def chemfile_read(self,filename,format_='LAMMPS Data'):
data = Trajectory(filename,format=format_)
frame=data.read()
topology=frame.topology
self.numberatom_permole=int(len(frame.atoms)/self.system.Number_Moles)
self.atoms=frame.atoms
self.bonds=topology.bonds[0:int(topology.bonds.shape[0]/self.system.Number_Moles)]+1
self.angles=topology.angles[0:int(topology.angles.shape[0]/self.system.Number_Moles)]+1
self.dihedrals=topology.dihedrals[0:int(topology.dihedrals.shape[0]/self.system.Number_Moles)]+1
def test_repr(self):
with Trajectory(get_data_path("topology.xyz")) as trajectory:
expected = "Trajectory('" + get_data_path(
"topology.xyz") + "', 'r', '')"
self.assertEqual(trajectory.__repr__(), expected)
with Trajectory(get_data_path("topology.xyz"), "r",
"XYZ") as trajectory:
expected = "Trajectory('" + get_data_path(
"topology.xyz") + "', 'r', 'XYZ')"
self.assertEqual(trajectory.__repr__(), expected)
with Trajectory("test-tmp.xyz", "w") as trajectory:
self.assertEqual(trajectory.__repr__(),
"Trajectory('test-tmp.xyz', 'w', '')")
os.unlink("test-tmp.xyz")
def test_errors(self):
with remove_warnings:
self.assertRaises(ChemfilesError, Trajectory,
get_data_path("not-here.xyz"))
self.assertRaises(ChemfilesError, Trajectory,
get_data_path("empty.unknown"))
with Trajectory("test-tmp.xyz", "w") as trajectory:
self.assertRaises(AttributeError, trajectory.write, None)
os.unlink("test-tmp.xyz")
def test_indexes(self):
# Create an input file
frame = Frame()
for i in range(120):
frame.add_atom(Atom('X'), [i % 10, i + 1 % 10, i + 2 % 10])
with Trajectory("filename.xyz", "w") as file:
file.write(frame)
path = os.path.join(ROOT, "..", "examples", "indexes.py")
# disable output
exec(open(path).read(), globals(), {'print': lambda _: None})
def test_select(self):
# Create an input file
frame = Frame()
NAMES = ["N", "Zn", "C", "O"]
for i in range(120):
frame.add_atom(Atom(NAMES[i % 4]),
[i % 10, i + 1 % 10, i + 2 % 10])
with Trajectory("input.arc", "w") as file:
file.write(frame)
path = os.path.join(ROOT, "..", "examples", "select.py")
exec(open(path).read(), globals())
def test_last_error(self):
chemfiles.misc._clear_errors()
self.assertEqual(chemfiles.misc._last_error(), "")
try:
with remove_warnings:
Trajectory("noextention")
except ChemfilesError:
pass
self.assertEqual(
chemfiles.misc._last_error(),
"file at 'noextention' does not have an extension, provide a "
"format name to read it",
)
chemfiles.misc._clear_errors()
self.assertEqual(chemfiles.misc._last_error(), "")
def test_write(self):
frame = Frame()
for i in range(4):
frame.add_atom(Atom("X"), [1, 2, 3])
with Trajectory("test-tmp.xyz", "w") as fd:
fd.write(frame)
expected_content = """4
Written by the chemfiles library
X 1 2 3
X 1 2 3
X 1 2 3
X 1 2 3
"""
with open("test-tmp.xyz") as fd:
self.assertEqual(fd.read(), expected_content)
os.unlink("test-tmp.xyz")
def test_warning(self):
def callback(message):
global LAST_MESSAGE
LAST_MESSAGE = message
chemfiles.set_warnings_callback(callback)
try:
Trajectory("noextention")
except ChemfilesError:
pass
self.assertEqual(
LAST_MESSAGE,
"file at 'noextention' does not have an extension, provide a "
"format name to read it",
)
chemfiles.misc._set_default_warning_callback()
def test_warning_with_exception(self):
def callback(message):
global LAST_MESSAGE
LAST_MESSAGE = message
raise Exception("test exception in callback")
chemfiles.set_warnings_callback(callback)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
try:
Trajectory("noextention")
except ChemfilesError:
pass
self.assertEqual(
LAST_MESSAGE,
"file at 'noextention' does not have an extension, provide a "
"format name to read it",
)
chemfiles.misc._set_default_warning_callback()
from chemfiles import Trajectory
file = Trajectory("filename.xyz")
frame = file.read()
print("There are {} atoms in the frame".format(len(frame.atoms)))
positions = frame.positions
# Do awesome science here with the positions
if frame.has_velocities():
