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 run(self):
"""
Minimize (or Adjust) the Selection or the current Part
"""
#bruce 050324 made this method from the body of MWsemantics.modifyMinimize
# and cleaned it up a bit in terms of how it finds the movie to use.
#bruce 050412 added 'Sel' vs 'All' now that we have two different Minimize buttons.
# In future the following code might become subclass-specific (and cleaner):
## fyi: this old code was incorrect, I guess since 'in' works by 'is' rather than '==' [not verified]:
## assert self.args in [['All'], ['Sel']], "%r" % (self.args,)
#bruce 051129 revising this to clarify it, though command-specific subclasses would be better
assert len(self.args) >= 1
cmd_subclass_code = self.args[0]
cmd_type = self.kws.get('type', 'Minimize')
# one of 'Minimize' or 'Adjust' or 'Adjust Atoms'; determines conv criteria, name [bruce 060705]
self.cmd_type = cmd_type # kluge, see comment where used
engine = self.kws.get('engine', MINIMIZE_ENGINE_UNSPECIFIED)
if (engine == MINIMIZE_ENGINE_UNSPECIFIED):
engine = env.prefs[Adjust_minimizationEngine_prefs_key]
if (engine == MINIMIZE_ENGINE_GROMACS_FOREGROUND):
self.useGromacs = True
self.background = False
elif (engine == MINIMIZE_ENGINE_GROMACS_BACKGROUND):
self.useGromacs = True
self.background = True
else:
self.useGromacs = False
self.background = False
assert cmd_subclass_code in ['All', 'Sel', 'Atoms'] #e and len(args) matches that?
# These words and phrases are used in history messages and other UI text;
# they should be changed by specific commands as needed.
# See also some computed words and phrases, e.g. self.word_Minimize,
# below the per-command if stamements. [bruce 060705]
# Also set flags for other behavior which differs between these commands.
if cmd_type.startswith('Adjust'):
self.word_minimize = "adjust"
self.word_minimization = "adjustment"
self.word_minimizing = "adjusting"
anchor_all_nonmoving_atoms = False
pass
else:
assert cmd_type.startswith('Minimize')
self.word_minimize = "minimize"
self.word_minimization = "minimization"
self.word_minimizing = "minimizing"
anchor_all_nonmoving_atoms = True
#bruce 080513 revision to implement nfr bug 2848 item 2
# (note: we might decide to add a checkbox for this into the UI,
# and just change its default value for Minimize vs Adjust)
pass
self.word_Minimize = _capitalize_first_word( self.word_minimize)
self.word_Minimizing = _capitalize_first_word( self.word_minimizing)
if cmd_subclass_code == 'All':
cmdtype = _MIN_ALL
cmdname = "%s All" % self.word_Minimize
elif cmd_subclass_code == 'Sel':
cmdtype = _MIN_SEL
cmdname = "%s Selection" % self.word_Minimize
elif cmd_subclass_code == 'Atoms':
#bruce 051129 added this case for Local Minimize (extending a kluge -- needs rewrite to use command-specific subclass)
cmdtype = _LOCAL_MIN
cmdname = "%s Atoms" % self.word_Minimize #bruce 060705; some code may assume this is always Adjust Atoms, as it is
# self.args is parsed later
else:
assert 0, "unknown cmd_subclass_code %r" % (cmd_subclass_code,)
self.cmdname = cmdname #e in principle this should come from a subclass for the specific command [bruce 051129 comment]
startmsg = cmdname + ": ..."
del cmd_subclass_code
# remove model objects inserted only for feedback from prior runs
# (both because it's a good feature, and to avoid letting them
# mess up this command) [bruce 080520]
from simulation.runSim import part_contains_pam_atoms
# kluge to use this function for this purpose
# (it's called later for other reasons)
hasPAM_junk = part_contains_pam_atoms( self.part,
kill_leftover_sim_feedback_atoms = True )
self.part.assy.update_parts() ###k is this always safe or good?
