def run(self):
if not self.part.molecules:
return
for chunk in self.part.molecules:
if chunk.atoms:
for atom in chunk.atoms.itervalues():
atom.setOverlayText("?")
chunk.showOverlayText = True
selection = self.part.selection_for_all()
simaspect = sim_aspect(
self.part, selection.atomslist(), cmdname_for_messages="CheckAtomTypes", anchor_all_nonmoving_atoms=False
)
movie = Movie(self.assy)
# self._movie = movie
writemovie(
self.part,
movie,
1,
simaspect=simaspect,
print_sim_warnings=True,
cmdname="Simulator",
cmd_type="Check AtomTypes",
useGromacs=False,
background=False,
useAMBER=True,
typeFeedback=True,
)
self.part.gl_update()
def run(self):
if not self.part.molecules:
return
for chunk in self.part.molecules:
if (chunk.atoms):
for atom in chunk.atoms.itervalues():
atom.setOverlayText("?")
chunk.showOverlayText = True
selection = self.part.selection_for_all()
simaspect = sim_aspect(self.part,
selection.atomslist(),
cmdname_for_messages="CheckAtomTypes",
anchor_all_nonmoving_atoms=False)
movie = Movie(self.assy)
#self._movie = movie
writemovie(self.part,
movie,
1,
simaspect=simaspect,
print_sim_warnings=True,
cmdname="Simulator",
cmd_type="Check AtomTypes",
useGromacs=False,
background=False,
useAMBER=True,
typeFeedback=True)
self.part.gl_update()
def makeSimMovie(self): ####@@@@ some of this should be a Movie method since it uses attrs of Movie...
#bruce 050324 made this from the Part method makeSimMovie.
# It's called only from self.run() above; not clear it should be a separate method,
# or if it is, that it's split from the caller at the right boundary.
suffix = self.part.movie_suffix()
if suffix is None: #bruce 050316 temporary kluge
msg = redmsg( "Simulator is not yet implemented for clipboard items.")
env.history.message(self.cmdname + ": " + msg)
return -1
###@@@ else use suffix below!
self.simcntl = SimSetup(self.win, self.part, suffix = suffix)
# this now has its own sticky params, doesn't need previous_movie [bruce 060601, fixing bug 1840]
# Open SimSetup dialog [and run it until user dismisses it]
movie = self.simcntl.movie # always a Movie object, even if user cancelled the dialog
if movie.cancelled:
# user hit Cancel button in SimSetup Dialog. No history msg went out; caller will do that.
movie.destroy()
return -1
r = writemovie(self.part, movie, print_sim_warnings = True, cmdname = self.cmdname)
# not passing mtype means "run dynamic sim (not minimize), make movie"
###@@@ bruce 050324 comment: maybe should do following in that function too
if not r:
# Movie file created. Initialize. ###@@@ bruce 050325 comment: following mods private attrs, needs cleanup.
movie.IsValid = True # Movie is valid.###@@@ bruce 050325 Q: what exactly does this (or should this) mean?
###@@@ bruce 050404: need to make sure this is a new obj-- if not always and this is not init False, will cause bugs
self.movie = movie # bruce 050324 added this
# it's up to caller to store self.movie in self.assy.current_movie if it wants to.
return r
def makeSimMovie(
self
): ####@@@@ some of this should be a Movie method since it uses attrs of Movie...
#bruce 050324 made this from the Part method makeSimMovie.
# It's called only from self.run() above; not clear it should be a separate method,
# or if it is, that it's split from the caller at the right boundary.
suffix = self.part.movie_suffix()
if suffix is None: #bruce 050316 temporary kluge
msg = redmsg(
"Simulator is not yet implemented for clipboard items.")
env.history.message(self.cmdname + ": " + msg)
return -1
###@@@ else use suffix below!
self.simcntl = SimSetup(self.win, self.part, suffix=suffix)
# this now has its own sticky params, doesn't need previous_movie [bruce 060601, fixing bug 1840]
# Open SimSetup dialog [and run it until user dismisses it]
movie = self.simcntl.movie # always a Movie object, even if user cancelled the dialog
if movie.cancelled:
# user hit Cancel button in SimSetup Dialog. No history msg went out; caller will do that.
movie.destroy()
return -1
r = writemovie(self.part,
movie,
print_sim_warnings=True,
cmdname=self.cmdname)
# not passing mtype means "run dynamic sim (not minimize), make movie"
###@@@ bruce 050324 comment: maybe should do following in that function too
if not r:
# Movie file created. Initialize. ###@@@ bruce 050325 comment: following mods private attrs, needs cleanup.
movie.IsValid = True # Movie is valid.###@@@ bruce 050325 Q: what exactly does this (or should this) mean?
