def reimage_traj(traj_file, traj_dir, save_dir, ext):
if ext == ".pdb":
file_lastname = traj_file.split("/")[len(traj_file.split("/")) - 1]
filename = file_lastname.split(".")[0]
h5_filename = file_lastname
new_h5_file = "%s/%s" % (save_dir, h5_filename)
if os.path.exists(new_h5_file):
print "already reimaged"
return
traj_pytraj = mdio.load(traj_file, top=traj_file)[:]
# traj_pytraj.fixatomorder()
traj_pytraj.autoimage()
traj_pytraj.save(new_h5_file)
print "saving %s" % h5_filename
else:
traj_file_lastname = traj_file.split("/")[len(traj_file.split("/")) - 1]
traj_filename = traj_file_lastname.split(".")[0]
traj_dcd = "%s/%s.dcd" % (traj_dir, traj_filename)
traj_pdb = "%s/%s.pdb" % (traj_dir, traj_filename)
traj = md.load(traj_file)
traj_frame = md.load_frame(traj_file, index=0)
traj.save_dcd(traj_dcd)
traj_frame.save_pdb(traj_pdb)
traj_pytraj = mdio.load(traj_dcd, top=traj_pdb)[:]
traj_pytraj.autoimage()
file_lastname = traj_file.split("/")[len(traj_file.split("/")) - 1]
filename = file_lastname.split(".")[0]
dcd_filename = "%s_temp.dcd" % filename
top_filename = "%s_temp.pdb" % filename
h5_filename = file_lastname
new_dcd_file = "%s/%s" % (save_dir, dcd_filename)
new_top_file = "%s/%s" % (save_dir, top_filename)
new_h5_file = "%s/%s" % (save_dir, h5_filename)
print new_dcd_file
print new_top_file
traj_pytraj.save(new_dcd_file)
traj_pytraj.save(new_top_file)
new_traj = md.load(new_dcd_file, top=traj_pdb)
new_traj.save(new_h5_file)
os.remove(traj_dcd)
os.remove(traj_pdb)
os.remove(new_dcd_file)
os.remove(new_top_file)
return
def get_frames_same_T():
# create a list of all remd trajs
flist = glob("../tests/data/Test_RemdTraj/rem.nc.*")
# make a list of TrajReadOnly instances
trajlist = []
for fh in flist:
topfile = "../tests/data/Test_RemdTraj/ala2.99sb.mbondi2.parm7"
# load trajectory and append to trajlist
trajlist.append(mdio.load(fh, topfile))
# make Trajectory instance that holds 492.2 T frames
# we need to reserve n_frames to hold the data
f4922 = Trajectory(n_frames=trajlist[0].n_frames)
assert f4922.n_frames == trajlist[0].n_frames
f4922.top = trajlist[0].top.copy()
# extract frames having T = 492.2
# use iteration for nested loops
for traj in trajlist:
for idx, frame in enumerate(traj):
if frame.temperature == 492.2:
# we don't use `append` method since we want to make sure
# frames are in the order of simulation time
f4922[idx] = frame
# make sure f4922 only hold frames having T = 492.2 K
arr0 = array(
'd',
[492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2])
assert f4922.temperatures == arr0
# make sure we reproduce cpptraj output
cpptraj = mdio.load("../tests/data/Test_RemdTraj/temp0.crd.492.20",
topfile)
print(f4922[5].coords[:10])
print(cpptraj[5].coords[:10])
for idx, framepy in enumerate(f4922):
assert_almost_equal(framepy.coords, cpptraj[idx].coords)
print("rmsd between pytraj Frame and cpptraj Frame = %s " %
framepy.rmsd(cpptraj[idx]))
# FIXME: `rmsd` do the fitting in the fly
# coords of frame would be changed
print("YES, we can reproduce cpptraj output")
def randions():
# get `traj` instance (Trajectory)
traj = load(filename="../tests/Test_RandomizeIons/adh206.tip3p.rst7.gz",
top="../tests/Test_RandomizeIons/adh206.ff10.tip3p.parm7.gz")
# get 1st frame from `traj`
frame0 = traj[0]
# randomize ions for frame0
randomize_ions(
traj=frame0,
top=traj.top,
command="randomizeions @Na+ around :1-16 by 5.0 overlap 3.0", )
# make sure to reproduce cpptraj output
savedframe = load(
filename="../tests/Test_RandomizeIons/random.crd.save",
top="../tests/Test_RandomizeIons/adh206.ff10.tip3p.parm7.gz")[0]
assert frame0.rmsd(savedframe) < 1E-3
def test_0(self):
from pytraj import io
fname = "./data/tz2.pdb"
traj = io.load(fname, fname)
ptpdb = pt.read_pdb_from_frame(traj.top, traj[0])
spdb = smd.read_pdb_saxs(fname)[0]
