def partChanged(self, selectedItem):
"""
Method called when user changed the partlib browser tree.
@param selectedItem: Item currently selected in the L{self.partLib}
@type selectedItem: L{self.partLib.FileItem}
@attention: This is called in the L{PM_TreeView.mouseReleaseEvent}. The
'selectionChanged' signal for self.partLib apparently was not emitted
so that code has been removed.
"""
#Copying some old code from deprecated MMKit.py -- ninad 2007-09-06
item = selectedItem
self.newModel = None
if isinstance(item, self.partLib.FileItem):
mmpFile = str(item.getFileObj())
if os.path.isfile(mmpFile):
self.newModel = \
Assembly(self.w,
os.path.normpath(mmpFile),
run_updaters = True # desirable for PartLib [bruce 080403]
)
self.newModel.set_glpane(
self.elementViewer) # sets its .o and .glpane
readmmp(self.newModel, mmpFile)
self.newModel.update_parts(
) #k not sure if needed after readmmp
self.newModel.checkparts()
if self.newModel.shelf.members:
for m in self.newModel.shelf.members[:]:
m.kill() #k guess about a correct way to handle them
self.newModel.update_parts() #k probably not needed
self.newModel.checkparts() #k probably not needed
self._updateElementViewer(self.newModel)
def partChanged(self, selectedItem):
"""
Method called when user changed the partlib browser tree.
@param selectedItem: Item currently selected in the L{self.partLib}
@type selectedItem: L{self.partLib.FileItem}
@attention: This is called in the L{PM_TreeView.mouseReleaseEvent}. The
'selectionChanged' signal for self.partLib apparently was not emitted
so that code has been removed.
"""
#Copying some old code from deprecated MMKit.py -- ninad 2007-09-06
item = selectedItem
self.newModel = None
if isinstance(item, self.partLib.FileItem):
mmpFile = str(item.getFileObj())
if os.path.isfile(mmpFile):
self.newModel = \
Assembly(self.w,
os.path.normpath(mmpFile),
run_updaters = True # desirable for PartLib [bruce 080403]
)
self.newModel.set_glpane(self.elementViewer) # sets its .o and .glpane
readmmp(self.newModel, mmpFile)
self.newModel.update_parts() #k not sure if needed after readmmp
self.newModel.checkparts()
if self.newModel.shelf.members:
for m in self.newModel.shelf.members[:]:
m.kill() #k guess about a correct way to handle them
self.newModel.update_parts() #k probably not needed
self.newModel.checkparts() #k probably not needed
self._updateElementViewer(self.newModel)
def _libPageView(self, isFile = False):
item = self.dirView.selectedItem()
if not isFile and not isinstance(item, self.FileItem):
self.newModel = None
self.elemGLPane.updateModel(self.newModel)
return
mmpfile = str(item.getFileObj())
if os.path.isfile(mmpfile):
#self.newModel = Assembly(self.w, "Assembly 1")
self.newModel = Assembly(self.w, os.path.normpath(mmpfile)) #ninad060924 to fix bug 1164
self.newModel.o = self.elemGLPane ## Make it looks "Assembly" used by glpane.
readmmp(self.newModel, mmpfile)
# What we did in Qt 3:
## #self.newModel = Assembly(self.w, "Assembly 1")
## self.newModel = Assembly(self.w, os.path.normpath(mmpfile)) #ninad060924 to fix bug 1164
## self.newModel.o = self.elemGLPane ## Make it looks "Assembly" used by glpane.
## readmmp(self.newModel, mmpfile)
## # The following is absolute nonsense, and is part of what's breaking the fix of bug 2028,
## # so it needs to be revised, to give this assy a standard structure.
## # We'll have to find some other way to draw the hotspot singlet
## # (e.g. a reasonable, straightforward way). So we did -- MMKitView.always_draw_hotspot is True.
## # [bruce 060627]
## ## # Move all stuff under assembly.tree into assy.shelf. This is needed to draw hotspot singlet
## ## def addChild(child):
## ## self.newModel.shelf.addchild(child)
## ##
## ## # Remove existing clipboard items from the libary part before adopting childern from 'tree'.
## ## self.newModel.shelf.members = []
## ## self.newModel.tree.apply2all(addChild)
## ##
## ## self.newModel.shelf.prior_part = None
## ## self.newModel.part = Part(self.newModel, self.newModel.shelf)
## if 1: #bruce 060627
self.newModel.update_parts() #k not sure if needed after readmmp)
self.newModel.checkparts()
if self.newModel.shelf.members:
if debug_flags.atom_debug:
print "debug warning: library part %r contains clipboard items" % mmpfile
# we'll see if this is common
# happens for e.g. nanokids/nanoKid-C39H42O2.mmp
for m in self.newModel.shelf.members[:]:
m.kill() #k guess about a correct way to handle them
self.newModel.update_parts() #k probably not needed
self.newModel.checkparts() #k probably not needed
else:
self.newModel = None
self.elemGLPane.updateModel(self.newModel)
def insertBaseFromMmp(filename, subgroup, tfm, position = position):
"""
Insert the atoms for a nucleic acid base from an MMP file into
a single chunk.