velocities = frame.velocities
# If the file contains information about the
# velocities, you will find them here.
import numpy as np
import math
from chemfiles import Trajectory, UnitCell, Atom, Topology, Frame, Selection
name = 'nt12-24-full.trj_wrap' #name of the trajectory wrapped around the nanotube axis
a = 24 #the a box length
# Read the traj
trajectory = Trajectory(name + '.xyz')
# Set the topology
topo = Trajectory("topology.pdb").read()
trajectory.set_topology(topo.topology())
# Select all
selection = Selection("all")
Ral = 6.5
with Trajectory(name + '_flat.xyz', 'w') as output:
for frame in trajectory:
nt = selection.evaluate(frame)
positions = frame.positions()
for atom in nt:
x = positions[atom][0]
y = positions[atom][1]
r = math.sqrt(x * x + y * y)
theta = math.atan2(y, x)
# This file is an example for the chemfiles library
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/usr/bin/env python
from chemfiles import Trajectory, Selection
trajectory = Trajectory("input.arc")
output = Trajectory("output.pdb", 'w')
selection = Selection("name Zn or name N")
for frame in trajectory:
to_remove = selection.evaluate(frame)
for i in reversed(sorted(to_remove)):
frame.remove(i)
output.write(frame)
# Benchmark the parsing of a mmCIF file given as an argument
import sys
import time
from chemfiles import Trajectory
mmcif_filepath = sys.argv[1]
start = time.time()
trajectory = Trajectory(mmcif_filepath, 'r', 'mmCIF')
for frame in trajectory:
pass
end = time.time()
print(end - start)
def test_close(self):
trajectory = Trajectory(get_data_path("water.xyz"))
trajectory.close()
self.assertRaises(ChemfilesError, trajectory.read)
from chemfiles import Trajectory, UnitCell, Atom, Topology, Frame, Selection
name = "nt12.opt"
a = 24.2
# Read the frame
frame = Trajectory(name+".xyz").read()
# Set the topology
topo = Trajectory("topology.pdb").read()
frame.set_topology(topo.topology())
# Get the positions
positions = frame.positions()
# Set the cell
cell = UnitCell(a, a, 42.43, 90, 90, 120)
frame.set_cell(cell)
# Select all except hydroxyl groups
#selection = Selection("atoms: name Al or name Obr or name Si")
selection = Selection("atoms: name Hext or name Oext or name Al or name Obr or name Si")
framework = selection.evaluate(frame)
with open(name+".cris",'w') as cris:
with open(name+".slice.xyz",'w') as slic:
with open(name+".framework.xyz",'w') as out:
cris.write(" .false.\n")
cris.write('{} {} 8.486 90.0 90.0 120.0\n'.format(a, a))
cris.write('{}\n'.format(len(framework)/5))
# Benchmark the parsing of a PDB file given as an argument
import sys
import time
from chemfiles import Trajectory
pdb_filepath = sys.argv[1]
start = time.time()
trajectory = Trajectory(pdb_filepath)
for frame in trajectory:
pass
end = time.time()
print(end - start)
import numpy as np
import math
from chemfiles import Trajectory, UnitCell, Atom, Topology, Frame, Selection
name='nt12-24-full.trj_wrap' #name of the trajectory wrapped around the nanotube axis
a=24 #the a box length
# Read the traj
trajectory = Trajectory(name+'.xyz')
# Set the topology
topo = Trajectory("topology.pdb").read()
trajectory.set_topology(topo.topology())
# Select all
selection = Selection("all")
Ral=6.5
with Trajectory(name+'_flat.xyz','w') as output:
for frame in trajectory:
nt = selection.evaluate(frame)
positions = frame.positions()
for atom in nt:
x=positions[atom][0]
y=positions[atom][1]
r=math.sqrt(x*x+y*y)
theta=math.atan2(y,x)
#!/usr/bin/env python
import numpy as np
from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory
topology = Topology()
topology.atoms.append(Atom("H"))
topology.atoms.append(Atom("O"))
topology.atoms.append(Atom("H"))
topology.add_bond(0, 1)
topology.add_bond(2, 1)
frame = Frame()
frame.resize(3)
frame.topology = topology
frame.positions[0, :] = np.array([1.0, 0.0, 0.0])
frame.positions[1, :] = np.array([0.0, 0.0, 0.0])
frame.positions[2, :] = np.array([0.0, 1.0, 0.0])
frame.add_atom(Atom("O"), [5.0, 0.0, 0.0])
frame.add_atom(Atom("C"), [6.0, 0.0, 0.0])
frame.add_atom(Atom("O"), [7.0, 0.0, 0.0])
frame.add_bond(3, 4)