# Make sure some chunks are in the part.
# (Valid for all cmdtypes -- Minimize only moves atoms, even if affected by jigs.)
if not self.part.molecules: # Nothing in the part to minimize.
env.history.message(greenmsg(cmdname + ": ") + redmsg("Nothing to %s." % self.word_minimize))
return
if cmdtype == _MIN_SEL:
selection = self.part.selection_from_glpane() # compact rep of the currently selected subset of the Part's stuff
if not selection.nonempty():
msg = greenmsg(cmdname + ": ") + redmsg("Nothing selected.") + \
" (Use %s All to %s the entire Part.)" % (self.word_Minimize, self.word_minimize)
#e might need further changes for Minimize Energy, if it's confusing that Sel/All is a dialog setting then
env.history.message( msg)
return
elif cmdtype == _LOCAL_MIN:
from operations.ops_select import selection_from_atomlist
junk, atomlist, ntimes_expand = self.args
selection = selection_from_atomlist( self.part, atomlist) #e in cleaned up code, selection object might come from outside
selection.expand_atomset(ntimes = ntimes_expand) # ok if ntimes == 0
# Rationale for adding monovalent atoms to the selection before
# instantiating the sim_aspect
#
# (Refer to comments for sim_aspect.__init__.) Why is it safe to add
# monovalent atoms to a selection? Let's look at what happens during a
# local minimization.
#
# While minimizing, we want to simulate as if the entire rest of the
# part is grounded, and only our selection of atoms is free to move. The
# most obvious approach would be to minimize all the atoms in the part
# while applying anchors to the atoms that aren't in the selection. But
# minimizing all the atoms, especially if the selection is small, is very
# wasteful. Applying the simulator to atoms is expensive and we want to
# minimize as few atoms as possible.
#
# [revision, bruce 080513: this discussion applies for Adjust,
# but the policy for Minimize is being changed to always include
# all atoms, even if most of them are anchored,
# re nfr bug 2848 item 2.]
#
# A more economical approach is to anchor the atoms for two layers going
# out from the selection. The reason for going out two layers, and not just
# one layer, is that we need bond angle terms to simulate accurately. When
# we get torsion angles we will probably want to bump this up to three
# layers. [Now we're doing three layers -- bruce 080507]
#
# Imagine labeling all the atoms in the selection with zero. Then take the
# set of unlabeled atoms that are bonded to a zero-labeled atom, and label
# all the atoms in that set with one. Next, take the set of yet-unlabeled
# atoms that are bonded to a one-labeled atom, and label the atoms in that
# set with two. The atoms labeled one and two become our first and second
# layers, and we anchor them during the minimization.
#
# In sim_aspect.__init__, the labels for zero, one and two correspond
# respectively to membership in the dictionaries self._moving_atoms,
# self._boundary1_atoms, and self._boundary2_atoms.
#
# If an atom in the selection is anchored, we don't need to go two layers
# out from that atom, only one layer. So we can label it with one, even
# though it's a member of the selection and would normally be labeled with
# zero. The purpose in doing this is to give the simulator a few less atoms
# to worry about.
#
# If a jig includes one of the selected atoms, but additionally includes
# atoms outside the selection, then it may not be obvious how to simulate
# that jig. For the present, the only jig that counts in a local
# minimization is an anchor, because all the other jigs are too complicated
# to simulate.
#
# The proposed fix here has the effect that monovalent atoms bonded to
# zero-labeled atoms are also labeled zero, rather than being labeled one,
# so they are allowed to move. Why is this OK to do?
#
# (1) Have we violated the assumption that the rest of the part is locked
# down? Yes, as it applies to those monovalent atoms, but they are
# presumably acceptable violations, since bug 1240 is regarded as a bug.
#
# (2) Have we unlocked any bond lengths or bond angles that should remain
# locked? Again, only those which involve (and necessarily end at) the
# monovalent atoms in question. The same will be true when we introduce
# torsion terms.
#
# (3) Have we lost any ground on the jig front? If a jig includes one or
# more of the monovalent atoms, possibly - but the only jigs we are
# simulating in this case is anchors, and those will be handled correctly.
# Remember that anchored atoms are only extended one layer, not two, but
# with a monovalent atom bonded to a selected atom, no extension is
# possible at all.
#
# One can debate about whether bug 1240 should be regarded as a bug. But
# having accepted it as a bug, one cannot object to adding these monovalents
# to the original selection.
#
# wware 060410 bug 1240
atoms = selection.selatoms
for atom in atoms.values():
# enumerate the monovalents bonded to atom
for atom2 in filter(lambda atom: not atom.is_singlet(), atom.baggageNeighbors()):
atoms[atom2.key] = atom2
else:
assert cmdtype == _MIN_ALL
selection = self.part.selection_for_all()
# like .selection_from_glpane() but for all atoms presently in the part [bruce 050419]
# no need to check emptiness, this was done above
self.selection = selection #e might become a feature of all CommandRuns, at some point