###@@@ bruce 050404: need to make sure this is a new obj-- if not always and this is not init False, will cause bugs
self.movie = movie # bruce 050324 added this
# it's up to caller to store self.movie in self.assy.current_movie if it wants to.
return r
def doMinimize(self, mtype = 1, simaspect = None):
#bruce 051115 renamed method from makeMinMovie
#bruce 051115 revised docstring to fit current code #e should clean it up more
"""
Minimize self.part (if simaspect is None -- no longer used)
or its given simaspect (simulatable aspect) (used for both Minimize Selection and Minimize All),
generating and showing a movie (no longer asked for) or generating and applying to part an xyz file.
The mtype flag means:
1 = tell writemovie() to create a single-frame XYZ file.
2 = tell writemovie() to create a multi-frame DPB moviefile.
[###@@@ not presently used, might not work anymore]
"""
assert mtype == 1 #bruce 051115
assert simaspect is not None #bruce 051115
#bruce 050324 made this from the Part method makeMinMovie.
suffix = self.part.movie_suffix()
if suffix is None: #bruce 050316 temporary kluge; as of circa 050326 this is not used anymore
msg = "%s is not yet implemented for clipboard items." % self.word_Minimize
env.history.message( redmsg( msg))
return
#e use suffix below? maybe no need since it's ok if the same filename is reused for this.
# bruce 050325 change: don't use or modify self.assy.current_movie,
# since we're not making a movie and don't want to prevent replaying
# the one already stored from some sim run.
# [this is for mtype == 1 (always true now) and might affect writemovie ###@@@ #k.]
# NOTE: the movie object is used to hold params and results from minimize,
# even if it makes an xyz file rather than a movie file.
# And at the moment it never makes a movie file when called from this code.
# [bruce 051115 comment about months-old situation]
movie = Movie(self.assy)
# do this in writemovie? no, the other call of it needs it passed in
# from the dialog... #k
# note that Movie class is misnamed since it's really a
# SimRunnerAndResultsUser... which might use .xyz or .dpb results...
# maybe rename it SimRun? ###e also, it needs subclasses for the
# different kinds of sim runs and their results... or maybe it needs
# a subobject which has such subclasses -- not yet sure. [bruce 050329]
self._movie = movie
#bruce 050415 kluge; note that class SimRun does the same thing.
# Probably it means that this class, SimRun, and this way of using
# class Movie should all be the same, or at least have more links
# than they do now. ###@@@
# Set update_cond for controlling realtime update settings for watching
# this "movie" (an ongoing sim). There are three possible ways
# (soon after A8 only the first one will be used) [bruce 060705]:
# - caller specified it.
# - if it didn't, use new common code to get it from General Prefs page.
# - if that fails, use older code for that.
#
# WARNING: it turns out this happens whether or not the checkbox pref
# says it should -- that is checked separately elsewhere! That's a bug,
# since we need to use a different checkbox depending on the command.
# let's see if we can consolidate the "enabling flag" into
# update_cond itself? so it is None or False if we won't update.
# this is now attempted...
if env.debug():
print "debug fyi: runSim/sim_commandruns watch_motion update_cond computed here " \
"(even if not watching motion)" #bruce 060705
try:
