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