def test_0(self):
IDX0 = 99
IDX1 = 98
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# write pdb files for TMalign program so we can compare our result to TMalign
# ./TMalign -A test_gdt_0.pdb -B test_gdt_1.pdb
mdio.writetraj(filename="test_gdt_0.pdb",
traj=traj[IDX0],
top=traj.top,
overwrite=True)
mdio.writetraj(filename="test_gdt_1.pdb",
traj=traj[IDX1],
top=traj.top,
overwrite=True)
# do our calculation
# score = 'gdtscore', 'tmscore' or 'maxsub'
score = 'tmscore'
print '%s = %s ' % (
score,
calc_score(traj[IDX0], traj[IDX1], "@CA", traj.top, score=score) /
1000.)
print calc_score(traj[IDX1], traj[IDX0], "@CA", traj.top,
score=score) / 1000.
# calculate RMSD
print "rmsd = ", traj[IDX0].rmsd(traj[IDX1])
def test_load_and_save_0(self):
print "test_load_and_save"
# need to load to FrameArray to save
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")[:]
trajiter = mdio.iterload(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top",
chunk=100)
print trajiter
print traj.size
indices = range(20, 30, 5) + [103, 78, 90, 82]
print type(indices)
print indices
mdio.writetraj(filename="./output/test_io_saved_.x",
traj=traj[:],
top="./data/Tc5b.top",
indices=indices,
overwrite=True)
# check frames
traj2 = mdio.load(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
print "test_load_and_save_0"
print traj2.size
print traj2.is_empty()
print len(indices)
assert traj2.size == len(indices)
def main():
# set frame index
IDX0 = 99
IDX1 = 98
# load traj
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# write pdb files for TMalign program so we can compare our results to TMalign
# ./TMalign -A test_gdt_0.pdb -B test_gdt_1.pdb
# turn off those if you don't like
mdio.writetraj(filename="test_gdt_0.pdb",
traj=traj[IDX0],
top=traj.top,
overwrite=True)
mdio.writetraj(filename="test_gdt_1.pdb",
traj=traj[IDX1],
top=traj.top,
overwrite=True)
# do our calculation
# option:
# score = 'gdtscore', 'tmscore' or 'maxsub'
# "@CA" : follow AMBER mask, change it if needed
score = 'tmscore'
print '%s = %s ' % (
score, calc_score(traj[IDX0], traj[IDX1], "@CA", traj.top,
score=score) / 1000.)
print calc_score(traj[IDX1], traj[IDX0], "@CA", traj.top,
score=score) / 1000.
def test_save_traj_from_file(self):
Trajout().help()
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")[:5]
print traj.size
mdio.writetraj(filename="test_0.binpos",
traj=traj,
top="./data/Tc5b.top",
fmt="BINPOS",
overwrite=True)
savedtraj = mdio.load("./test_0.binpos", traj.top)
print "test_0.binpos size = ", savedtraj.size
print traj.size
assert savedtraj.size == traj.size
def test_load_and_save_0(self):
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")[:110]
indices = range(20, 30, 5) + [103, 78, 90, 82]
print indices
#for i in indices:
# print traj[i]
mdio.writetraj(filename="./output/test_io_saved_.x",
traj=traj,
top="./data/Tc5b.top",
indices=indices,
overwrite=True)
# check frames
traj2 = mdio.load(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
# TODO : check error
assert traj2.size == len(indices)
def test_2(self):
"""test write FrameArray"""
farray = FrameArray("data/md1_prod.Tc5b.x",
"./data/Tc5b.top",
indices=range(10))
writetraj("test_write_output.x", farray, farray.top, overwrite=True)
writetraj("test_pdb_1.dummyext",
farray[0],
farray.top,
overwrite=True,
fmt='pdb')
# test 'save'
print farray
farray.save("test_write_output_save_method.x", overwrite=True)
