def test_mm_options_as_string(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
igb = 8
mm_options = sander.gas_input(igb)
mm_options_str = 'mm_options = sander.gas_input(8)'
e0 = pt.energy_decomposition(traj, mm_options=mm_options, dtype='dict')
e1 = pt.energy_decomposition(traj,
mm_options=mm_options_str,
dtype='dict')
assert sorted(e0) == sorted(e1)
def test_frame_indices(self):
traj = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
frame_indices = [0, 6, 7, 4, 5]
data_without_frame_indices = pt.energy_decomposition(traj, igb=8)
data_with_frame_indices = pt.energy_decomposition(
traj, igb=8, frame_indices=frame_indices)
data_with_frame_indices_2 = pt.energy_decomposition(
traj[frame_indices], igb=8)
for key in data_without_frame_indices:
aa_eq(data_without_frame_indices[key][frame_indices],
data_with_frame_indices[key])
aa_eq(data_without_frame_indices[key][frame_indices],
data_with_frame_indices_2[key])
def test_GB_QMMM(self):
# compare to saved test: GB + QMMM
topfile = os.path.join(amberhome, "test/qmmm2/lysine_PM3_qmgb2/prmtop")
rstfile = os.path.join(amberhome,
"test/qmmm2/lysine_PM3_qmgb2/lysine.crd")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(1)
options.cut = 99.0
options.ifqnt = 1
qm_options = sander.qm_input()
qm_options.iqmatoms[:3] = [8, 9, 10]
qm_options.qm_theory = "PM3"
qm_options.qmcharge = 0
qm_options.qmgb = 2
qm_options.adjust_q = 0
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
qm_options=qm_options)
assert_close(edict['bond'][0], 0.0016, tol=3E-4)
assert_close(edict['vdw'][0], 0.1908, tol=3E-4)
assert_close(edict['vdw_14'][0], 3.7051, tol=3E-4)
assert_close(edict['elec'][0], -4.1241, tol=3E-4)
assert_close(edict['elec_14'][0], 65.9137, tol=3E-4)
assert_close(edict['gb'][0], -80.1406, tol=3E-4)
assert_close(edict['scf'][0], -11.9100, tol=3E-4)
def test_PME_QMMM(self):
# compare to saved test: PME + QMMM
topfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/prmtop")
rstfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/inpcrd")
traj = pt.load(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
options.ifqnt = 1
options.jfastw = 4
qm_options = sander.QmInputOptions()
qm_options.qm_theory = "PDDG-PM3"
qm_options.qmmask = ":1-2"
qm_options.qmcharge = 0
qm_options.scfconv = 1e-10
qmmm_tight_p_conv = 1
qm_options.qmmm_int = 5
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
qm_options=qm_options)
assert_close(edict['bond'][0], 605.7349, tol=3E-4)
assert_close(edict['vdw_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec'][0], -7409.7167, tol=3E-1)
assert_close(edict['scf'][0], -37.1277, tol=3E-4)
def test_PME_QMMM(self):
# compare to saved test: PME + QMMM
topfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/prmtop")
rstfile = os.path.join(amberhome,
"test/qmmm2/MechEm_nma-spcfwbox/inpcrd")
traj = pt.load(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
options.ifqnt = 1
options.jfastw = 4
qm_options = sander.QmInputOptions()
qm_options.qm_theory = "PDDG-PM3"
qm_options.qmmask = ":1-2"
qm_options.qmcharge = 0
qm_options.scfconv = 1e-10
qmmm_tight_p_conv = 1
qm_options.qmmm_int = 5
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
qm_options=qm_options)
assert_close(edict['bond'][0], 605.7349, tol=3E-4)
assert_close(edict['vdw_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec_14'][0], 0.0000, tol=3E-4)
assert_close(edict['elec'][0], -7409.7167, tol=3E-1)
assert_close(edict['scf'][0], -37.1277, tol=3E-4)
def test_GB_QMMM(self):
# compare to saved test: GB + QMMM
topfile = os.path.join(amberhome, "test/qmmm2/lysine_PM3_qmgb2/prmtop")
rstfile = os.path.join(amberhome,
"test/qmmm2/lysine_PM3_qmgb2/lysine.crd")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(1)
options.cut = 99.0
options.ifqnt = 1
qm_options = sander.qm_input()