# Only the client code knows where to find the correct realtime
# update settings widgets (or someday, knows whether these values
# come from widgets at all, vs from a script).
# It should figure out the update_cond
# (False if we should not watch motion),
# and tell us in self.kws['update_cond'].
update_cond = self.kws['update_cond']
assert update_cond or (update_cond is False) # a callable or False [remove when works]
# WARNING: as of 080321, this apparently fails routinely
# for Adjust All, and then the first fallback in the
# except clause also fails (userPrefs.watch_motion_buttongroup
# attributeerror), and then its fallback finally works.
# Cleanup is severely needed. [bruce 080321 comment]
except:
## print_compact_traceback("bug ...: ")
if env.debug():
print "debug: fyi: sim_commandruns grabbing userPrefs data"
# For A8, this is normal, since only (at most) Minimize Energy sets self.kws['update_cond'] itself.
# This will be used routinely in A8 by Adjust All and Adjust Selection, and maybe Adjust Atoms (not sure).
#
# Just get the values from the "Adjust" prefs page.
# But at least try to do that using new common code.
try:
from widgets.widget_controllers import realtime_update_controller
userPrefs = env.mainwindow().userPrefs
from utilities.prefs_constants import Adjust_watchRealtimeMinimization_prefs_key
###@@@ should depend on command, or be in movie...
ruc = realtime_update_controller(
( userPrefs.watch_motion_buttongroup,
# Note: watch_motion_buttongroup exists in MinimizeEnergyProp.py
# and in SimSetup.py and now its back in Preferences.py,
# so this is no longer a bug (for "Adjust All"). [mark 2008-06-04]
userPrefs.update_number_spinbox,
userPrefs.update_units_combobox ),
None, # checkbox ###@@@ maybe not needed, since UserPrefs sets up the connection #k
Adjust_watchRealtimeMinimization_prefs_key )
update_cond = ruc.get_update_cond_from_widgets()
# note, if those widgets are connected to env.prefs, that's not handled here or in ruc;
# I'm not sure if they are. Ideally we'd tell ruc the prefs_keys and have it handle that too,
# perhaps making it a long-lived object (though that might not be necessary).
assert update_cond or (update_cond is False) # a callable or False
except:
# even that didn't work. Complain, then fall back to otherwise-obsolete old code.
msg = "bug using realtime_update_controller in sim_commandruns, will use older code instead: "
print_compact_traceback(msg)
# This code works (except for always using the widgets from the General Prefs page,
# even for Minimize Energy), but I'll try to replace it with calls to common code.
# [bruce 060705]
# This code for setting update_cond is duplicated (inexactly)
# in SimSetup.createMoviePressed() in SimSetup.py.
userPrefs = env.mainwindow().userPrefs
update_units = userPrefs.update_units_combobox.currentText()
update_number = userPrefs.update_number_spinbox.value()
if userPrefs.update_asap_rbtn.isChecked():
update_cond = ( lambda simtime, pytime, nframes:
simtime >= max(0.05, min(pytime * 4, 2.0)) )
elif update_units == 'frames':
update_cond = ( lambda simtime, pytime, nframes, _nframes = update_number: nframes >= _nframes )
elif update_units == 'seconds':
update_cond = ( lambda simtime, pytime, nframes, _timelimit = update_number: simtime + pytime >= _timelimit )
elif update_units == 'minutes':
update_cond = ( lambda simtime, pytime, nframes, _timelimit = update_number * 60: simtime + pytime >= _timelimit )
elif update_units == 'hours':
update_cond = ( lambda simtime, pytime, nframes, _timelimit = update_number * 3600: simtime + pytime >= _timelimit )
else:
print "don't know how to set update_cond from (%r, %r)" % (update_number, update_units)
update_cond = None
# new as of 060705, in this old code
if not env.prefs[Adjust_watchRealtimeMinimization_prefs_key]:
