def generateNewTrajectory(top_file_path, traj_file_path, output_traj_file_name): trajid = loadTopology(top_file_path) input_traj_file_type = getFileType(traj_file_path) molecule.read(trajid, input_traj_file_type, traj_file_path, beg=start, end=stop, skip=stride, waitfor=-1) output_traj_file_type = getFileType(output_traj_file_name) selection = atomsel.atomsel(query, molid=trajid) molecule.write(trajid, output_traj_file_type, output_traj_file_name, beg=1, end=-1, selection=selection)
def save(self, filename, filetype=None, first=0, last=-1, step=1, waitfor=-1, sel=None):
"""
Save timesteps to the given file. The filetype will be guessed from
the filename extension; this can be overridden by setting the filetype
option. first, last, and step control which timesteps to save. Returns
the number of frames written before the command completes.
"""
if filetype is None:
filetype = self._guessFiletype(filename)
####################################################
# XXX AtomSel is no longer imported automatically,
# so the following piece of code will fail when
# using the save() method with a selection.
# if the selection is an atomsel builtin type, it
# can be passed on directly. otherwise we get a
# reasonable error message. so this chunk is no
# longer needed. AK. 2009/07/21
####################################################
# if sel:
# if isinstance(sel, VMD.AtomSel.AtomSel):
# sel=sel.list()
# else:
# try:
# sel=tuple(sel)
# except:
# sel=None
####################################################
nframes = molecule.write(self.id, filetype, filename, first, last, step, waitfor, selection=sel)
if nframes < 0:
raise IOError, "Unable to save file: %s" % filename
return nframes
def write(self, filename, filetype=None):
"""Write the atoms in the selection to filename. Filetype is guessed
from the filename, or can be specified with filetype."""
if filetype is None:
filetype = 'pdb'
ind=filename.rfind('.')
if ind >= 0:
filetype = filename[ind+1:]
if molecule.write(self.__molid, filetype, filename, self.__frame, \
self.__frame, 1, -1, selection=self.__list) != 1:
raise IOError, "Unable to write selection to file '%s'." % filename
return self
def write(self, filename, filetype=None):
"""Write the atoms in the selection to filename. Filetype is guessed
from the filename, or can be specified with filetype."""
if filetype is None:
filetype = 'pdb'
ind = filename.rfind('.')
if ind >= 0:
filetype = filename[ind + 1:]
if molecule.write(self.__molid, filetype, filename, self.__frame, \
self.__frame, 1, -1, selection=self.__list) != 1:
raise IOError, "Unable to write selection to file '%s'." % filename
return self
def save(self,
filename,
filetype=None,
first=0,
last=-1,
step=1,
waitfor=-1,
sel=None):
"""
Save timesteps to the given file. The filetype will be guessed from
the filename extension; this can be overridden by setting the filetype
option. first, last, and step control which timesteps to save. Returns
the number of frames written before the command completes.
"""
if filetype is None:
filetype = self._guessFiletype(filename)
####################################################
# XXX AtomSel is no longer imported automatically,
# so the following piece of code will fail when
# using the save() method with a selection.
# if the selection is an atomsel builtin type, it
# can be passed on directly. otherwise we get a
# reasonable error message. so this chunk is no
# longer needed. AK. 2009/07/21
####################################################
# if sel:
# if isinstance(sel, VMD.AtomSel.AtomSel):
# sel=sel.list()
# else:
# try:
# sel=tuple(sel)
# except:
# sel=None
####################################################
nframes = molecule.write(self.id,
filetype,
filename,
first,
last,
step,
waitfor,
selection=sel)
if nframes < 0:
raise IOError, "Unable to save file: %s" % filename
return nframes
def save(self, filename, filetype=None, first=0, last=-1, step=1, waitfor=-1, sel=None):
"""
Save timesteps to the given file. The filetype will be guessed from
the filename extension; this can be overridden by setting the filetype
option. first, last, and step control which timesteps to save. Returns
the number of frames written before the command completes.
"""
if filetype is None:
filetype = self._guessFiletype(filename)
if sel:
if isinstance(sel, VMD.AtomSel.AtomSel):
sel=sel.list()
else:
try:
sel=tuple(sel)
except:
sel=None
nframes = molecule.write(self.id, filetype, filename, first, last, step, waitfor, selection=sel)
if nframes < 0:
raise IOError, "Unable to save file: %s" % filename
return nframes
def maeToPdb(input_mae_path, output_pdb_file_path):
molid = molecule.load('mae', input_mae_path)
molecule.write(molid, 'pdb', output_pdb_file_path)
print("Finished Conversion for: " + str(input_mae_path))
#### Read in input topology, trajectory files, outTraj file
top_file = sys.argv[1]
traj_file = sys.argv[2]
out_traj_file = sys.argv[3]
if ("-crys" in sys.argv):
include_crys = True
else:
include_crys = False
#### load topology and trajectories
traj_molid = molecule.load('pdb', top_file)
molecule.read(traj_molid, 'netcdf', traj_file, beg=0, end=-1, waitfor=-1)
#### align all frames
refsel = atomsel("protein", molid=traj_molid, frame=0)
for i in range(molecule.numframes(traj_molid)):
molecule.set_frame(traj_molid, i)
b = atomsel("protein", molid=traj_molid, frame=i)
T = b.fit(refsel)
atomsel("all", molid=traj_molid, frame=i).move(T)
#### Read out file
if (include_crys == True):
molecule.write(traj_molid, 'dcd', out_traj_file, beg=0, end=-1)
else:
molecule.write(traj_molid, 'dcd', out_traj_file, beg=1, end=-1)
toc = time.clock()
print("Time for wrapAlign.py = " + str(toc - tic))
def generateNewTopology(top_file_path, output_top_file_name): trajid = loadTopology(top_file_path) output_top_file_type = getFileType(output_top_file_name) selection = atomsel.atomsel(query, molid=trajid) molecule.write(trajid, output_top_file_type, output_top_file_name, selection=selection)
for index, traj_fragment_file in enumerate(traj_fragments_list):
print("Fragment Index " + str(index) + " : " + traj_fragment_file)
molecule.read(traj_molid,
getFileType(traj_fragment_file),
traj_fragment_file,
beg=0,
end=-1,
skip=100,
waitfor=-1)
if (traj_file_type == "dcd"):
evaltcl('package require pbctools')
evaltcl(
'pbc wrap -compound residue -center com -centersel "protein" -all')
#### align all frames
refsel = atomsel("protein", molid=traj_molid, frame=0)
for i in range(molecule.numframes(traj_molid)):
molecule.set_frame(traj_molid, i)
b = atomsel("protein", molid=traj_molid, frame=i)
T = b.fit(refsel)
atomsel("all", molid=traj_molid, frame=i).move(T)
#### Read out file
molecule.write(traj_molid,
getFileType(out_traj_file),
out_traj_file,
beg=0,
end=-1)
