def test_rmsfit_with_autoimage_compared_to_cpptraj(self):
# assert to cpptraj: need to set mass
traj = self.traj.copy()
txt = '''
parm {0}
trajin {1}
autoimage
rms first {2} mass
trajout tmp.nc
'''.format(traj.top.filename, traj.filename, self.mask)
with tempfolder():
state = pt.datafiles.load_cpptraj_output(txt, dtype='state')
state.run()
# need to load to memory (not iterload)
saved_traj = pt.load('tmp.nc', traj.top)
fa1 = traj[:]
fa1.autoimage()
pt.superpose(fa1, ref=0, mask=self.mask, mass=True)
aa_eq(fa1.xyz, saved_traj.xyz)
fa_saved_nowat = saved_traj['!:WAT']
fa1_nowat = fa1['!:WAT']
aa_eq(fa_saved_nowat.xyz, fa1_nowat.xyz)
def test_rmsfit_with_autoimage_compared_to_cpptraj(self):
# assert to cpptraj: need to set mass
traj = self.traj.copy()
txt = '''
parm {0}
trajin {1}
autoimage
rms first {2} mass
trajout tmp.nc
'''.format(traj.top.filename, traj.filename, self.mask)
with tempfolder():
state = pt.datafiles.load_cpptraj_output(txt, dtype='state')
state.run()
# need to load to memory (not iterload)
saved_traj = pt.load('tmp.nc', traj.top)
fa1 = traj[:]
fa1.autoimage()
pt.superpose(fa1, ref=0, mask=self.mask, mass=True)
aa_eq(fa1.xyz, saved_traj.xyz)
fa_saved_nowat = saved_traj['!:WAT']
fa1_nowat = fa1['!:WAT']
aa_eq(fa_saved_nowat.xyz, fa1_nowat.xyz)
def to_ParmEd(pytraj_top):
# TODO: exten to gromacs, charmm too
# need to change extension
"""convert to ParmEd object"""
from pytraj.utils.context import tempfolder
from pytraj.Topology import ParmFile
import parmed as chem
# I am not a fan of saving/loading again but this might be best choice
with tempfolder():
fname = "tmp_pytrajtop.prmtop"
ParmFile().writeparm(pytraj_top, fname, format="")
return chem.load_file(fname)
def prmtop_from_tleap(filename, leapin=None, verbose=False):
'''make prmtop file from pdb
Parameters
----------
filename : str, pdb filename
leapin : str, optional, default None
leap input
if None, use::
source leaprc.ff14SB
set default PBradii mbondi3
x = loadpdb {pdbfile}
saveamberparm x {pdbfile}.prmtop {pdbfile}.rst7
quit
verbose : bool, default False
if False, suppress tleap output
'''
import os
import subprocess
import pytraj as pt
if leapin is None:
leapin = leap_template
amberhome = os.environ.get('AMBERHOME')
if amberhome is None:
raise RuntimeError('must set AMBERHOME')
tleap = amberhome + '/bin/tleap'
filename = os.path.abspath(filename)
with tempfolder():
leapin = leapin.format(pdbfile=filename)
with open("tmp_leap.in", 'w') as f:
f.write(leapin)
with open(os.devnull, 'wb') as devnull:
if not verbose:
subprocess.check_call(
[tleap, ' -f tmp_leap.in'],
stdout=devnull,
stderr=subprocess.STDOUT)
else:
x = subprocess.check_call([tleap, ' -f tmp_leap.in'])
if verbose:
print(x)
return pt.load_topology("tmp.top")
def read_gaussian_output(filename=None, top=None):
"""return a `pytraj.trajectory.Trajectory` object
Parameters
----------
fname : str, filename
top : {str, Topology}, optional, default None
pytraj.Topology or a filename or None
if None, use `antechamber` to generate mol2 file, need set $AMBERHOME env
Requires
--------
cclib (``pip install cclib``)
>>> import pytraj as pt
>>> pt.tools.read_gaussian_output("gau.out", "mytest.pdb") # doctest: +SKIP
"""
import cclib
from pytraj.trajectory.trajectory import Trajectory
from pytraj.utils.context import tempfolder
from pytraj.utils.get_common_objects import get_topology
_top = get_topology(None, top)
gau = cclib.parser.Gaussian(filename)
go = gau.parse()
if _top is None: # pragma: no cover
try:
amberhome = os.environ['AMBERHOME']
except KeyError:
raise KeyError("must set AMBERHOME")
fpath = os.path.abspath(filename)
with tempfolder():
at = amberhome + "/bin/antechamber"
out = "-i %s -fi gout -o tmp.mol2 -fo mol2 -at amber" % fpath
cm = " ".join((at, out))
os.system(cm)
return Trajectory(xyz=go.atomcoords, top="tmp.mol2")
else:
return Trajectory(xyz=go.atomcoords, top=_top)
def read_gaussian_output(filename=None, top=None):
"""return a `pytraj.trajectory.Trajectory` object
Parameters
----------
fname : str, filename
top : {str, Topology}, optional, default None
pytraj.Topology or a filename or None
if None, use `antechamber` to generate mol2 file, need set $AMBERHOME env
Requires
--------
cclib (``pip install cclib``)
>>> import pytraj as pt
>>> pt.tools.read_gaussian_output("gau.out", "mytest.pdb") # doctest: +SKIP
"""
import cclib
from pytraj.trajectory import Trajectory
from pytraj.utils.context import tempfolder
from pytraj.get_common_objects import get_topology
_top = get_topology(None, top)
gau = cclib.parser.Gaussian(filename)
go = gau.parse()
if _top is None: # pragma: no cover
try:
amberhome = os.environ['AMBERHOME']
except KeyError:
raise KeyError("must set AMBERHOME")
fpath = os.path.abspath(filename)
with tempfolder():
at = amberhome + "/bin/antechamber"
out = "-i %s -fi gout -o tmp.mol2 -fo mol2 -at amber" % fpath
cm = " ".join((at, out))
os.system(cm)
return Trajectory(xyz=go.atomcoords, top="tmp.mol2")
else:
return Trajectory(xyz=go.atomcoords, top=_top)
def minimize(traj, engine='sander', input=None, top=None):
"""
>>> from pytraj.amber_wrap import minimize
>>> minimize(traj)
>>> minimize(traj, engine='pmemd')
"""
from pytraj import Trajectory
if not isinstance(traj, Trajectory):
raise ValueError("support only mutable Trajectory")
_top = get_topology(traj, top)
if input is not None:
min_in = input
else:
min_in = MIN_IN
if engine in ['sander', 'pmemd']:
_engine = "$AMBERHOME/bin/" + engine
else:
_engine = engine
with tempfolder():
with open("min.in", 'w') as fh:
fh.write(min_in)
pt.write_parm("tmp.prmtop", _top)
for frame in traj:
pt.write_traj("tmp_frame.rst7", frame, top=_top, overwrite=True)
os.system(
"%s -O -p tmp.prmtop -c tmp_frame.rst7.1 -r min.r -i min.in" %
(_engine))
f0 = pt.load("min.r", traj.top)[0]
# update coords
frame.xyz[:] = f0.xyz
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