# At this point, the conditions are met to try to do the command.
env.history.message(greenmsg( startmsg)) #bruce 050412 doing this earlier
# Disable some QActions (menu items/toolbar buttons) during minimize.
self.win.disable_QActions_for_sim(True)
try:
simaspect = sim_aspect( self.part,
selection.atomslist(),
cmdname_for_messages = cmdname,
anchor_all_nonmoving_atoms = anchor_all_nonmoving_atoms
)
#bruce 051129 passing cmdname
# note: atomslist gets atoms from selected chunks, not only selected atoms
# (i.e. it gets atoms whether you're in Select Atoms or Select Chunks mode)
# history message about singlets written as H (if any);
#bruce 051115 updated comment: this is used for both Minimize All and Minimize Selection as of long before 051115;
# for Run Sim this code is not used (so this history message doesn't go out for it, though it ought to)
# but the bug254 X->H fix is done (though different code sets the mapping flag that makes it happen).
nsinglets_H = simaspect.nsinglets_H()
if nsinglets_H: #bruce 051209 this message code is approximately duplicated elsewhere in this file
info = fix_plurals( "(Treating %d bondpoint(s) as Hydrogens, during %s)" % (nsinglets_H, self.word_minimization) )
env.history.message( info)
nsinglets_leftout = simaspect.nsinglets_leftout()
assert nsinglets_leftout == 0 # for now
# history message about how much we're working on; these atomcounts include singlets since they're written as H
nmoving = simaspect.natoms_moving()
nfixed = simaspect.natoms_fixed()
info = fix_plurals( "(%s %d atom(s)" % (self.word_Minimizing, nmoving))
if nfixed:
them_or_it = (nmoving == 1) and "it" or "them"
if anchor_all_nonmoving_atoms:
msg2 = "holding remaining %d atom(s) fixed" % nfixed
else:
msg2 = "holding %d atom(s) fixed around %s" % (nfixed, them_or_it)
info += ", " + fix_plurals(msg2 )
info += ")"
env.history.message( info)
self.doMinimize(mtype = 1, simaspect = simaspect)
# mtype = 1 means single-frame XYZ file.
# [this also sticks results back into the part]
#self.doMinimize(mtype = 2) # 2 = multi-frame DPB file.
finally:
self.win.disable_QActions_for_sim(False)
simrun = self._movie._simrun #bruce 050415 klugetower
if not simrun.said_we_are_done:
env.history.message("Done.")
return
def run(self):
"""
Minimize (or Adjust) the Selection or the current Part
"""
#bruce 050324 made this method from the body of MWsemantics.modifyMinimize
# and cleaned it up a bit in terms of how it finds the movie to use.
#bruce 050412 added 'Sel' vs 'All' now that we have two different Minimize buttons.
# In future the following code might become subclass-specific (and cleaner):
## fyi: this old code was incorrect, I guess since 'in' works by 'is' rather than '==' [not verified]:
## assert self.args in [['All'], ['Sel']], "%r" % (self.args,)
#bruce 051129 revising this to clarify it, though command-specific subclasses would be better
assert len(self.args) >= 1
cmd_subclass_code = self.args[0]
cmd_type = self.kws.get('type', 'Minimize')
# one of 'Minimize' or 'Adjust' or 'Adjust Atoms'; determines conv criteria, name [bruce 060705]
self.cmd_type = cmd_type # kluge, see comment where used
engine = self.kws.get('engine', MINIMIZE_ENGINE_UNSPECIFIED)
if (engine == MINIMIZE_ENGINE_UNSPECIFIED):
engine = env.prefs[Adjust_minimizationEngine_prefs_key]
if (engine == MINIMIZE_ENGINE_GROMACS_FOREGROUND):
self.useGromacs = True
self.background = False
elif (engine == MINIMIZE_ENGINE_GROMACS_BACKGROUND):
self.useGromacs = True
self.background = True
else:
self.useGromacs = False
self.background = False
assert cmd_subclass_code in ['All', 'Sel',
'Atoms'] #e and len(args) matches that?
