def performance(mode,_self=cmd):
pymol=_self._pymol
cmd=_self
mode = int(mode)
if mode==0: # maximum quality
cmd.set('line_smooth',1)
cmd.set('depth_cue',1)
cmd.set('specular',1)
cmd.set('surface_quality',1)
cmd.set('stick_quality',15)
cmd.set('sphere_quality',2)
cmd.set('cartoon_sampling',14)
cmd.set('ribbon_sampling',10)
cmd.set('transparency_mode',2)
cmd.set('stick_ball',1)
cmd.do("rebuild")
elif mode==33:
cmd.set('line_smooth',1)
cmd.set('depth_cue',1)
cmd.set('specular',1)
cmd.set('surface_quality',0)
cmd.set('stick_quality',8)
cmd.set('sphere_quality',1)
cmd.set('cartoon_sampling',7)
cmd.set('ribbon_sampling',1)
cmd.set('transparency_mode',2)
cmd.set('stick_ball',0)
cmd.do("rebuild")
elif mode==66: # good perfomance
cmd.set('line_smooth',0)
cmd.set('depth_cue',0)
cmd.set('specular',1)
cmd.set('surface_quality',0)
cmd.set('stick_quality',8)
cmd.set('sphere_quality',1)
cmd.set('cartoon_sampling',6)
cmd.set('ribbon_sampling',1)
cmd.set('transparency_mode',2)
cmd.set('stick_ball',0.0)
cmd.do("rebuild")
else: # maximum performance
cmd.set('line_smooth',0)
cmd.set('depth_cue',0)
cmd.set('specular',0)
cmd.set('surface_quality',-1) # new
cmd.set('stick_quality',5)
cmd.set('sphere_quality',0)
cmd.set('ribbon_sampling',1)
cmd.set('cartoon_sampling',3)
cmd.set('transparency_mode',0)
cmd.set('stick_ball',0.0)
cmd.do("rebuild")
def alignsg(sele):
allsg = cmd.get_model("(("+sele+") and (name VSG))").atom
allsf = cmd.get_model("(("+sele+") and (name S5,S6,S7,S8))").atom
while allsg:
closest = [9e9,None,None]
for sga in allsg:
for sfa in allsf:
sg = Vec(sga.coord)
sf = Vec(sfa.coord)
if (sg-sf).length() < closest[0]:
closest = [(sg-sf).length(),sga,sfa]
sga,sfa = closest[1:]
allsg.remove(sga)
allsf.remove(sfa)
if closest[0] > 10.0: break
cmd.do("alter_state 1, (("+sele+") and (resi %s and name %s))"%(sga.resi,sga.name)+",x=%f"%sfa.coord[0])
cmd.do("alter_state 1, (("+sele+") and (resi %s and name %s))"%(sga.resi,sga.name)+",y=%f"%sfa.coord[1])
cmd.do("alter_state 1, (("+sele+") and (resi %s and name %s))"%(sga.resi,sga.name)+",z=%f"%sfa.coord[2])
def alignsg(sele):
allsg = cmd.get_model("((" + sele + ") and (name VSG))").atom
allsf = cmd.get_model("((" + sele + ") and (name S5,S6,S7,S8))").atom
while allsg:
closest = [9e9, None, None]
for sga in allsg:
for sfa in allsf:
sg = Vec(sga.coord)
sf = Vec(sfa.coord)
if (sg - sf).length() < closest[0]:
closest = [(sg - sf).length(), sga, sfa]
sga, sfa = closest[1:]
allsg.remove(sga)
allsf.remove(sfa)
if closest[0] > 10.0: break
cmd.do("alter_state 1, ((" + sele + ") and (resi %s and name %s))" %
(sga.resi, sga.name) + ",x=%f" % sfa.coord[0])
cmd.do("alter_state 1, ((" + sele + ") and (resi %s and name %s))" %
(sga.resi, sga.name) + ",y=%f" % sfa.coord[1])
cmd.do("alter_state 1, ((" + sele + ") and (resi %s and name %s))" %
(sga.resi, sga.name) + ",z=%f" % sfa.coord[2])
def parse(self, line):
if self.control == None:
self.blurt("your control is unlinked")
return
commandQue = []
if line == "":
line = self.lastcmd
self.lastcmd = line
# slice the input to a managable size
line = line[0:128]
# bug: input with multiple commands (\n seperated) are ignored
if line.rfind("\n") > -1:
return False
words = line.split()
punct = "\' \" , . ? !".split() # incomplete
# = special case! this is to remain compatable with cmd.py's do_help ===
if len(words) > 0:
if words[0] == "help":
cmd, arg, line = self.parseline(line)
return self.do_help(arg)
# === end special case ===
# checking to see if ands in words refer to items
referedTo, words = self.getReferedTo(words)
ands = self.findall(words, "and")
group = []
for i in ands:
if isinstance(words[i - 1], mc.Thing):
if isinstance(words[i + 1], mc.Thing):
group.append(words[i - 1])
group.append(words[i + 1])
# group is a list of items that were refered to
if len(group) > 0:
commandQue = []
for thing in group:
cmd = self.getCommand(words, [thing])
commandQue.append(cmd)
if None in commandQue:
return self.default()
else:
for cmd in commandQue:
cmd.do()
return True
return
if len(ands) > 0:
start = 0
chunk = []
vfyAnd = []
for i in ands:
chunk.append(words[start:i])
start = i + 1
if len(words[start:]) > 0:
chunk.append(words[start:])
# ok, we have some chunks!
for i in chunk:
cmd = self.getCommand(i, referedTo)
vfyAnd.append(cmd)
# with a reasonable amount of certainty, we can say "and" here
# is used to split apart multiple actions if getCommand does not
# return False for any chunk
#if None not in vfyAnd:
# bug: this is only temporary...
commandQue = vfyAnd
else:
# simply process words as a single command
cmd = self.getCommand(words, referedTo)
commandQue.append(cmd)
# if we have a unknown or failing command, then fail the whole parse
if None in commandQue:
return self.default()
else:
for cmd in commandQue:
cmd.do()
return True
def do(py_file):
out, err = cmd.do("nix-build %s/pip.nix --argstr path %s" % (os.path.dirname(__file__), os.path.dirname(py_file)))
# TODO: handle err
return os.path.join(out.split("\n")[0], "wheelhouse")