qm_options.iqmatoms[:3] = [8, 9, 10]
qm_options.qm_theory = "PM3"
qm_options.qmcharge = 0
qm_options.qmgb = 2
qm_options.adjust_q = 0
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
qm_options=qm_options)
assert_close(edict['bond'][0], 0.0016, tol=3E-4)
assert_close(edict['vdw'][0], 0.1908, tol=3E-4)
assert_close(edict['vdw_14'][0], 3.7051, tol=3E-4)
assert_close(edict['elec'][0], -4.1241, tol=3E-4)
assert_close(edict['elec_14'][0], 65.9137, tol=3E-4)
assert_close(edict['gb'][0], -80.1406, tol=3E-4)
assert_close(edict['scf'][0], -11.9100, tol=3E-4)
def test_frame_indices(self):
traj = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
frame_indices = [0, 6, 7, 4, 5]
data_without_frame_indices = pt.energy_decomposition(traj, igb=8)
data_with_frame_indices = pt.energy_decomposition(
traj,
igb=8,
frame_indices=frame_indices)
data_with_frame_indices_2 = pt.energy_decomposition(
traj[frame_indices],
igb=8)
for key in data_without_frame_indices:
aa_eq(data_without_frame_indices[key][frame_indices],
data_with_frame_indices[key])
aa_eq(data_without_frame_indices[key][frame_indices],
data_with_frame_indices_2[key])
def test_sander_pmap_simple(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
fname = traj.top.filename
serial = pt.energy_decomposition(traj, prmtop=fname)['dihedral']
parallel = pt.pmap(n_cores=4,
func=pt.energy_decomposition,
traj=traj,
prmtop=fname)['dihedral']
aa_eq(serial, parallel)
def test_sander_pmap_simple(self):
traj = pt.iterload('./data/Tc5b.x', './data/Tc5b.top')
fname = traj.top.filename
serial = pt.energy_decomposition(traj, prmtop=fname)['dihedral']
parallel = pt.pmap(n_cores=4,
func=pt.energy_decomposition,
traj=traj,
prmtop=fname)['dihedral']
aa_eq(serial, parallel)
def main():
folder = sys.argv[1]
files = glob("{}/min*rst7".format(folder))
parm = glob("{}/*.parm7".format(folder))[0]
traj = pt.iterload(files, top=parm)
energies = pt.energy_decomposition(traj, igb=8)["tot"]
for fn, potential in zip(files, energies):
print(fn, potential)
def test_PME(self):
# compare to saved test: PME
topfile = os.path.join(amberhome, "test/4096wat/prmtop")
rstfile = os.path.join(amberhome, "test/4096wat/eq1.x")
traj = pt.iterload(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
edict = pt.energy_decomposition(traj=traj, mm_options=options)
assert_close(edict['bond'][0], 0., tol=3E-4)
assert_close(edict['vdw'][0], 6028.9517, tol=3E-4)
assert_close(edict['elec'][0], -45371.5995, tol=3E-4)
def test_0(self):
if os.path.exists(amberhome):
from pytraj.amber_wrapper import minimize
traj = pt.iterload("./data/Ala3/Ala3.crd", "./data/Ala3/Ala3.top")
t0 = traj[:1]
if has_("sander"):
print('egb: ', pt.energy_decomposition(t0, igb=8)['gb'])
minimize(t0)
self.assertRaises(ValueError, lambda: minimize(traj))
if has_("sander"):
print('egb: ', pt.energy_decomposition(t0, igb=8)['gb'])
# load saved file
saved_coords = pt.load("./data/Ala3/min/min.r", traj.top).xyz
aa_eq(t0.xyz, saved_coords, decimal=5)
def test_0(self):
if os.path.exists(amberhome):
from pytraj.amber_wrapper import minimize
traj = pt.iterload("./data/Ala3/Ala3.crd", "./data/Ala3/Ala3.top")
t0 = traj[:1]
if has_("sander"):
print('egb: ', pt.energy_decomposition(t0, igb=8)['gb'])
minimize(t0)
self.assertRaises(ValueError, lambda: minimize(traj))
if has_("sander"):
print('egb: ', pt.energy_decomposition(t0, igb=8)['gb'])
# load saved file
saved_coords = pt.load("./data/Ala3/min/min.r", traj.top).xyz
aa_eq(t0.xyz, saved_coords, decimal=5)
def test_PME(self):
# compare to saved test: PME
topfile = os.path.join(amberhome, "test/4096wat/prmtop")
rstfile = os.path.join(amberhome, "test/4096wat/eq1.x")
traj = pt.iterload(rstfile, topfile)
options = sander.pme_input()
options.cut = 8.0
edict = pt.energy_decomposition(traj=traj, mm_options=options)
