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
def distance(frame):
# FIXME: this should use Selection("resid 50 and [chainname] A") which will
# be available in chemfiles 0.10 (the next release)
r50 = Selection("resid 50 and index < 1000").evaluate(frame)
r60 = Selection("resid 60 and index < 1000").evaluate(frame)
min = float('inf')
for i in r50:
for j in r60:
r = frame.distance(i, j)
if r < min:
min = r
return min
def ramachandran(frame):
phi_selection = Selection(
"dihedrals: name(#1) C and name(#2) N and name(#3) CA and name(#4) C")
phi_angles = []
for (i, j, k, m) in phi_selection.evaluate(frame):
# 57.29578 to convert from radians to degrees
phi_angles.append(frame.dihedral(i, j, k, m) * 57.29578)
psi_selection = Selection(
"dihedrals: name(#1) N and name(#2) CA and name(#3) C and name(#4) N")
psi_angles = []
for (i, j, k, m) in psi_selection.evaluate(frame):
psi_angles.append(frame.dihedral(i, j, k, m) * 57.29578)
# FIXME: the sign of the angles is inverted w.r.t. the MDAnalysis results
return phi_angles, psi_angles
def count(frame):
selection = Selection("resname ALA")
return len(selection.evaluate(frame))
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)
def test_evaluate(self):
frame = testing_frame()
selection = Selection("name H")
res = selection.evaluate(frame)
self.assertEqual(res, [0, 3])
selection = Selection("bonds: all")
res = selection.evaluate(frame)
self.assertIn((0, 1), res)
self.assertIn((1, 2), res)
self.assertIn((2, 3), res)
selection = Selection("angles: all")
res = selection.evaluate(frame)
self.assertIn((0, 1, 2), res)
self.assertIn((1, 2, 3), res)
selection = Selection("dihedrals: all")
res = selection.evaluate(frame)
self.assertEqual([(0, 1, 2, 3)], res)
def test_string(self):
self.assertEqual(Selection("name H").string, "name H")
def test_size(self):
self.assertEqual(Selection("name H").size, 1)
self.assertEqual(Selection("pairs: all").size, 2)
self.assertEqual(Selection("dihedrals: all").size, 4)
def test_copy(self):
# Just checking that we can call copy.copy on a selction
selection = Selection("name H")
copy.copy(selection)
def test_repr(self):
self.assertEqual(Selection("name H").__repr__(), "Selection('name H')")
def count(f):
len(Selection("resname ALA and name CA").evaluate(f))
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)
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))
slic.write('{}\n\n'.format(len(framework) / 5))
out.write('{}\n\n'.format(len(framework)))
for (ind, i) in enumerate(framework):
atom = frame.atom(i)
if atom.name() == "Al":
atom.set_charge(1.5750)
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))
slic.write('{}\n\n'.format(len(framework)/5))
out.write('{}\n\n'.format(len(framework)))
for (ind,i) in enumerate(framework):
atom = frame.atom(i)
if atom.name() == "Al":
atom.set_charge(1.5750)
# 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()