frame.add_bond(4, 5)
frame.cell = UnitCell(10, 10, 10)
with Trajectory("water-co2.pdb", 'w') as trajectory:
trajectory.write(frame)
# This trajectory is an example for the chemtrajectorys library
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/usr/bin/env python
from chemfiles import Trajectory
trajectory = Trajectory("filename.xyz")
frame = trajectory.read()
less_than_five = []
positions = frame.positions()
for i in range(len(frame)):
if positions[i, 0] < 5:
less_than_five.append(i)
print("Atoms with x < 5: ")
for i in less_than_five:
print(" - {}".format(i))
# This trajectory is an example for the chemtrajectorys library
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/usr/bin/env python
from chemfiles import Trajectory
with Trajectory("filename.xyz") as trajectory:
frame = trajectory.read()
less_than_five = []
for i in range(len(frame.atoms)):
if frame.positions[i, 0] < 5:
less_than_five.append(i)
print("Atoms with x < 5: ")
for i in less_than_five:
print(" - {}".format(i))
from chemfiles import Trajectory, UnitCell, Atom, Topology, Frame, Selection
name = "nt12.opt"
a = 24.2
# Read the frame
frame = Trajectory(name + ".xyz").read()
# Set the topology
topo = Trajectory("topology.pdb").read()
frame.set_topology(topo.topology())
# Get the positions
positions = frame.positions()
# Set the cell
cell = UnitCell(a, a, 42.43, 90, 90, 120)
frame.set_cell(cell)
# Select all except hydroxyl groups
#selection = Selection("atoms: name Al or name Obr or name Si")
selection = Selection(
"atoms: name Hext or name Oext or name Al or name Obr or name Si")
framework = selection.evaluate(frame)
with open(name + ".cris", 'w') as cris:
with open(name + ".slice.xyz", 'w') as slic:
with open(name + ".framework.xyz", 'w') as out:
cris.write(" .false.\n")
cris.write('{} {} 8.486 90.0 90.0 120.0\n'.format(a, a))
cris.write('{}\n'.format(len(framework) / 5))
def parse(filepath):
t = Trajectory(filepath)
for _ in range(t.nsteps):
t.read()
return 0, 0, 0, 0, 0, 0, 0
if state == 8:
return x, y, x, y - 1, x, y, height + 1
if state == 9:
return x, y, x + 0.866, y + 0.5, x, y, height + 1
if state == 10:
return x, y, x - 0.866, y + 0.5, x, y, height + 1
if state == 11:
return x, y, x, y - 1, x + 0.866, y + 0.5, height
if state == 12:
return x, y, x - 0.866, y + 0.5, x + 0.866, y + 0.5, height
if state == 13:
return x, y, x - 0.866, y + 0.5, x, y - 1, height
with Trajectory('conf.xyz', 'w') as output:
with open('conf.dat', 'r') as conf:
ring = 0
skip = 0
for line in conf:
if line.startswith("Step:") and skip % 100 == 0:
frame = Frame()
ring = 0
elif line.startswith("####"):
if skip % 100 == 0:
output.write(frame)
skip += 1
elif skip % 100 == 0:
row = map(int, line.split())
for column, state in enumerate(row):
if state < 7:
def test_read(self):
trajectory = Trajectory(get_data_path("water.xyz"))
self.assertEqual(trajectory.nsteps, 100)
self.assertEqual(trajectory.path, get_data_path("water.xyz"))
frame = trajectory.read()
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.positions[0].all(),
np.array([0.417219, 8.303366, 11.737172]).all())
self.assertEqual(frame.positions[124].all(),
np.array([5.099554, -0.045104, 14.153846]).all())
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.atoms[0].name, "O")
self.assertEqual(frame.atoms[1].name, "H")
trajectory.set_cell(UnitCell(30, 30, 30))
frame = trajectory.read_step(41)
self.assertEqual(frame.cell.lengths, (30.0, 30.0, 30.0))
self.assertEqual(frame.positions[0].all(),
np.array([0.761277, 8.106125, 10.622949]).all())
self.assertEqual(frame.positions[124].all(),
np.array([5.13242, 0.079862, 14.194161]).all())
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.topology.bonds_count(), 0)
frame.guess_bonds()
self.assertEqual(frame.topology.bonds_count(), 181)
self.assertEqual(frame.topology.angles_count(), 87)
topology = Topology()
for i in range(297):
topology.atoms.append(Atom("Cs"))
trajectory.set_topology(topology)
frame = trajectory.read_step(10)
self.assertEqual(frame.atoms[10].name, "Cs")
trajectory.set_topology(get_data_path("topology.xyz"), "XYZ")