# These words and phrases are used in history messages and other UI text;
# they should be changed by specific commands as needed.
# See also some computed words and phrases, e.g. self.word_Minimize,
# below the per-command if stamements. [bruce 060705]
# Also set flags for other behavior which differs between these commands.
if cmd_type.startswith('Adjust'):
self.word_minimize = "adjust"
self.word_minimization = "adjustment"
self.word_minimizing = "adjusting"
anchor_all_nonmoving_atoms = False
pass
else:
assert cmd_type.startswith('Minimize')
self.word_minimize = "minimize"
self.word_minimization = "minimization"
self.word_minimizing = "minimizing"
anchor_all_nonmoving_atoms = True
#bruce 080513 revision to implement nfr bug 2848 item 2
# (note: we might decide to add a checkbox for this into the UI,
# and just change its default value for Minimize vs Adjust)
pass
self.word_Minimize = _capitalize_first_word(self.word_minimize)
self.word_Minimizing = _capitalize_first_word(self.word_minimizing)
if cmd_subclass_code == 'All':
cmdtype = _MIN_ALL
cmdname = "%s All" % self.word_Minimize
elif cmd_subclass_code == 'Sel':
cmdtype = _MIN_SEL
cmdname = "%s Selection" % self.word_Minimize
elif cmd_subclass_code == 'Atoms':
#bruce 051129 added this case for Local Minimize (extending a kluge -- needs rewrite to use command-specific subclass)
cmdtype = _LOCAL_MIN
cmdname = "%s Atoms" % self.word_Minimize #bruce 060705; some code may assume this is always Adjust Atoms, as it is
# self.args is parsed later
else:
assert 0, "unknown cmd_subclass_code %r" % (cmd_subclass_code, )
self.cmdname = cmdname #e in principle this should come from a subclass for the specific command [bruce 051129 comment]
startmsg = cmdname + ": ..."
del cmd_subclass_code
# remove model objects inserted only for feedback from prior runs
# (both because it's a good feature, and to avoid letting them
# mess up this command) [bruce 080520]
from simulation.runSim import part_contains_pam_atoms
# kluge to use this function for this purpose
# (it's called later for other reasons)
hasPAM_junk = part_contains_pam_atoms(
self.part, kill_leftover_sim_feedback_atoms=True)
self.part.assy.update_parts() ###k is this always safe or good?
# Make sure some chunks are in the part.
# (Valid for all cmdtypes -- Minimize only moves atoms, even if affected by jigs.)
if not self.part.molecules: # Nothing in the part to minimize.
env.history.message(
greenmsg(cmdname + ": ") +
redmsg("Nothing to %s." % self.word_minimize))
return
if cmdtype == _MIN_SEL:
selection = self.part.selection_from_glpane(
) # compact rep of the currently selected subset of the Part's stuff
if not selection.nonempty():
msg = greenmsg(cmdname + ": ") + redmsg("Nothing selected.") + \
" (Use %s All to %s the entire Part.)" % (self.word_Minimize, self.word_minimize)
#e might need further changes for Minimize Energy, if it's confusing that Sel/All is a dialog setting then
env.history.message(msg)
return
elif cmdtype == _LOCAL_MIN:
