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 replot(self):
if self.fig is None or self.ax is None:
return
self.ax.cla()
self.ax.set_xlabel('Frame')
if self.observable is not None:
self.ax.plot(self.observable, 'r.')
self.ax.plot(self.change_times, 0.5 * (self.ylim[0] + self.ylim[1])
* np.ones(len(self.change_times)), 'ro')
self.ax.set_xlim((0, molecule.numframes(self.molid)))
self.ax.set_ylim(self.ylim)
self.fig.canvas.draw()
self.dataplot = self.fig.canvas.copy_from_bbox(self.ax.bbox)
def numFrames(self): """ Returns the number of coordinate frames in the molecule. """ return molecule.numframes(self.id)
#### 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 set_times(molid, times):
import molecule
offset = molecule.numframes(molid) - len(times)
assert offset == 1 or offset == 0 # frame 0 may be the system file
for i, t in enumerate(times):
molecule.set_physical_time(t, molid, i+offset)
def showtime(self, frame, old_frame):
if not self.loaded_frames:
# Initialize display
self.loaded_frames = True
numframes = molecule.numframes(self.molid)
self.pairs = [set() for i in range(numframes)]
self.gray_res_sels = ['none' for i in range(numframes)]
self.color_res_sels = ['none' for i in range(numframes)]
first_frame = 0
for i, time in enumerate(self.change_times):
while first_frame < numframes and first_frame < time:
first_frame += 1
if first_frame > numframes - min(6, self.window + 1):
break
if first_frame < min(5, self.window):
continue
begin = max(first_frame - self.window, 0)
for j in range(i-1,-1,-1):
if self.change_times[j] <= begin:
break
if len(self.changes[self.change_times[j]] & self.changes[self.change_times[i]]) > 0:
begin = 0
while begin < first_frame and begin < self.change_times[j]:
begin += 1
break
end = min(first_frame + self.window, numframes)
for j in range(i+1, len(self.change_times)):
if self.change_times[j] > end-1:
break
if len(self.changes[self.change_times[j]] & self.changes[self.change_times[i]]) > 0:
end = numframes
while end > first_frame and end-1 >= self.change_times[j]:
end -= 1
break
if begin >= first_frame or end <= first_frame + 1:
continue
all_changed = []
for pair in self.changes[time]:
a0_all = self._info_to_ids(pair[0])
a1_all = self._info_to_ids(pair[1])
for a0 in a0_all:
for a1 in a1_all:
before_dists = [float(v) for v in vmd.VMDevaltcl(
'measure bond {%d %d} molid %d first %d last %d'
% (a0, a1, self.molid, begin,
first_frame-1)).split()]
before_med = np.median(before_dists)
after_dists = [float(v) for v in vmd.VMDevaltcl(
'measure bond {%d %d} molid %d first %d last %d'
% (a0, a1, self.molid, first_frame,
end-1)).split()]
after_med = np.median(after_dists)
if self.label_before_after is not None:
label_before, label_after = \
self.label_before_after(
before_med, after_med, a0, a1)
else:
label_before = False
label_after = False
if label_before:
self.pairs[first_frame-1].add((a0,a1))
if label_after:
self.pairs[first_frame].add((a0,a1))
all_changed += list(a0_all) + list(a1_all)
for f in range(begin, end):
sel = 'same residue as index'
for changed_atom in all_changed:
sel += ' %d' % changed_atom
if self.disp_h:
sel = ' or (%s)' % sel
else:
sel = ' or ((' + sel + ') and not (element H and' + \
' withinbonds 1 of element C))'
if f == first_frame - 1 or f == first_frame:
self.color_res_sels[f] += sel
else:
self.gray_res_sels[f] += sel
old_frame = None
gray_repid = molrep.repindex(self.molid, self.gray_rep)
if gray_repid == -1:
# User deleted molrep to display residues--recreate this molrep
molrep.addrep(self.molid, style='Licorice', color='ColorID 2',
selection='none', material='Opaque')
self.gray_rep = molrep.get_repname(self.molid,
molrep.num(self.molid)-1)
gray_repid = molrep.repindex(self.molid, self.gray_rep)
old_frame = None
color_repid = molrep.repindex(self.molid, self.color_rep)
if color_repid == -1:
# User deleted molrep to display residues--recreate this molrep
molrep.addrep(self.molid, style='Licorice', color='Element',
selection='none', material='Opaque')
self.color_rep = molrep.get_repname(self.molid,
molrep.num(self.molid)-1)
color_repid = molrep.repindex(self.molid, self.color_rep)
old_frame = None
if old_frame is None \
or self.gray_res_sels[old_frame] != self.gray_res_sels[frame]:
molrep.modrep(self.molid, gray_repid, sel=self.gray_res_sels[frame])
if old_frame is None or \
self.color_res_sels[old_frame] != self.color_res_sels[frame]:
molrep.modrep(self.molid, color_repid,
sel=self.color_res_sels[frame])
if old_frame is None or self.pairs[old_frame] != self.pairs[frame]:
labels = label.listall(label.BOND)
for l in labels:
label.delete(label.BOND, l)
os.environ['VMD_QUIET_STARTUP'] = '1'
molid_pair = (self.molid, self.molid)
for pair in self.pairs[frame]:
label.add(label.BOND, molid_pair, pair)
os.environ.pop('VMD_QUIET_STARTUP')
# Update plot of indicator variable
if self.fig is None or self.fig.canvas.window is None:
# Figure has not been created or was closed by user--create new
# figure
self.fig = plt.figure()
# Need to replot everything if the figure window is resized
self.fig.canvas.mpl_connect('resize_event', lambda ev,
s=self: s.replot())
self.fig.show()
self.ax = self.fig.add_subplot(111)
self.line = self.ax.axvline(0, animated=True, color='r',
linewidth=2)
self.replot()
self.fig.canvas.restore_region(self.dataplot)
self.line.set_xdata(frame)
self.ax.draw_artist(self.line)
self.fig.canvas.blit(self.ax.bbox)
def numFrames(self):
""" Returns the number of coordinate frames in the molecule. """
return molecule.numframes(self.id)