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
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 test_run_0(self):
# load traj
farray = pt.load(filename="./data/tz2.truncoct.nc",
top="./data/tz2.truncoct.parm7")[:2]
fold = farray.copy()
act = allactions.Action_Image()
ptrajin = """
center :2-11
image center familiar com :6
"""
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
top = farray.top
# add two actions: Action_Strip and Action_Distance
alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top)
alist.add(allactions.Action_Image(),
ArgList("center familiar com :6"),
top=top)
# do checking
alist.check_topology(top)
farray2 = Trajectory()
frame0 = Frame()
# testing how fast to do the actions
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.n_frames)"
for frame in farray:
# perform actions for each frame
# we make a copy since we want to keep orginal Frame
frame0 = frame.copy()
alist.compute(frame0)
# we need to keep the modified frame in farray2
farray2.append(frame0)
# make sure that Action_Strip does its job in stripping
assert farray2.n_frames == farray.n_frames
fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save",
"data/tz2.truncoct.parm7")
assert fsaved.n_frames == 2
def test_run_0(self):
# load traj
farray = pt.load(filename="./data/tz2.truncoct.nc",
top="./data/tz2.truncoct.parm7")[:2]
fold = farray.copy()
act = allactions.Action_Image()
ptrajin = """
center :2-11
image center familiar com :6
"""
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
top = farray.top
# add two actions: Action_Strip and Action_Distance
alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top)
alist.add(allactions.Action_Image(),
ArgList("center familiar com :6"),
top=top)
# do checking
alist.check_topology(top)
farray2 = Trajectory()
frame0 = Frame()
# testing how fast to do the actions
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.n_frames)"
for frame in farray:
# perform actions for each frame
# we make a copy since we want to keep orginal Frame
frame0 = frame.copy()
alist.compute(frame0)
# we need to keep the modified frame in farray2
farray2.append(frame0)
# make sure that Action_Strip does its job in stripping
assert farray2.n_frames == farray.n_frames
fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save",
"data/tz2.truncoct.parm7")
assert fsaved.n_frames == 2
def test_ComparetoMDtraj(self):
import mdtraj as md
traj = pt.load(filename="./data/Tc5b.x",
top="./data/Tc5b.top")
m_top = md.load_prmtop("./data/Tc5b.top")
m_traj = md.load_mdcrd("./data/Tc5b.x", m_top)
m_traj.xyz = m_traj.xyz * 10 # convert `nm` to `Angstrom` unit
arr0 = pt.rmsd(traj, ref=0)
arr1 = pt.rmsd(traj, ref=0)
arr2 = pt.rmsd(traj, )
a_md0 = md.rmsd(m_traj, m_traj, 0)
aa_eq(arr0, arr1)
aa_eq(arr0, arr2)
aa_eq(arr0, a_md0)
arr0 = pt.rmsd(traj, ref=-1)
arr1 = pt.rmsd(traj, ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1)
aa_eq(arr0, arr1)
aa_eq(arr0, a_md)
mask = ":3-18@CA,C"
atm = traj.top(mask)
arr0 = pt.rmsd(traj, ref=-1, mask=mask)
arr1 = pt.rmsd(traj, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(traj, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(traj, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
arr0 = pt.rmsd(fa, ref=-1, mask=mask)
arr1 = pt.rmsd(fa, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(fa, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(fa, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
mask = "!@H="
atm = fa.top(mask)
arr0 = pt.rmsd(fa, ref=4, mask=mask)
a_md = md.rmsd(m_traj, m_traj, 4, atm.indices)
# exclude 0-th frame for ref
aa_eq(arr0, a_md)
def test_ComparetoMDtraj(self):
import mdtraj as md
traj = pt.load(filename=tc5b_trajin, top=tc5b_top)
m_top = md.load_prmtop(tc5b_top)
m_traj = md.load_mdcrd(tc5b_trajin, m_top)
m_traj.xyz = m_traj.xyz * 10 # convert `nm` to `Angstrom` unit
arr0 = pt.rmsd(traj, ref=0)
arr1 = pt.rmsd(traj, ref=0)
arr2 = pt.rmsd(traj, )
a_md0 = md.rmsd(m_traj, m_traj, 0)
aa_eq(arr0, arr1)
aa_eq(arr0, arr2)
aa_eq(arr0, a_md0)
arr0 = pt.rmsd(traj, ref=-1)
arr1 = pt.rmsd(traj, ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1)
aa_eq(arr0, arr1)
aa_eq(arr0, a_md)
mask = ":3-18@CA,C"
atm = traj.top(mask)
arr0 = pt.rmsd(traj, ref=-1, mask=mask)
arr1 = pt.rmsd(traj, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(traj, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(traj, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
arr0 = pt.rmsd(fa, ref=-1, mask=mask)
arr1 = pt.rmsd(fa, mask=atm.indices, ref=-1)
arr2 = pt.rmsd(fa, mask=list(atm.indices), ref=-1)
arr3 = pt.rmsd(fa, mask=tuple(atm.indices), ref=-1)
a_md = md.rmsd(m_traj, m_traj, -1, atm.indices)
aa_eq(arr0, a_md)
aa_eq(arr1, a_md)
aa_eq(arr2, a_md)
aa_eq(arr3, a_md)
fa = Trajectory(traj)
mask = "!@H="
atm = fa.top(mask)
arr0 = pt.rmsd(fa, ref=4, mask=mask)
a_md = md.rmsd(m_traj, m_traj, 4, atm.indices)
# exclude 0-th frame for ref
aa_eq(arr0, a_md)
def load_MDAnalysis(universe, top=None):
"""load MDAnalysis' Universe object to pytra's traj object
Notes
-----
All coords will be loaded
See Also
--------
load_MDAnalysisIterator
"""
from MDAnalysis import Universe
from pytraj.Trajectory import Trajectory
from ..Frame import Frame
# don't import here since we import load_pseudo_parm in
# TrajectoryMDAnalysisIterator
# MDAnalysis needs numpy. So we always have numpy when using this
if not isinstance(universe, Universe):
raise ValueError("must be a Universe")
# creat pseudotop
if top is None:
raise ValueError("need a Topology or pdb/mol2/...")