update_cond = False
pass
# now do this with update_cond, however it was computed
movie.update_cond = update_cond
# semi-obs comment, might still be useful [as of 050406]:
# Minimize Selection [bruce 050330] (ought to be a distinct
# command subclass...) this will use the spawning code in writemovie
# but has its own way of writing the mmp file.
# To make this clean, we need to turn writemovie into more than one
# method of a class with more than one subclass, so we can override
# one of them (writing mmp file) and another one (finding atom list).
# But to get it working I might just kluge it
# by passing it some specialized options... ###@@@ not sure
movie._cmdname = self.cmdname
#bruce 050415 kluge so writemovie knows proper progress bar caption to use
# (not really wrong -- appropriate for only one of several
# classes Movie should be split into, i.e. one for the way we're using it here,
# to know how to run the sim, which is perhaps really self (a SimRunner),
# once the code is fully cleaned up.
# [review: is that the same SimRunner which is by 080321
# a real class in runSim?]
# write input for sim, and run sim
# this also sets movie.alist from simaspect
r = writemovie(self.part,
movie,
mtype,
simaspect = simaspect,
print_sim_warnings = True,
cmdname = self.cmdname,
cmd_type = self.cmd_type,
useGromacs = self.useGromacs,
background = self.background)
if r:
# We had a problem writing the minimize file.
# Simply return (error message already emitted by writemovie). ###k
return
if mtype == 1: # Load single-frame XYZ file.
if (self.useGromacs):
if (self.background):
return
tracefileProcessor = movie._simrun.tracefileProcessor
newPositions = readGromacsCoordinates(movie.filename + "-out.gro", movie.alist, tracefileProcessor)
else:
newPositions = readxyz( movie.filename, movie.alist )
# movie.alist is now created in writemovie [bruce 050325]
# retval is either a list of atom posns or an error message string.
assert type(newPositions) in [type([]),type("")]
if type(newPositions) == type([]):
#bruce 060102 note: following code is approximately duplicated somewhere else in this file.
movie.moveAtoms(newPositions)
# bruce 050311 hand-merged mark's 1-line bugfix in assembly.py (rev 1.135):
self.part.changed() # Mark - bugfix 386
self.part.gl_update()
else:
#bruce 050404: print error message to history
env.history.message(redmsg( newPositions))
else: # Play multi-frame DPB movie file.
###@@@ bruce 050324 comment: can this still happen? [no] is it correct [probably not]
# (what about changing mode to movieMode, does it ever do that?) [don't know]
# I have not reviewed this and it's obviously not cleaned up (since it modifies private movie attrs).
# But I will have this change the current movie, which would be correct in theory, i think, and might be needed
# before trying to play it (or might be a side effect of playing it, this is not reviewed either).
###e bruce 050428 comment: if self.assy.current_movie exists, should do something like close or destroy it... need to review
self.assy.current_movie = movie
# If cueMovie() returns a non-zero value, something went wrong loading the movie.
if movie.cueMovie():
return
movie._play()
movie._close()
return
def doMinimize(self, mtype=1, simaspect=None):
#bruce 051115 renamed method from makeMinMovie
#bruce 051115 revised docstring to fit current code #e should clean it up more
"""
Minimize self.part (if simaspect is None -- no longer used)
or its given simaspect (simulatable aspect) (used for both Minimize Selection and Minimize All),
generating and showing a movie (no longer asked for) or generating and applying to part an xyz file.
The mtype flag means:
1 = tell writemovie() to create a single-frame XYZ file.
2 = tell writemovie() to create a multi-frame DPB moviefile.
[###@@@ not presently used, might not work anymore]
"""
assert mtype == 1 #bruce 051115
assert simaspect is not None #bruce 051115
#bruce 050324 made this from the Part method makeMinMovie.
suffix = self.part.movie_suffix()
if suffix is None: #bruce 050316 temporary kluge; as of circa 050326 this is not used anymore
msg = "%s is not yet implemented for clipboard items." % self.word_Minimize
env.history.message(redmsg(msg))
return
#e use suffix below? maybe no need since it's ok if the same filename is reused for this.
# bruce 050325 change: don't use or modify self.assy.current_movie,
# since we're not making a movie and don't want to prevent replaying
# the one already stored from some sim run.
# [this is for mtype == 1 (always true now) and might affect writemovie ###@@@ #k.]
# NOTE: the movie object is used to hold params and results from minimize,
# even if it makes an xyz file rather than a movie file.
# And at the moment it never makes a movie file when called from this code.
# [bruce 051115 comment about months-old situation]
movie = Movie(self.assy)
# do this in writemovie? no, the other call of it needs it passed in
# from the dialog... #k
# note that Movie class is misnamed since it's really a
# SimRunnerAndResultsUser... which might use .xyz or .dpb results...
# maybe rename it SimRun? ###e also, it needs subclasses for the
# different kinds of sim runs and their results... or maybe it needs
# a subobject which has such subclasses -- not yet sure. [bruce 050329]
self._movie = movie
#bruce 050415 kluge; note that class SimRun does the same thing.