# reproduce result?
f0 = mdio.load("test_write_output.x", "./data/Tc5b.top")
f1 = mdio.load("test_write_output_save_method.x", "./data/Tc5b.top")
from numpy.testing import assert_almost_equal as assert_ae
assert_ae(f0[:, :, :], f1[:, :, :])
def test_load_and_save_1(self):
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")
trajiter = mdio.iterload(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top",
chunk=100)
print trajiter
indices = range(20, 30, 5) + [103, 78, 90, 82]
mdio.writetraj(filename="./output/test_io_saved.pdb",
traj=traj,
top="./data/Tc5b.top",
fmt='pdbfile',
indices=indices,
overwrite=True)
# check frames
traj = mdio.load(filename="./output/test_io_saved.pdb",
top="./data/Tc5b.top")
assert traj.size == len(indices)
assert traj.top.n_atoms == 304
def test_action(self):
distaction = allactions.Action_Distance()
boxaction = allactions.Action_Box()
boxaction.help()
toplist = TopologyList()
framelist = FrameList()
dsetlist = DataSetList()
dflist = DataFileList()
# add stuff
toplist.add_parm("./data/Tc5b.top")
framelist.add_reference(ArgList("./data/Tc5b.nat.crd"), toplist)
distaction.read_input(ArgList(":2@CA :10@CA"), toplist, framelist,
dsetlist, dflist, 0)
boxaction.read_input(ArgList("x 1000. y 1000. alpha 500."), toplist,
framelist, dsetlist, dflist, 0)
distaction.process(toplist[0])
idx = 0
farray = FrameArray("./data/Tc5b.nat.crd", "./data/Tc5b.top")
distaction.do_action(0, farray[idx])
frame0 = farray[idx]
# update Frame instance with new Box info
boxaction.do_action(idx, frame0)
print frame0.get_box()
mdio.writetraj(filename="test_withbox.r",
traj=frame0,
top=farray.top,
fmt='AMBERRESTART',
overwrite=True)
frame0.set_nobox()
print frame0.get_box()
mdio.writetraj(filename="test.r",
traj=frame0,
top=farray.top,
fmt='AMBERRESTART',
overwrite=True)
def test_strip_atoms(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
frame1 = traj[1]
frame2 = traj[2]
frame3 = traj[3]
frame1 = frame0.strip_atoms("!@CA", traj.top, copy=True)
frame2 = Frame(frame0)
print frame2.n_atoms
print frame1.n_atoms
print frame1
assert frame1.n_atoms == 20
assert frame0.n_atoms == 304
frame0.strip_atoms("!@CA", traj.top, copy=False)
assert frame0.n_atoms == 20
_, mat, v1, v2 = frame2.rmsd(frame3, get_mvv=True)
print mat, v1, v2
print frame2[:10]
print mdio.writetraj("./test_0_before.pdb", traj=frame2, top=traj.top, overwrite=True)
frame2.trans_rot_trans(v1, mat, v2)
print frame2[:10]
print mdio.writetraj("./test_0_afeter.pdb", traj=frame2, top=traj.top, overwrite=True)
print Trajout().help()
from pycpptraj import io as mdio
from pycpptraj import Trajout
Trajout().help()
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# etract first 10 frames and write to CHARMM format
subtraj = traj[:10]
mdio.writetraj(filename="./output/subtraj_0_CHARMM.dcd", traj=subtraj,
top=traj.top,
fmt="CHARMMDCD",
overwrite=True)
# make sure we can load the traj,
# use AMBER top is fine
charmm_traj = mdio.load("./output/subtraj_0_CHARMM.dcd", "./data/Tc5b.top")
# calculate rmsd between old and saved traj for 1st frame
print charmm_traj[0].rmsd(subtraj[0])
assert charmm_traj[0].rmsd(subtraj[0]) < 1E-6
# another way
subtraj.save("./output/subtraj_1_CHARMM.dcd", overwrite=True)
charmm_traj_1 = mdio.load("./output/subtraj_1_CHARMM.dcd", "./data/Tc5b.top")
print charmm_traj_1[0].rmsd(subtraj[0])
assert charmm_traj_1[0].rmsd(subtraj[0]) < 1E-6
