def load_mdtraj(m_traj, autoconvert=False, top=None):
"""load_mdtraj traj object
Parameters
----------
m_traj : Trajectory object from mdtraj
autoconvert : bool, default=False
convert from "nm" (mdtraj )to "Angstrom" (pytraj)
top : pytraj.Topology, default None
if `top` is provided, the converting will be much faster
"""
import numpy as np
from mdtraj import Trajectory as MDTrajectory
from pytraj.trajectory import Trajectory
if autoconvert:
unit = 10.
else:
unit = 1.
if not isinstance(m_traj, MDTrajectory):
raise ValueError("must be mdtraj's Trajectory object")
else:
if isinstance(top, string_types):
pseudotop = _load_Topology(top)
else:
pseudotop = top
if pseudotop is None:
raise ValueError("need Topology or pdb, mol2, ... files")
traj = Trajectory(xyz=m_traj.xyz.astype('f8'), top=pseudotop)
if m_traj.unitcell_lengths is not None and m_traj.unitcell_angles is not None:
traj.unitcells = np.hstack((unit * m_traj.unitcell_lengths,
m_traj.unitcell_angles)).astype('f8')
return traj
def load_parmed(parm, traj=True, **kwd):
"""return pytraj's Topology or Trajectory objects
Parameters
----------
parm : ParmEd's Structure object
traj: bool, default True
if True, return pytraj.Trajectory
if False, return Topology
>>> import parmed as pmd
>>> import pytraj as pt
>>> p = pmd.download_PDB("1l2y")
>>> traj = pt.load_parmed(p)
"""
with tempfolder():
fname = 'tmp.parm7'
parm.save(fname)
top = _load_Topology(fname)
if traj:
from pytraj import Trajectory
coords = parm.get_coordinates()
traj = Trajectory(xyz=coords, top=top)
traj.unitcells = parm.get_box()
return traj
else:
return top
def load_mdtraj(m_traj, autoconvert=False, top=None):
"""load_mdtraj traj object
Parameters
----------
m_traj : Trajectory object from mdtraj
autoconvert : bool, default=False
convert from "nm" (mdtraj )to "Angstrom" (pytraj)
top : pytraj.Topology, default None
if `top` is provided, the converting will be much faster
"""
import numpy as np
from mdtraj import Trajectory as MDTrajectory
from pytraj.trajectory import Trajectory
from pytraj.compat import string_types
if autoconvert:
unit = 10.
else:
unit = 1.
if not isinstance(m_traj, MDTrajectory):
raise ValueError("must be mdtraj's Trajectory object")
else:
if isinstance(top, string_types):
pseudotop = _load_Topology(top)
else:
pseudotop = top
if pseudotop is None:
raise ValueError("need Topology or pdb, mol2, ... files")
traj = Trajectory(xyz=m_traj.xyz.astype('f8'), top=pseudotop)
if m_traj.unitcell_lengths is not None and m_traj.unitcell_angles is not None:
traj.unitcells = np.hstack((unit * m_traj.unitcell_lengths,
m_traj.unitcell_angles)).astype('f8')
return traj