from operations.ops_select import selection_from_atomlist
junk, atomlist, ntimes_expand = self.args
selection = selection_from_atomlist(
self.part, atomlist
) #e in cleaned up code, selection object might come from outside
selection.expand_atomset(ntimes=ntimes_expand) # ok if ntimes == 0
# Rationale for adding monovalent atoms to the selection before
# instantiating the sim_aspect
#
# (Refer to comments for sim_aspect.__init__.) Why is it safe to add
# monovalent atoms to a selection? Let's look at what happens during a
# local minimization.
#
# While minimizing, we want to simulate as if the entire rest of the
# part is grounded, and only our selection of atoms is free to move. The
# most obvious approach would be to minimize all the atoms in the part
# while applying anchors to the atoms that aren't in the selection. But
# minimizing all the atoms, especially if the selection is small, is very
# wasteful. Applying the simulator to atoms is expensive and we want to
# minimize as few atoms as possible.
#
# [revision, bruce 080513: this discussion applies for Adjust,
# but the policy for Minimize is being changed to always include
# all atoms, even if most of them are anchored,
# re nfr bug 2848 item 2.]
#
# A more economical approach is to anchor the atoms for two layers going
# out from the selection. The reason for going out two layers, and not just
# one layer, is that we need bond angle terms to simulate accurately. When
# we get torsion angles we will probably want to bump this up to three
# layers. [Now we're doing three layers -- bruce 080507]
#
# Imagine labeling all the atoms in the selection with zero. Then take the
# set of unlabeled atoms that are bonded to a zero-labeled atom, and label
# all the atoms in that set with one. Next, take the set of yet-unlabeled
# atoms that are bonded to a one-labeled atom, and label the atoms in that
# set with two. The atoms labeled one and two become our first and second
# layers, and we anchor them during the minimization.
#
# In sim_aspect.__init__, the labels for zero, one and two correspond
# respectively to membership in the dictionaries self._moving_atoms,
# self._boundary1_atoms, and self._boundary2_atoms.
#
# If an atom in the selection is anchored, we don't need to go two layers
# out from that atom, only one layer. So we can label it with one, even
# though it's a member of the selection and would normally be labeled with
# zero. The purpose in doing this is to give the simulator a few less atoms
# to worry about.
#
# If a jig includes one of the selected atoms, but additionally includes
# atoms outside the selection, then it may not be obvious how to simulate
# that jig. For the present, the only jig that counts in a local
# minimization is an anchor, because all the other jigs are too complicated
# to simulate.
#
# The proposed fix here has the effect that monovalent atoms bonded to
# zero-labeled atoms are also labeled zero, rather than being labeled one,
# so they are allowed to move. Why is this OK to do?
#
# (1) Have we violated the assumption that the rest of the part is locked
# down? Yes, as it applies to those monovalent atoms, but they are
# presumably acceptable violations, since bug 1240 is regarded as a bug.
#
# (2) Have we unlocked any bond lengths or bond angles that should remain
# locked? Again, only those which involve (and necessarily end at) the
# monovalent atoms in question. The same will be true when we introduce
# torsion terms.
#
# (3) Have we lost any ground on the jig front? If a jig includes one or
# more of the monovalent atoms, possibly - but the only jigs we are
# simulating in this case is anchors, and those will be handled correctly.
# Remember that anchored atoms are only extended one layer, not two, but
# with a monovalent atom bonded to a selected atom, no extension is
# possible at all.
#
# One can debate about whether bug 1240 should be regarded as a bug. But
# having accepted it as a bug, one cannot object to adding these monovalents
# to the original selection.
#
# wware 060410 bug 1240
atoms = selection.selatoms
for atom in atoms.values():
# enumerate the monovalents bonded to atom
for atom2 in filter(lambda atom: not atom.is_singlet(),
atom.baggageNeighbors()):
atoms[atom2.key] = atom2
else:
assert cmdtype == _MIN_ALL
selection = self.part.selection_for_all()
# like .selection_from_glpane() but for all atoms presently in the part [bruce 050419]
# no need to check emptiness, this was done above
self.selection = selection #e might become a feature of all CommandRuns, at some point
# At this point, the conditions are met to try to do the command.
env.history.message(
greenmsg(startmsg)) #bruce 050412 doing this earlier
# Disable some QActions (menu items/toolbar buttons) during minimize.
self.win.disable_QActions_for_sim(True)
try:
simaspect = sim_aspect(
self.part,
selection.atomslist(),
cmdname_for_messages=cmdname,
anchor_all_nonmoving_atoms=anchor_all_nonmoving_atoms)
#bruce 051129 passing cmdname
# note: atomslist gets atoms from selected chunks, not only selected atoms
# (i.e. it gets atoms whether you're in Select Atoms or Select Chunks mode)
# history message about singlets written as H (if any);
#bruce 051115 updated comment: this is used for both Minimize All and Minimize Selection as of long before 051115;
# for Run Sim this code is not used (so this history message doesn't go out for it, though it ought to)
# but the bug254 X->H fix is done (though different code sets the mapping flag that makes it happen).
nsinglets_H = simaspect.nsinglets_H()
if nsinglets_H: #bruce 051209 this message code is approximately duplicated elsewhere in this file
info = fix_plurals(
"(Treating %d bondpoint(s) as Hydrogens, during %s)" %
(nsinglets_H, self.word_minimization))
env.history.message(info)
nsinglets_leftout = simaspect.nsinglets_leftout()
assert nsinglets_leftout == 0 # for now
# history message about how much we're working on; these atomcounts include singlets since they're written as H
nmoving = simaspect.natoms_moving()
nfixed = simaspect.natoms_fixed()
info = fix_plurals("(%s %d atom(s)" %
(self.word_Minimizing, nmoving))
if nfixed:
them_or_it = (nmoving == 1) and "it" or "them"
if anchor_all_nonmoving_atoms:
msg2 = "holding remaining %d atom(s) fixed" % nfixed
else:
msg2 = "holding %d atom(s) fixed around %s" % (nfixed,
them_or_it)
info += ", " + fix_plurals(msg2)
info += ")"
env.history.message(info)
self.doMinimize(mtype=1, simaspect=simaspect)
# mtype = 1 means single-frame XYZ file.
# [this also sticks results back into the part]
#self.doMinimize(mtype = 2) # 2 = multi-frame DPB file.
finally:
self.win.disable_QActions_for_sim(False)
simrun = self._movie._simrun #bruce 050415 klugetower
if not simrun.said_we_are_done:
env.history.message("Done.")
return