def make_fake_topology(n_atoms):
'''make fake Topology, just for writing xyz array to supported formats
(netcdf, dcd, trr, ...)
>>> import pytraj as pt
>>> top = pt.tools.make_fake_topology(100)
>>> top.n_atoms
100
>>> isinstance(top, pt.Topology)
True
>>> import numpy as np
>>> xyz = np.random.rand(10*100*3).reshape(10, 100, 3)
>>> traj0 = pt.Trajectory(xyz=xyz, top=top)
>>> pt.write_traj('output/test.nc', traj0, overwrite=True)
>>> traj = pt.iterload('output/test.nc', top=top)
>>> traj.n_atoms
100
'''
from pytraj import Atom, Residue, Topology
top = Topology()
for _ in range(n_atoms):
atom = Atom(name='X', type='X', charge=0., mass=0., resid=0)
residue = Residue('Y', 0)
top.add_atom(atom, residue)
return top
def split_traj_by_residues(traj, start=0, stop=-1, step=1):
'''return a generator
Examples
--------
>>> import pytraj as pt
>>> traj = pt.datafiles.load_rna()
>>> g = pt.tools.split_traj_by_residues(traj)
>>> t0 = next(g)
>>> print(t0.top.n_residues)
1
'''
from pytraj.externals.six.moves import range
from pytraj.utils.cyutils import get_positive_idx
_stop = get_positive_idx(stop, traj.top.n_residues)
for i in range(start, _stop, step):
j = ':' + str(i + 1)
# example: traj[':3']
yield traj[j]
def n_grams(a, n):
"""n_grams
Parameters
----------
a : sequence
n : number of elements
asarray : bool, default False
if False: return an iterator
if True: return a numpy array
Examples
--------
>>> list(n_grams([2, 3, 4 ,5], 2))
[(2, 3), (3, 4), (4, 5)]
Notes
-----
adapted from: http://sahandsaba.com/thirty-python-language-features-and-tricks-you-may-not-know.html
"""
z = (islice(a, i, None) for i in range(n))
return zip(*z)