def init():
display.set(size=[1024,768])
display.set(projection='Perspective')
color.set_colormap('Display',{'Background': 'white'})
axes.set_location('OFF')
display.set(depthcue=False)
display.set(nearclip=0.01)
for m in molecule.listall():
molecule.delete(m)
def ssrecalcu(molid, frame):
molecule.ssrecalc(molid)
#load the O atom from O.pdb
O=load('pdb','O.pdb')
#Move the O atom into the right place
all=atomsel()
all.moveby([x,y,z0])
#Set resid to 0 (for now, doesn't matter, just needs to be something
# so that the simulation program isn't unhappy
all=atomsel()
all.set('resid',0)
#So far we have 26 molecfules (1 graphene, 25 O). We need to combine them into one thing
#so that we can treat them together. We use topotools to do this
combined=evaltcl('::TopoTools::mergemols %s'%list2tcl(molecule.listall()))
import animate
#Set the segname of everything to CNT (doesn't matter now, just to make sim happy)
all=atomsel()
all.set('segname','CNT')
all.set('resname','CNT')
#Set the occupacy of everything to 0
all.set('occupancy',0)
#Set the occupancy of just the CA atoms to 1, which we'll use as a flag to keep them fixed
all=atomsel('type CA')
all.set('occupancy',1)
def moleculeList(): """ Returns a Molecule instance for all current molecules. """ return [Molecule(id=id) for id in molecule.listall()]
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)
def moleculeList():
""" Returns a Molecule instance for all current molecules. """
return [Molecule(id=id) for id in molecule.listall()]