print (ptpdb)
print (spdb[0][0])
def randions():
# get `traj` instance (Trajectory)
traj = load(filename="../tests/Test_RandomizeIons/adh206.tip3p.rst7.gz",
top="../tests/Test_RandomizeIons/adh206.ff10.tip3p.parm7.gz")
# get 1st frame from `traj`
frame0 = traj[0]
# randomize ions for frame0
randomize_ions(
traj=frame0,
top=traj.top,
command="randomizeions @Na+ around :1-16 by 5.0 overlap 3.0",
)
# make sure to reproduce cpptraj output
savedframe = load(
filename="../tests/Test_RandomizeIons/random.crd.save",
top="../tests/Test_RandomizeIons/adh206.ff10.tip3p.parm7.gz")[0]
assert frame0.rmsd(savedframe) < 1E-3
def test_0(self):
print (smd.calc_saxs_md.__doc__)
traj0 = io.load("./data/solu.pdb", "./data/solu.pdb")
traj1 = io.load("./data/solv.pdb", "./data/solv.pdb")
@Timer()
def test():
v = smd.calc_saxs_md(solute_traj=traj0,
solvent_traj=traj1,
explicit_hydrogen=True,
dtype='ndarray')
test()
# make sure to reproduce saxs's data
v = smd.calc_saxs_md(solute_traj=traj0,
solvent_traj=traj1,
explicit_hydrogen=True,
dtype='ndarray')
import numpy as np
from pytraj.testing import aa_eq
saved_data = np.loadtxt("./data/saxs.out", skiprows=9).transpose()
print (v)
aa_eq(v, saved_data[1])
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("../tests/data/Tc5b.x",
"../tests/data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `optionsl` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def reimage(traj_dir):
new_dir = "%s_reimaged" %(traj_dir)
if not os.path.exists(new_dir):
os.makedirs(new_dir)
files = get_trajectory_files(traj_dir, ext = ".pdb")
for i in range(0, len(files)):
print i
pdb = files[i]
name = pdb.split("/")[len(pdb.split("/"))-1]
conformation = mdio.load(pdb, pdb)
f0 = conformation[0]
adict['autoimage']("", f0, conformation.top)
new_file = "%s/%s" %(new_dir, name)
mdio.save(new_file, traj = f0, top = conformation.top)
return new_dir
def reimage(traj_dir):
new_dir = "%s_reimaged" % (traj_dir)
if not os.path.exists(new_dir):
os.makedirs(new_dir)
files = get_trajectory_files(traj_dir, ext=".pdb")
for i in range(0, len(files)):
print(i)
pdb = files[i]
name = pdb.split("/")[len(pdb.split("/")) - 1]
conformation = mdio.load(pdb, pdb)
f0 = conformation[0]
adict['autoimage']("", f0, conformation.top)
new_file = "%s/%s" % (new_dir, name)
mdio.save(new_file, traj=f0, top=conformation.top)
return new_dir
def test_1(self):
from pytraj import io
import numpy as np
print ("use pytraj")
# load traj
traj = io.load("./test.pdb", "test.pdb")
n_atoms = traj.top.n_atoms
# creat dummy B-factors
b_array = np.zeros(n_atoms)
# create dummy r_array
r_array = np.asarray([atom.gb_radius for atom in traj.top])
#print (r_array[0])
# read pdb for 1st frame
pdb = read_pdb_from_frame(traj.top, traj[0], b_array, r_array)
#print (len(pdb))
#print (pdb[0])
#print (pdb)
# read dx, find all guv.* files in current folder
v_dx = sx.read_dx("./")
# v_dx is a list of dictionary
# in C++ saxs, this is a vector of struct
print (len(v_dx))
d1 = v_dx[0]
print (d1.keys())
# get info
x, y, z = d1['ngrid']
print (x * y * z)
print (d1['conc'])
print (d1['type'])
print (d1['delta'])
print (d1['origin'])
arr0 = np.asarray(d1['value'])
assert arr0.shape[0] == (x * y * z)
# calculate vcoor_max, vcoor_min: dummy example
v_max, v_min = sx.calc_extreme_pdb(pdb)
def test_0(self):
from pytraj import io
import numpy as np
print ("use pytraj")
# load traj
traj = io.load("./test.pdb", "test.pdb")
v_dx = sx.read_dx("./")
# v_dx is a list of dictionary
# in C++ saxs, this is a vector of struct
d1 = v_dx[0]
x, y, z = d1['ngrid']
print (x * y * z)
print (d1['conc'])
print (d1['type'])
print (d1['delta'])
print (d1['origin'])
arr0 = np.asarray(d1['value'])
assert arr0.shape[0] == (x * y * z)
print ("shape of grids = %s %s %s" % (x, y, z))
"""calculat RMSD for 8 replica trajs using 1 cores.
