def addRep(self, rep):
""" Add the given rep to the molecule. Modifications to the rep will
affect all molecules to which the rep has been added."""
if rep.molecules.has_key(self.id):
raise ValueError, "This molecule already has this rep"
molrep.addrep(self.id, style=rep.style, color=rep.color, selection=rep.selection, material=rep.material)
repid = molrep.num(self.id)-1
repname = molrep.get_repname(self.id, repid)
rep.assign_molecule(self.id, repname)
def addRep(self, rep):
""" Add the given rep to the molecule. Modifications to the rep will
affect all molecules to which the rep has been added."""
if rep.molecules.has_key(self.id):
raise ValueError, "This molecule already has this rep"
molrep.addrep(self.id,
style=rep.style,
color=rep.color,
selection=rep.selection,
material=rep.material)
repid = molrep.num(self.id) - 1
repname = molrep.get_repname(self.id, repid)
rep.assign_molecule(self.id, repname)
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 __init__(self, changes, molid, vmd_frames, window, label_before_after,
observable):
if molid not in molecule.listall():
raise RuntimeError, "Invalid molid %d" % molid
self.molid = molid
self.tk = timekeeper(molid)
self.tk.register(self)
self.disp_h = False
self.changes = {}
for time, change in changes.items():
# Map change time (frame in original trajectory file) to VMD frame
if vmd_frames is None:
vmd_time = time + 1
else:
if len(vmd_frames) != 4 or vmd_frames[0] >= vmd_frames[1] or \
vmd_frames[0] < 0 or vmd_frames[2] < 1:
raise RuntimeError, "Invalid vmd_frames input"
vmd_time = (float(time) - vmd_frames[0]) / vmd_frames[2]
if vmd_time < 0 or vmd_time > vmd_frames[1]:
continue
if vmd_frames[3]:
vmd_time += 1
self.changes[vmd_time]=change
for pair in change:
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:
if atomsel('index %d' % a0).get('element') == 'H' and \
'C' not in atomsel('withinbonds 1 of index %d'
% a0).get('element'):
self.disp_h = True
if atomsel('index %d' % a1).get('element') == 'H' and \
'C' not in atomsel('withinbonds 1 of index %d'
% a1).get('element'):
self.disp_h = True
self.change_times = sorted(self.changes.keys())
self.loaded_frames = False
# To display residues and lines in VMD
self.window = window
self.label_before_after = label_before_after
self.pairs = []
self.gray_res_sels = []
self.color_res_sels = []
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)
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)
# To plot an indicator variable with a moving line
self.fig = None
self.ax = None
self.line = None
self.observable = observable
if observable is not None:
ymin = min(observable)
ymax = max(observable)
self.ylim = (1.1 * ymin - 0.1 * ymax, 1.1 * ymax - 0.1 * ymin)
else:
self.ylim = (0,2)
else:
FINISHED_CYCLES = ITERATIONS
for CURCYCLE in FINISHED_CYCLES:
# sysprep
SYSPREP_LMPDAT = SYSPREP_LMPDAT_RAW.format(MAINDIR, CURCYCLE)
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)