def load_traj(TOP, TRAJ, beg_frame, end_frame, stride):
"""
Loads in topology and trajectory into VMD
Parameters
----------
TOP: MD Topology
TRAJ: MD Trajectory
beg_frame: int
end_frame: int
stride: int
Returns
-------
trajid: int
simulation molid object
"""
top_file_type = get_file_type(TOP)
traj_file_type = get_file_type(TRAJ)
trajid = molecule.load(top_file_type, TOP)
if TRAJ is not None:
molecule.read(trajid,
traj_file_type,
TRAJ,
beg=beg_frame,
end=end_frame,
skip=stride,
waitfor=-1)
else:
molecule.read(trajid,
top_file_type,
TOP,
beg=beg_frame,
end=end_frame,
skip=stride,
waitfor=-1)
return trajid
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 load_traj(top_path, traj_path):
top_file_type = getFileType(top_path)
trajid = molecule.load(top_file_type, top_path)
if (traj_path != None):
traj_file_type = getFileType(traj_path)
molecule.read(trajid,
traj_file_type,
traj_path,
beg=start,
end=stop,
skip=stride,
waitfor=-1)
def getWaterLocations(f, TOP, TRAJ, printNumFrames):
print("Start getWaterLocations()")
molid = molecule.load(getFileType(TOP), TOP)
molecule.read(molid, getFileType(TRAJ), TRAJ, beg=1, end=-1, skip=1, waitfor=-1)
n_frames = molecule.numframes(molid)
if(printNumFrames): f.write("numFrames:" + str(n_frames) + "\n")
grid = create_grid(n_frames)
print_file_header(f)
waters = atomsel.atomsel('water', molid= molid)
# waters = atomsel.atomsel('resname IP3', molid= molid)
coords = getAllCoords(molid, n_frames)
return grid, waters, coords, n_frames
def load_traj(top_path, traj_path):
"""
Load trajectory and topology into VMD display
"""
top_file_type = getFileType(top_path)
trajid = molecule.load(top_file_type, top_path)
if (traj_path != None):
traj_file_type = getFileType(traj_path)
molecule.read(trajid,
traj_file_type,
traj_path,
beg=start,
end=stop,
skip=stride,
waitfor=-1)
def load(self, filename, filetype=None, first=0, last=-1, step=1, waitfor=-1, volsets=[0]):
"""
Load molecule data from 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 coordinates frames to load,
if any.
"""
if filetype is None:
filetype = self._guessFiletype(filename)
if molecule.read(self.id, filetype, filename, first, last, step, waitfor, volsets) < 0:
raise IOError, "Unable to load file: %s" % filename
return self
def load_traj(struct_file_name, traj_file_names):
struct_file_name = struct_file_name.replace("_strip_waters", "")
top_file_type = getFileType(struct_file_name)
print("topo name", struct_file_name)
trajid = molecule.load(top_file_type, struct_file_name)
for traj_index, traj_file_name in enumerate(traj_file_names):
if (traj_index > 0): break
traj_file_name = traj_file_name.replace("_strip_waters", "")
print("traj name", traj_file_name)
traj_file_type = getFileType(traj_file_name)
molecule.read(trajid,
traj_file_type,
traj_file_name,
beg=start,
end=stop,
skip=stride,
waitfor=-1)
print("Finished Loading Trajectory")
molrep.delrep(0, 0)
if (display_mode == "-d"):
molrep.addrep(0,
style='NewRibbons',
color='ColorID 8',
selection="protein")
# molrep.addrep(0, style = 'HBonds 3.0 110', selection = 'protein and not carbon', color = 'Type')
molrep.addrep(
0,
style='HBonds 3.8 70',
selection="(water within 3.5 of protein) or protein and not carbon",
color="Type")
molrep.set_autoupdate(0, 1, 1)
elif (display_mode == "-s"):
molrep.addrep(0,
style="VDW",
selection="name CA",
material="Transparent")
else:
print("Input Format Incorrect")
exit(1)
animate.goto(0)
def load(self,
filename,
filetype=None,
first=0,
last=-1,
step=1,
waitfor=-1,
volsets=[0]):
"""
Load molecule data from 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 coordinates frames to load,
if any.
"""
if filetype is None:
filetype = self._guessFiletype(filename)
if molecule.read(self.id, filetype, filename, first, last, step,
waitfor, volsets) < 0:
raise IOError, "Unable to load file: %s" % filename
return self
if (len(sys.argv) < 4):
print "Usage: python wrapAlignAmber.py <topology file> <trajectory file> <out wrapped trajectory file>"
sys.exit()
#### 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)
ag_vmd.vmd_load_molecule(SYSPREP_LMPDAT,
style="Lines 1.000",
molid=CURCYCLE)
molrep.set_visible(CURCYCLE, 0, False)
# add representations
for CSEL in SELECTIONS:
molrep.addrep(CURCYCLE,
style=CSEL["style"],
color=CSEL["color"],
selection=CSEL["selection"],
material=CSEL["material"])
# quenching
QUENCH_DCD = QUENCH_DCD_RAW.format(MAINDIR, CURCYCLE)
molecule.read(CURCYCLE, "dcd", QUENCH_DCD, beg=0, end=-1, waitfor=-1)
# annealing - heating up
EQUIL_ANNEAL_DCD = EQUIL_ANNEAL_DCD_RAW.format(MAINDIR, CURCYCLE)
molecule.read(CURCYCLE,
"dcd",
EQUIL_ANNEAL_DCD,
beg=0,
end=-1,
waitfor=-1)
# annealing - productive
ANNEAL_DIR = "{}/anneal_{}".format(MAINDIR, CURCYCLE)
PROD_ANNEAL_DCDS = get_files(
"{0}/anneal_{1}/".format(ANNEAL_DIR, CURCYCLE),
PROD_ANNEAL_DCD_RAW.format(CURCYCLE))
#### load topology and trajectories
traj_molid = molecule.load(getFileType(top_file), top_file)
if (traj_file_type == "nc"):
traj_fragments_list = glob.glob(traj_dir + "/Prod_*/Prod_*.nc")
elif (traj_file_type == "dcdconvert"):
traj_fragments_list = glob.glob(traj_dir + "/Prod_*/Prod_*.dcd")
elif (traj_file_type == "dcd"):
traj_fragments_list = glob.glob(traj_dir + "/*.dcd")
traj_fragments_list.sort(key=natural_keys)
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)