist(b0)
g1 = networkx.from_edgelist(b1)
for i in range(len(g0.nodes())):
for k0, k1, components, smiles, cas, temperature, pressure, density, perm in data.itertuples(
):
print(k0, k1, components, smiles, cas, temperature, pressure, density)
mol2_filename = "./tmpmol2/%s.mol2" % cas
frcmod_filename = "./tmpmol2/%s.frcmod" % cas
openmoltools.openeye.smiles_to_antechamber(smiles, mol2_filename,
frcmod_filename)
PATH0 = "/home/kyleb/liquid_benchmark_4_8/"
PATH1 = "/home/kyleb/liquid_benchmark_3_14/"
PATH2 = "./tmpmol2/"
for k0, k1, components, smiles, cas, temperature, pressure, density, perm in data.itertuples(
):
print(k0, k1, components, smiles, cas, temperature, pressure, density)
mol2_filename = PATH0 + "/monomers/%s.mol2" % cas
prmtop0 = chemistry.load_file(mol2_filename)
charges0 = np.array([a.charge for a in prmtop0.atoms])
mol2_filename = PATH1 + "/monomers/%s.mol2" % cas
prmtop1 = chemistry.load_file(mol2_filename)
charges1 = np.array([a.charge for a in prmtop1.atoms])
mol2_filename = PATH2 + "/%s.mol2" % cas
prmtop2 = chemistry.load_file(mol2_filename)
charges2 = np.array([a.charge for a in prmtop2.atoms])
print(cas)
print(np.std((charges0.min(), charges1.min(), charges2.min())))
print(charges0.min(), charges1.min(), charges2.min())
