def vmd_load_molecule(coordsfile,
filetype="lammpsdata",
dcd=None,
selection="all",
scale=1.0,
molid=0,
vmd_material="Basic1Pantone",
style="CPK 1.000000 0.300000 12.000000 12.000000"):
"""
"""
if not molecule.exists(molid):
# load molecule in vmd
if dcd is not None:
molecule.load(filetype, coordsfile, "dcd", dcd)
else:
molecule.load(filetype, coordsfile)
molrep.modrep(molid,
0,
style=style,
material=vmd_material,
color="Name",
sel=selection)
#trans.scale(scale)
VMD.evaltcl("scale to {}".format(scale))
def changeMaterial(self, material):
""" Change the material for the rep to 'material'."""
for id,name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, material=material):
raise ValueError, "Invalid material'%s'" % material
self.material = str(material)
def changeSelection(self, selection):
""" Change the atom selection of the rep to 'selection'."""
for id,name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, sel=selection):
raise ValueError, "Invalid selection '%s'" % selection
self.selection = str(selection)
def changeColor(self, color):
""" Change the coloring method the rep to 'color'."""
for id,name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, color=color):
raise ValueError, "Invalid color '%s'" % color
self.color = str(color)
def changeStyle(self, style):
""" Change the draw style of the rep to 'style'."""
for id,name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, style=style):
raise ValueError, "Invalid style '%s'" % style
self.style = str(style)
def changeMaterial(self, material):
""" Change the material for the rep to 'material'."""
for id, name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, material=material):
raise ValueError, "Invalid material'%s'" % material
self.material = str(material)
def changeSelection(self, selection):
""" Change the atom selection of the rep to 'selection'."""
for id, name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, sel=selection):
raise ValueError, "Invalid selection '%s'" % selection
self.selection = str(selection)
def changeColor(self, color):
""" Change the coloring method the rep to 'color'."""
for id, name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, color=color):
raise ValueError, "Invalid color '%s'" % color
self.color = str(color)
def changeStyle(self, style):
""" Change the draw style of the rep to 'style'."""
for id, name in self.molecules.items():
repid = molrep.repindex(id, name)
if not molrep.modrep(id, repid, style=style):
raise ValueError, "Invalid style '%s'" % style
self.style = str(style)
VMD.evaltcl("display shadows off")
color_display = color.get_colormap("Display")
color_display["Background"] = "white"
color.set_colormap("Display", color_display)
display.set(depthcue=0)
# load mol and change its representation
# geometry optimized cbz
licor_style = "Licorice 0.1 50 50"
sel_no_h = "not element H"
if molecule.exists(0) != 1:
molecule.load("xyz", cbz_gOpt)
molrep.modrep(0,
0,
sel=sel_no_h,
style=licor_style,
material="AOChalky",
color="ColorID 7")
if molecule.exists(1) != 1:
#molecule.load("lammpsdata", cbz_gaff2_lmpdat, "dcd", cbz_gaff2_dcd)
molecule.load("lammpsdata", cbz_gaff2_lmpdat)
molrep.modrep(1,
0,
sel=sel_no_h,
style=licor_style,
material="AOChalky",
color="ColorID 0")
if molecule.exists(2) != 1:
#molecule.load("lammpsdata", cbz_gaff_lmpdat, "dcd", cbz_gaff_dcd)
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)