assert_close(edict['bond'][0], 0., tol=3E-4)
assert_close(edict['vdw'][0], 6028.9517, tol=3E-4)
assert_close(edict['elec'][0], -45371.5995, tol=3E-4)
def test_gbneck2nu(self):
# compare to saved test: GBneck2nu
topfile = os.path.join(amberhome, "test/gbneck2nu/1hji/prmtop")
rstfile = os.path.join(amberhome, "test/gbneck2nu/1hji/min.r")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(8)
options.cut = 9999.0
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
prmtop=topfile)
assert_close(edict['gb'][0], -2287.6880, tol=3E-4)
assert_close(edict['gb'][0], -2287.6880, tol=3E-4)
assert_close(edict['elec'][0], -1659.5740, tol=3E-4)
assert_close(edict['vdw'][0], 384.2512, tol=3E-4)
def test_gbneck2nu(self):
# compare to saved test: GBneck2nu
topfile = os.path.join(amberhome, "test/gbneck2nu/1hji/prmtop")
rstfile = os.path.join(amberhome, "test/gbneck2nu/1hji/min.r")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(8)
options.cut = 9999.0
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
prmtop=topfile)
assert_close(edict['gb'][0], -2287.6880, tol=3E-4)
assert_close(edict['gb'][0], -2287.6880, tol=3E-4)
assert_close(edict['elec'][0], -1659.5740, tol=3E-4)
assert_close(edict['vdw'][0], 384.2512, tol=3E-4)
def test_GB(self):
# compare to saved test: GB
topfile = os.path.join(amberhome, "test/gb7_trx/prmtop_an")
rstfile = os.path.join(amberhome, "test/gb7_trx/trxox.2.4ns.x")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(7)
options.cut = 9999.0
options.saltcon = 0.2
options.gbsa = 1
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
prmtop=topfile)
assert_close(edict['bond'][0], 631.8993, tol=3E-4)
assert_close(edict['angle'][0], 898.2543, tol=3E-4)
assert_close(edict['surf'][0], 33.8338, tol=3E-4)
assert_close(edict['gb'][0], -1943.0838, tol=3E-4)
# dummy test to make sure `energy_decomposition` can work with list
edict2 = pt.energy_decomposition(traj=[
traj,
],
mm_options=options,
prmtop=topfile,
top=traj.top)
edict3 = pt.energy_decomposition(traj=traj(),
mm_options=options,
prmtop=topfile,
top=traj.top)
edict4 = pt.energy_decomposition(traj=[traj[:5], traj[5:]],
mm_options=options,
prmtop=topfile,
top=traj.top)
edict5 = pt.energy_decomposition(traj=[traj[:5],
traj(start=5)],
mm_options=options,
prmtop=topfile,
top=traj.top)
# test dtype
dslist = pt.energy_decomposition(traj=[
traj,
],
mm_options=options,
prmtop=topfile,
top=traj.top,
dtype='dataset')
assert edict == edict2
assert edict == edict3
assert edict == edict4
assert sorted(dslist.to_dict()) == sorted(edict)
def test_sander_pmap_with_options(self):
'''need to write mm_options as text
'''
code_local = '''
mm_options = sander.gas_input(8)
'''
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
for code in [code_global, code_local]:
data_parallel = pt.pmap(pt.energy_decomposition,
traj,
mm_options=code,
n_cores=3,
dtype='dict')
mm_options = sander.gas_input(8)
data_serial = pt.energy_decomposition(traj,
mm_options=mm_options,
dtype='dict')
aa_eq(pt.tools.dict_to_ndarray(data_parallel),
pt.tools.dict_to_ndarray(data_serial))
def test_sander_pmap_with_options(self):
'''need to write mm_options as text
'''
code_local = '''
mm_options = sander.gas_input(8)
'''
traj = pt.iterload('./data/Tc5b.x', './data/Tc5b.top')
for code in [code_global, code_local]:
data_parallel = pt.pmap(pt.energy_decomposition,
traj,
mm_options=code,
n_cores=3,
dtype='dict')
mm_options = sander.gas_input(8)
data_serial = pt.energy_decomposition(traj,
mm_options=mm_options,
dtype='dict')
aa_eq(
pt.tools.dict_to_ndarray(data_parallel),
pt.tools.dict_to_ndarray(data_serial))
def test_GB(self):
# compare to saved test: GB
topfile = os.path.join(amberhome, "test/gb7_trx/prmtop_an")
rstfile = os.path.join(amberhome, "test/gb7_trx/trxox.2.4ns.x")
traj = pt.load(rstfile, topfile)
options = sander.gas_input(7)