# Probably it means that this class, SimRun, and this way of using
# class Movie should all be the same, or at least have more links
# than they do now. ###@@@
# Set update_cond for controlling realtime update settings for watching
# this "movie" (an ongoing sim). There are three possible ways
# (soon after A8 only the first one will be used) [bruce 060705]:
# - caller specified it.
# - if it didn't, use new common code to get it from General Prefs page.
# - if that fails, use older code for that.
#
# WARNING: it turns out this happens whether or not the checkbox pref
# says it should -- that is checked separately elsewhere! That's a bug,
# since we need to use a different checkbox depending on the command.
# let's see if we can consolidate the "enabling flag" into
# update_cond itself? so it is None or False if we won't update.
# this is now attempted...
if env.debug():
print "debug fyi: runSim/sim_commandruns watch_motion update_cond computed here " \
"(even if not watching motion)" #bruce 060705
try:
# Only the client code knows where to find the correct realtime
# update settings widgets (or someday, knows whether these values
# come from widgets at all, vs from a script).
# It should figure out the update_cond
# (False if we should not watch motion),
# and tell us in self.kws['update_cond'].
update_cond = self.kws['update_cond']
assert update_cond or (update_cond is False
) # a callable or False [remove when works]
# WARNING: as of 080321, this apparently fails routinely
# for Adjust All, and then the first fallback in the
# except clause also fails (userPrefs.watch_motion_buttongroup
# attributeerror), and then its fallback finally works.
# Cleanup is severely needed. [bruce 080321 comment]
except:
## print_compact_traceback("bug ...: ")
if env.debug():
print "debug: fyi: sim_commandruns grabbing userPrefs data"
# For A8, this is normal, since only (at most) Minimize Energy sets self.kws['update_cond'] itself.
# This will be used routinely in A8 by Adjust All and Adjust Selection, and maybe Adjust Atoms (not sure).
#
# Just get the values from the "Adjust" prefs page.
# But at least try to do that using new common code.
try:
from widgets.widget_controllers import realtime_update_controller
userPrefs = env.mainwindow().userPrefs
from utilities.prefs_constants import Adjust_watchRealtimeMinimization_prefs_key
###@@@ should depend on command, or be in movie...
ruc = realtime_update_controller(
(
userPrefs.watch_motion_buttongroup,
# Note: watch_motion_buttongroup exists in MinimizeEnergyProp.py
# and in SimSetup.py and now its back in Preferences.py,
# so this is no longer a bug (for "Adjust All"). [mark 2008-06-04]
userPrefs.update_number_spinbox,
userPrefs.update_units_combobox),
None, # checkbox ###@@@ maybe not needed, since UserPrefs sets up the connection #k
Adjust_watchRealtimeMinimization_prefs_key)
update_cond = ruc.get_update_cond_from_widgets()
# note, if those widgets are connected to env.prefs, that's not handled here or in ruc;
# I'm not sure if they are. Ideally we'd tell ruc the prefs_keys and have it handle that too,
# perhaps making it a long-lived object (though that might not be necessary).
assert update_cond or (update_cond is False
) # a callable or False
except:
# even that didn't work. Complain, then fall back to otherwise-obsolete old code.
msg = "bug using realtime_update_controller in sim_commandruns, will use older code instead: "
print_compact_traceback(msg)