else:
pseudotop = top
# creat atom group
ag = universe.atoms
farray = Trajectory()
farray.top = pseudotop
for _ in universe.trajectory:
frame = Frame(farray.top.n_atoms)
# set box for each Frame
frame.boxview[:] = farray.top.box[:]
# load xyz coords, let numpy do automatically casting
frame.xyz[:] = ag.positions
# we don't need to make copy=True since we already created
# frame and `farray` can 'keep' it
farray.append(frame, copy=False)
return farray
def load_MDAnalysis(its_obj, top=None):
"""load MDAnalysis' Universe object to pytra's traj object
Notes
-----
All coords will be loaded
See Also
--------
load_MDAnalysisIterator
"""
from MDAnalysis import Universe
from pytraj.Trajectory import Trajectory
from ..Frame import Frame
# don't import here since we import load_pseudo_parm in
# TrajectoryMDAnalysisIterator
# MDAnalysis needs numpy. So we always have numpy when using this
if not isinstance(its_obj, Universe):
raise ValueError("must be a Universe")
# creat pseudotop
if top is None:
raise ValueError("need a Topology or pdb/mol2/...")
else:
pseudotop = top
# creat atom group
ag = its_obj.atoms
farray = Trajectory()
farray.top = pseudotop
for _ in its_obj.trajectory:
frame = Frame(farray.top.n_atoms)
# set box for each Frame
frame.boxview[:] = farray.top.box[:]
# load xyz coords, let numpy do automatically casting
frame.xyz[:] = ag.positions
# we don't need to make copy=True since we already created
# frame and `farray` can 'keep' it
farray.append(frame, copy=False)
return farray
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
def load_ParmEd(parmed_obj, as_traj=False, **kwd):
"""return pytraj's Topology or Trajectory objects
Parameters
---------
parmed_obj : ParmEd's Structure object
as_traj: bool, default False
if True, return pytraj.trajectory.Trajectory
if False, return Topology
>>> import parmed as pmd
>>> import pytraj as pt
>>> p = pmd.download_PDB("1l2y")
>>> top = pt.load_ParmEd(p)
"""
import parmed as pmd
from parmed.amber import AmberParm
if isinstance(parmed_obj, string_types):
# reserve **kwd for `structure=True`
parmed_obj = pmd.load_file(parmed_obj, **kwd)
# faster
with tempfolder():
if isinstance(parmed_obj, AmberParm):
fname = 'tmp.parm7'
else:
fname = 'tmppdb.psf'
parmed_obj.save(fname)
top = _load_Topology(fname)
if as_traj:
from pytraj import Trajectory
coords = parmed_obj.coordinates
coords = coords.reshape(1, *coords.shape)
return Trajectory(xyz=coords, top=top)
else:
return top
def test_assert(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = Trajectory.from_iterable(iterframe_master(traj), top=traj.top)
for f0, f1 in zip(fa, traj):
aa_eq(f0.xyz, f1.xyz)
def test_len(self):
traj = Trajectory(fn("Tc5b.x"), tc5b_top)
top = traj.top
assert len(top) == top.n_atoms
import numpy as np
import unittest
import pytraj as pt
from pytraj.externals.six import zip
from pytraj import Topology, Trajectory, Atom
from pytraj.core.elements import mass_atomic_number_dict
from pytraj.testing import aa_eq
# local
from utils import fn
import pytest
TRAJ = Trajectory(fn("Tc5b.x"), fn("Tc5b.top"))
tc5b_top = fn('Tc5b.top')
class TestTopology(unittest.TestCase):
def test_empty_top(self):
top = Topology()
assert top.is_empty() == True
top = pt.load_topology(tc5b_top)
assert top.is_empty() == False
def test_1(self):
top = pt.load_topology(tc5b_top)
#
top.strip("!@CA")
assert top.n_atoms == 20
for atom in top.atoms:
def test_nobox(self):
from pytraj import Trajectory
traj = Trajectory()
traj._allocate(10, 10)
def test_nobox(self):
from pytraj import Trajectory
traj = Trajectory()
traj._allocate(10, 10)