options.cut = 9999.0
options.saltcon = 0.2
options.gbsa = 1
edict = pt.energy_decomposition(traj=traj,
mm_options=options,
prmtop=topfile)
assert_close(edict['bond'][0], 631.8993, tol=3E-4)
assert_close(edict['angle'][0], 898.2543, tol=3E-4)
assert_close(edict['surf'][0], 33.8338, tol=3E-4)
assert_close(edict['gb'][0], -1943.0838, tol=3E-4)
# dummy test to make sure `energy_decomposition` can work with list
edict2 = pt.energy_decomposition(traj=[traj, ],
mm_options=options,
prmtop=topfile,
top=traj.top)
edict3 = pt.energy_decomposition(traj=traj(),
mm_options=options,
prmtop=topfile,
top=traj.top)
edict4 = pt.energy_decomposition(traj=[traj[:5], traj[5:]],
mm_options=options,
prmtop=topfile,
top=traj.top)
edict5 = pt.energy_decomposition(traj=[traj[:5], traj(start=5)],
mm_options=options,
prmtop=topfile,
top=traj.top)
# test dtype
dslist = pt.energy_decomposition(traj=[traj, ],
mm_options=options,
prmtop=topfile,
top=traj.top,
dtype='dataset')
assert edict == edict2
assert edict == edict3
assert edict == edict4
assert sorted(dslist.to_dict()) == sorted(edict)
def main(argv):
args = sys.argv
native = ''
outfile = ''
try:
opts, args=getopt.getopt(sys.argv[1:], "ho:n:o:", ["in:file:n=", "out:file:scorefile="])
except getopt.GetoptError:
print('Unknown flag given.\nKnown flags:\n\t-h\n\t-n <native>')
sys.exit()
for opt, arg in opts:
if opt == '-h':
print('Something.py --in:file:s <input_pdb_id> --out:file:scorefile <output_filename>')
sys.exit()
elif opt in ("-n", "--in:file:n"):
native = arg
elif opt in ("-o", "--out:file:scorefile"):
outfile = arg
if native == '':
print('No native rst7 supplied.')
sys.exit()
if outfile == '':
outfile = 'Scores.sc'
print( "===== Native RST7: %s =====" % native )
os.chdir(PATH_TO_DECOYDISC)
min_decoys = os.popen('ls min*.rst7').readlines() ## List of rst7s ["<rst7_1>\n", "<rst7_2>\n", ...]
for m in range(len(min_decoys)):
min_decoys[m] = min_decoys[m].rstrip()
if native in min_decoys:
min_decoys.remove(native)
print("== Analyzing %i mols==" % len(min_decoys))
min_decoys.insert(0, native)
parmfile = '_'.join(native.split('_')[1:]).rstrip('rst7') + 'parm7'
print("\t=== Loading Trajectories ===")
traj = pt.iterload(min_decoys, parmfile)
print("\t=== Getting RMSDs ===")
ca_rmsd_data = pt.rmsd(traj, mask=['@CA'])
print("\t=== Getting Energy Decomposition ===")
energy_data = pt.energy_decomposition(traj, igb=8)
print("\t\tFinished")
with open(outfile,'w') as scorefile:
header = 'pdb\t'
for s in energy_data.keys():
header += s + '\t'
header += 'rmsd\n'
scorefile.write(header)
for pdb_index in range(len(min_decoys)):
scoreline = min_decoys[pdb_index]+'\t'
for s in energy_data.keys():
scoreline += '%s\t' % str(energy_data[s][pdb_index])
scoreline += '%s\n' % str(ca_rmsd_data[pdb_index])
scorefile.write(scoreline)
traj = pt.iterload("./data/Ala3/Ala3.crd", "./data/Ala3/Ala3.top")
print(traj.n_atoms, traj.top.n_residues)
print(pt.multidihedral(traj).to_dict())
t0 = traj[:1]
deg_ene = []
flist = []
for deg in range(-180, 180, 5):
pt.rotate_dihedral(t0, "custom:3:omega:" + str(deg))
flist.append(t0[0].copy())
en = pt.energy_decomposition(t0, igb=8,
prmtop=traj.top.filename)['dihedral'][0]
deg_ene.append((deg, en))
arr = np.array(deg_ene).T
pt.write_traj("test.pdb",
flist,
top=traj.top,
overwrite=True,
options='model')
arr[1] = arr[1] - np.min(arr[1])
except ImportError:
pass
flist = []
try:
import sander
import parmed
# scan from -180 to 180, every 5 deg
# calculate dihedral energy for each conformation
#
for deg in range(-180, 180, 5):
pt.rotate_dihedral(t0, "custom:3:omega:" + str(deg))
flist.append(t0[0].copy())
en = pt.energy_decomposition(t0,
igb=8,
verbose=False,
parm=traj.top.filename)['dihedral'][0]
print(deg, en)
deg_ene.append((deg, en))
arr = np.array(deg_ene).T
print(len(flist))