Reference frame is the 1st frame of remd.x.000
System: 17443 atoms, 1000 frames, netcdf, 8 replicas (000 to 007), 200Mb/replica
python test_serial.py
"""
import numpy as np
from pytraj import io
import pytraj.common_actions as pyca
root_dir = "../../tests/data/nogit/remd/"
top_name = root_dir + "myparm.top"
# 8 replicas, 1000 frames
size = 8
sarr = np.empty((size, 1000))
REF = None
for i in range(size):
fname = root_dir + "/remd.x.00" + str(i) # 000, 001, 002, 003 ...
straj = io.load(fname, root_dir + "/myparm.parm7")
if i == 0:
REF = straj[0]
sarr[i] = straj.calc_rmsd(REF, "@CA")
np.savetxt("./serial_rmsd.txt", sarr.flatten())
"""calculat RMSD for 8 replica trajs using 1 cores.
Reference frame is the 1st frame of remd.x.000
System: 17443 atoms, 1000 frames, netcdf, 8 replicas (000 to 007), 200Mb/replica
python test_serial.py
"""
import numpy as np
from pytraj import io
import pytraj.common_actions as pyca
root_dir = "../../tests/data/nogit/remd/"
top_name = root_dir + "myparm.top"
# 8 replicas, 1000 frames
size = 8
sarr = np.empty((size, 1000))
REF = None
for i in range(size):
fname = root_dir + "/remd.x.00" + str(i) # 000, 001, 002, 003 ...
straj = io.load(fname, root_dir + "/myparm.parm7")
if i == 0:
REF = straj[0]
sarr[i] = straj.calc_rmsd(REF, "@CA")
np.savetxt("./serial_rmsd.txt", sarr.flatten())
from pytraj import io as mdio
traj = mdio.load("../tests/data/Tc5b.x", "../tests/data/Tc5b.top")[:]
# get x coord of 0-th atom of 0-th frame
print(traj[0, 0, 0])
# get new Trajectory with only CA atoms
print(traj['@CA'])
# get new Trajectory with only CA with several frames
print(traj[2:7, '@CA'])
print(traj[[1, 5, 7, 9], '@CA'])
import numpy as np
from pytraj import io
from pytraj import Frame
import pytraj.common_actions as pyca
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.rank
size = comm.size
root_dir = "../../tests/data/nogit/remd/"
fname = root_dir + "/remd.x.00" + str(rank) # 000, 001, 002, 003 ...
top_name = root_dir + "myparm.top"
traj = io.load(fname, top_name)
n_atoms = traj.top.n_atoms
n_frames = traj.n_frames
if rank == 0:
ref = traj[0]
ref_xyz = np.asarray(ref.xyz, dtype=np.float64)
else:
ref = None
ref_xyz = np.empty((n_atoms, 3), dtype=np.float64)
# broadcast ref_xyz to other cores from master
comm.Bcast([ref_xyz, MPI.DOUBLE])
if rank != 0:
# need to reconstruct ref
# (require: mpi4py, numpy) # python serial_cal_molsurf_0.py from pytraj import io import pytraj.common_actions as pyca root_dir = "../../tests/data/nogit/remd/" traj_name = root_dir + "/remd.x.000" parm_name = root_dir + "myparm.top" traj = io.load(traj_name, parm_name) arr = pyca.calc_molsurf(traj, "@CA") print(arr[:10])