# This code works (except for always using the widgets from the General Prefs page,
# even for Minimize Energy), but I'll try to replace it with calls to common code.
# [bruce 060705]
# This code for setting update_cond is duplicated (inexactly)
# in SimSetup.createMoviePressed() in SimSetup.py.
userPrefs = env.mainwindow().userPrefs
update_units = userPrefs.update_units_combobox.currentText()
update_number = userPrefs.update_number_spinbox.value()
if userPrefs.update_asap_rbtn.isChecked():
update_cond = (lambda simtime, pytime, nframes: simtime >=
max(0.05, min(pytime * 4, 2.0)))
elif update_units == 'frames':
update_cond = (lambda simtime, pytime, nframes, _nframes=
update_number: nframes >= _nframes)
elif update_units == 'seconds':
update_cond = (
lambda simtime, pytime, nframes, _timelimit=
update_number: simtime + pytime >= _timelimit)
elif update_units == 'minutes':
update_cond = (
lambda simtime, pytime, nframes, _timelimit=
update_number * 60: simtime + pytime >= _timelimit)
elif update_units == 'hours':
update_cond = (
lambda simtime, pytime, nframes, _timelimit=
update_number * 3600: simtime + pytime >= _timelimit)
else:
print "don't know how to set update_cond from (%r, %r)" % (
update_number, update_units)
update_cond = None
# new as of 060705, in this old code
if not env.prefs[Adjust_watchRealtimeMinimization_prefs_key]:
update_cond = False
pass
# now do this with update_cond, however it was computed
movie.update_cond = update_cond
# semi-obs comment, might still be useful [as of 050406]:
# Minimize Selection [bruce 050330] (ought to be a distinct
# command subclass...) this will use the spawning code in writemovie
# but has its own way of writing the mmp file.
# To make this clean, we need to turn writemovie into more than one
# method of a class with more than one subclass, so we can override
# one of them (writing mmp file) and another one (finding atom list).
# But to get it working I might just kluge it
# by passing it some specialized options... ###@@@ not sure
movie._cmdname = self.cmdname
#bruce 050415 kluge so writemovie knows proper progress bar caption to use
# (not really wrong -- appropriate for only one of several
# classes Movie should be split into, i.e. one for the way we're using it here,
# to know how to run the sim, which is perhaps really self (a SimRunner),
# once the code is fully cleaned up.
# [review: is that the same SimRunner which is by 080321
# a real class in runSim?]
# write input for sim, and run sim
# this also sets movie.alist from simaspect
r = writemovie(self.part,
movie,
mtype,
simaspect=simaspect,
print_sim_warnings=True,
cmdname=self.cmdname,
cmd_type=self.cmd_type,
useGromacs=self.useGromacs,
background=self.background)
if r:
# We had a problem writing the minimize file.
# Simply return (error message already emitted by writemovie). ###k
return
if mtype == 1: # Load single-frame XYZ file.
if (self.useGromacs):
if (self.background):
return
tracefileProcessor = movie._simrun.tracefileProcessor
newPositions = readGromacsCoordinates(
movie.filename + "-out.gro", movie.alist,
tracefileProcessor)
else:
newPositions = readxyz(movie.filename, movie.alist)
# movie.alist is now created in writemovie [bruce 050325]
# retval is either a list of atom posns or an error message string.
assert type(newPositions) in [type([]), type("")]
if type(newPositions) == type([]):
#bruce 060102 note: following code is approximately duplicated somewhere else in this file.
movie.moveAtoms(newPositions)
# bruce 050311 hand-merged mark's 1-line bugfix in assembly.py (rev 1.135):
self.part.changed() # Mark - bugfix 386
self.part.gl_update()
else:
#bruce 050404: print error message to history
env.history.message(redmsg(newPositions))
else: # Play multi-frame DPB movie file.
###@@@ bruce 050324 comment: can this still happen? [no] is it correct [probably not]
# (what about changing mode to movieMode, does it ever do that?) [don't know]
# I have not reviewed this and it's obviously not cleaned up (since it modifies private movie attrs).
# But I will have this change the current movie, which would be correct in theory, i think, and might be needed
# before trying to play it (or might be a side effect of playing it, this is not reviewed either).
###e bruce 050428 comment: if self.assy.current_movie exists, should do something like close or destroy it... need to review
self.assy.current_movie = movie
# If cueMovie() returns a non-zero value, something went wrong loading the movie.
if movie.cueMovie():
return
movie._play()
movie._close()
return