# write multiple pdb to a single file to visualize
# rotation with vmd.
pt.write_traj("output/test.pdb", flist,
top=traj.top,
overwrite=True,
options='model')
elif 'decoys.set2' in pdb:
pdb_dirs[index] = pdb.replace('decoys.set2', 'decoys.set2.init')
else:
pdb_dirs[index] = pdb
# get min filenames
_min_files = [pdb_dir + '/no_restraint/' + 'min_NoH_' + x
for pdb_dir, x in zip(pdb_dirs, df[2])]
end = '_0001'
min_files = []
for mf in _min_files:
if '0001_0001' in mf:
min_files.append(mf.replace('0001_0001', '0001') + '.rst7')
elif '0002_0001' in mf:
min_files.append(mf.replace('0002_0001', '0002') + '.rst7')
else:
min_files.append(mf)
epots = []
for pdb_dir, mf in zip(pdb_dirs, min_files):
if os.path.exists(mf):
parmfile = glob(pdb_dir + '/*.parm7')[0]
traj = pt.iterload(mf, parmfile)
epots.append(pt.energy_decomposition(traj, igb=8)['tot'][0])
else:
epots.append(None)
pt.to_pickle(epots, 'epots.pk')
# import MPI to get rank
from mpi4py import MPI
import pytraj as pt
from pytraj.testing import aa_eq
try:
import sander
comm = MPI.COMM_WORLD
# end. you are free to update anything below here
# split remd.x.000 to N cores and do calc_surf in parallel
root_dir = "../../tests/data/"
traj_name = root_dir + "tz2.nc"
parm_name = root_dir + "tz2.parm7"
# load to TrajectoryIterator
traj = pt.iterload(traj_name, parm_name)
inp = sander.gas_input(8)
# gather the data
# if rank != 0: data is None
data = pt.pmap_mpi(pt.energy_decomposition, traj, mm_options=inp)
if comm.rank == 0:
# make sure to reproduce serial output
serial_data = pt.energy_decomposition(traj, mm_options=inp)
aa_eq(pt.tools.dict_to_ndarray(data), pt.tools.dict_to_ndarray(serial_data))
except ImportError:
print('does not have sander. skip this example')
else:
pdb_dirs[index] = pdb
# get min filenames
_min_files = [
pdb_dir + '/no_restraint/' + 'min_NoH_' + x
for pdb_dir, x in zip(pdb_dirs, df[2])
]
end = '_0001'
min_files = []
for mf in _min_files:
if '0001_0001' in mf:
min_files.append(mf.replace('0001_0001', '0001') + '.rst7')
elif '0002_0001' in mf:
min_files.append(mf.replace('0002_0001', '0002') + '.rst7')
else:
min_files.append(mf)
epots = []
for pdb_dir, mf in zip(pdb_dirs, min_files):
if os.path.exists(mf):
parmfile = glob(pdb_dir + '/*.parm7')[0]
traj = pt.iterload(mf, parmfile)
epots.append(pt.energy_decomposition(traj, igb=8)['tot'][0])
else:
epots.append(None)
pt.to_pickle(epots, 'epots.pk')
import pytraj as pt
import numpy as np
traj = pt.iterload("RAN.rst7", "RAN.parm7")
print(traj.n_atoms, traj.top.n_residues)
print(pt.calc_chin(traj))
t0 = traj[:1]
deg_ene = []
flist = []
for deg in range(-180, 180, 5):
pt._rotate_dih(t0, dihtype='chin', deg=deg, resid='1')
flist.append(t0[0].copy())
en = pt.energy_decomposition(flist,
top=traj.top,
igb=8,
parm='./RAN.parm7')['dihedral']
chin = pt.calc_chin(flist, top=traj.top).values
en = en - en.min()
from matplotlib import pyplot as plt
plt.plot(chin, en, '--bo')
plt.show()
def main(argv):
args = sys.argv
native = ''
outfile = ''
try:
opts, args = getopt.getopt(sys.argv[1:], "ho:n:o:",
["in:file:n=", "out:file:scorefile="])
except getopt.GetoptError:
print('Unknown flag given.\nKnown flags:\n\t-h\n\t-n <native>')
sys.exit()
for opt, arg in opts:
if opt == '-h':
print(
'Something.py --in:file:s <input_pdb_id> --out:file:scorefile <output_filename>'
)
sys.exit()
elif opt in ("-n", "--in:file:n"):
native = arg
elif opt in ("-o", "--out:file:scorefile"):
outfile = arg
if native == '':
print('No native rst7 supplied.')