frame = trajectory.read()
self.assertEqual(frame.atoms[100].name, "Rd")
def test_read(self):
trajectory = Trajectory(get_data_path("water.xyz"))
self.assertEqual(trajectory.nsteps, 100)
self.assertEqual(trajectory.path, get_data_path("water.xyz"))
frame = trajectory.read()
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(
frame.positions[0].all(),
np.array([0.417219, 8.303366, 11.737172]).all()
)
self.assertEqual(
frame.positions[124].all(),
np.array([5.099554, -0.045104, 14.153846]).all()
)
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.atoms[0].name, "O")
self.assertEqual(frame.atoms[1].name, "H")
trajectory.set_cell(UnitCell(30, 30, 30))
frame = trajectory.read_step(41)
self.assertEqual(frame.cell.lengths, (30.0, 30.0, 30.0))
self.assertEqual(
frame.positions[0].all(),
np.array([0.761277, 8.106125, 10.622949]).all()
)
self.assertEqual(
frame.positions[124].all(),
np.array([5.13242, 0.079862, 14.194161]).all()
)
self.assertEqual(len(frame.atoms), 297)
self.assertEqual(frame.topology.bonds_count(), 0)
frame.guess_bonds()
self.assertEqual(frame.topology.bonds_count(), 181)
self.assertEqual(frame.topology.angles_count(), 87)
topology = Topology()
for i in range(297):
topology.atoms.append(Atom("Cs"))
trajectory.set_topology(topology)
frame = trajectory.read_step(10)
self.assertEqual(frame.atoms[10].name, "Cs")
trajectory.set_topology(get_data_path("topology.xyz"), "XYZ")
frame = trajectory.read()
self.assertEqual(frame.atoms[100].name, "Rd")
# Benchmark the counting of alanine residues in a PDB file
import time
from chemfiles import Trajectory, Selection
def count(frame):
selection = Selection("resname ALA")
return len(selection.evaluate(frame))
pdb_filepath = "data/1AKE.pdb"
frame = Trajectory(pdb_filepath).read()
start = time.time()
count(frame)
end = time.time()
print(end - start)
def test_protocols(self):
with Trajectory(get_data_path("water.xyz")) as trajectory:
for frame in trajectory:
self.assertEqual(len(frame.atoms), 297)
def test_close(self):
trajectory = Trajectory(get_data_path("water.xyz"))
trajectory.close()
self.assertRaises(ChemfilesError, trajectory.read)
import sys
from shared import timeit
from chemfiles import Selection, Trajectory
def distance(f):
ai = Selection("resid 50").evaluate(f)
bi = Selection("resid 60").evaluate(f)
min_dist = float("inf")
for i in ai:
for j in bi:
d = f.distance(i, j)
if d < min_dist:
min_dist = d
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
f = Trajectory(pdbfile).read()
print(timeit(distance, f, repeats=repeats))
# Benchmark the parsing of a MMTF file given as an argument
import sys
import time
from chemfiles import Trajectory
mmtf_filepath = sys.argv[1]
start = time.time()
trajectory = Trajectory(mmtf_filepath)
for frame in trajectory:
pass
end = time.time()
print(end - start)
import numpy as np
from chemfiles import Topology, Frame, Atom, UnitCell, Trajectory
topology = Topology()
topology.add_atom(Atom("H"))
topology.add_atom(Atom("O"))
topology.add_atom(Atom("H"))
topology.add_bond(0, 1)
topology.add_bond(2, 1)
frame = Frame()
frame.resize(3)
frame.set_topology(topology)
positions = frame.positions()
positions[0, :] = np.array([1.0, 0.0, 0.0])
positions[1, :] = np.array([0.0, 0.0, 0.0])
positions[2, :] = np.array([0.0, 1.0, 0.0])
frame.add_atom(Atom("O"), [5.0, 0.0, 0.0])
frame.add_atom(Atom("C"), [6.0, 0.0, 0.0])
frame.add_atom(Atom("O"), [7.0, 0.0, 0.0])
frame.add_bond(3, 4)
frame.add_bond(4, 5)
frame.set_cell(UnitCell(10, 10, 10))
trajectory = Trajectory("water-co2.pdb", 'w')
trajectory.write(frame)
# This file is an example for the chemfiles library
# Any copyright is dedicated to the Public Domain.
# http://creativecommons.org/publicdomain/zero/1.0/
#!/usr/bin/env python
from chemfiles import Trajectory, Selection
trajectory = Trajectory("input.arc")
output = Trajectory("output.pdb", 'w')
selection = Selection("name Zn or name N")
for frame in trajectory:
to_remove = selection.evaluate(frame)
for i in reversed(sorted(to_remove)):
frame.remove(i)
output.write(frame)
trajectory.close()
output.close()