sys.exit()
if outfile == '':
outfile = 'Scores.sc'
print("===== Native RST7: %s =====" % native)
os.chdir(PATH_TO_DECOYDISC)
min_decoys = os.popen('ls min*.rst7').readlines(
) ## List of rst7s ["<rst7_1>\n", "<rst7_2>\n", ...]
for m in range(len(min_decoys)):
min_decoys[m] = min_decoys[m].rstrip()
if native in min_decoys:
min_decoys.remove(native)
print("== Analyzing %i mols==" % len(min_decoys))
min_decoys.insert(0, native)
parmfile = '_'.join(native.split('_')[1:]).rstrip('rst7') + 'parm7'
print("\t=== Loading Trajectories ===")
traj = pt.iterload(min_decoys, parmfile)
print("\t=== Getting RMSDs ===")
ca_rmsd_data = pt.rmsd(traj, mask=['@CA'])
print("\t=== Getting Energy Decomposition ===")
energy_data = pt.energy_decomposition(traj, igb=8)
print("\t\tFinished")
with open(outfile, 'w') as scorefile:
header = 'pdb\t'
for s in energy_data.keys():
header += s + '\t'
header += 'rmsd\n'
scorefile.write(header)
for pdb_index in range(len(min_decoys)):
scoreline = min_decoys[pdb_index] + '\t'
for s in energy_data.keys():
scoreline += '%s\t' % str(energy_data[s][pdb_index])
scoreline += '%s\n' % str(ca_rmsd_data[pdb_index])
scorefile.write(scoreline)
print(traj.n_atoms, traj.top.n_residues)
print(pt.multidihedral(traj).to_dict())
t0 = traj[:1]
deg_ene = []
flist = []
for deg in range(-180, 180, 5):
pt.rotate_dihedral(t0, "custom:3:omega:" + str(deg))
flist.append(t0[0].copy())
en = pt.energy_decomposition(t0,
igb=8,
prmtop=traj.top.filename)['dihedral'][0]
deg_ene.append((deg, en))
arr = np.array(deg_ene).T
pt.write_traj("test.pdb",
flist,
top=traj.top,
overwrite=True,
options='model')
arr[1] = arr[1] - np.min(arr[1])
except ImportError:
pass
# mmgbsa EGB should match (or be close): -402.71625 kcal/mol
# for first 10 frames
import pytraj as pt
traj = pt.iterload('tz2.nc', 'tz2.parm7')
gb = pt.energy_decomposition(traj, igb=8)['gb']
print(gb[0])
# import MPI to get rank
from mpi4py import MPI
import pytraj as pt
from pytraj.testing import aa_eq
try:
import sander
comm = MPI.COMM_WORLD
# end. you are free to update anything below here
# split remd.x.000 to N cores and do calc_surf in parallel
root_dir = "../../tests/data/"
traj_name = root_dir + "tz2.nc"
parm_name = root_dir + "tz2.parm7"
# load to TrajectoryIterator
traj = pt.iterload(traj_name, parm_name)
inp = sander.gas_input(8)
# gather the data
# if rank != 0: data is None
data = pt.pmap_mpi(pt.energy_decomposition, traj, mm_options=inp)
if comm.rank == 0:
# make sure to reproduce serial output
serial_data = pt.energy_decomposition(traj, mm_options=inp)
aa_eq(pt.tools.dict_to_ndarray(data),
pt.tools.dict_to_ndarray(serial_data))
except ImportError:
print('does not have sander. skip this example')