- If atomistic, the atoms for each base are in a separate chunk.
- If PAM5, the pseudo atoms for each base-pair are together in a
chunk.
@param filename: The mmp filename containing the base
(or base-pair).
@type filename: str
@param subgroup: The part group to add the atoms to.
@type subgroup: L{Group}
@param tfm: Transform applied to all new base atoms.
@type tfm: V
@param position: The origin in space of the DNA duplex, where the
3' end of strand A is 0, 0, 0.
@type position: L{V}
"""
try:
ok, grouplist = readmmp(assy, filename, isInsert = True)
except IOError:
raise PluginBug("Cannot read file: " + filename)
if not grouplist:
raise PluginBug("No atoms in DNA base? " + filename)
viewdata, mainpart, shelf = grouplist
for member in mainpart.members:
# 'member' is a chunk containing a set of base-pair atoms.
for atm in member.atoms.values():
atm._posn = tfm(atm._posn) + position
if atm.element.symbol in ('Se3', 'Ss3', 'Ss5'):
if atm.getDnaBaseName() == "a":
baseLetter = currentBaseLetter
else:
try:
baseLetter = \
basesDict[currentBaseLetter]['Complement']
except:
# If complement not found, just assign same
# letter.
baseLetter = currentBaseLetter
if 0:
print "Ss(%r) being set to %r." \
% (atm.getDnaBaseName(), baseLetter)
atm.setDnaBaseName(baseLetter)
member.name = currentBaseLetter
subgroup.addchild(member)
baseList.append(member)
# Clean up.
del viewdata
shelf.kill()
def insertBaseFromMmp(filename, subgroup, tfm, position=position):
"""
Insert the atoms for a nucleic acid base from an MMP file into
a single chunk.
- If atomistic, the atoms for each base are in a separate chunk.
- If PAM5, the pseudo atoms for each base-pair are together in a
chunk.
@param filename: The mmp filename containing the base
(or base-pair).
@type filename: str
@param subgroup: The part group to add the atoms to.
@type subgroup: L{Group}
@param tfm: Transform applied to all new base atoms.
@type tfm: V
@param position: The origin in space of the DNA duplex, where the
3' end of strand A is 0, 0, 0.
@type position: L{V}
"""
try:
ok, grouplist = readmmp(assy, filename, isInsert=True)
except IOError:
raise PluginBug("Cannot read file: " + filename)
if not grouplist:
raise PluginBug("No atoms in DNA base? " + filename)
viewdata, mainpart, shelf = grouplist
for member in mainpart.members:
# 'member' is a chunk containing a set of base-pair atoms.
for atm in member.atoms.values():
atm._posn = tfm(atm._posn) + position
if atm.element.symbol in ('Se3', 'Ss3', 'Ss5'):
if atm.getDnaBaseName() == "a":
baseLetter = currentBaseLetter
else:
try:
baseLetter = \
basesDict[currentBaseLetter]['Complement']
except:
# If complement not found, just assign same
# letter.
baseLetter = currentBaseLetter
if 0:
print "Ss(%r) being set to %r." \
% (atm.getDnaBaseName(), baseLetter)
atm.setDnaBaseName(baseLetter)
member.name = currentBaseLetter
subgroup.addchild(member)
baseList.append(member)
# Clean up.
del viewdata
shelf.kill()
def read_mmp_single_part(assy, filename):
from files.mmp.files_mmp import readmmp
# start incredible kluge block
history = env.history
#bruce 050901 revised this.
# It depends on there being only one active history object at a time.
# (Before 050913, that object was stored as both env.history and win.history.)
oldmessage = history.message
from utilities.constants import noop
history.message = noop # don't bother user with this file being nonstd (bad, should pass a flag, so other errors seen)
try:
ok, grouplist = readmmp(assy, filename, isInsert = True)
finally:
history.message = oldmessage
if grouplist:
viewdata, mainpart, shelf = grouplist
return mainpart.steal_members() # a python list of whatever toplevel stuff was in the mmp file
return None
def insert_output(self, outfiles, params, name):
## return self.create_methane_test(params, name)
if debug_run():
print "inserting output from", outfiles ###@@@
# modified from dna generator's local function insertmmp(filename, tfm)
assert len(outfiles) == 1 # for now
filename = outfiles[0]
assert filename.endswith(
'.mmp'
) # for now; in future, also permit .pdb or anything else we know how to read
assy = self.win.assy #k
from files.mmp.files_mmp import readmmp
ok_junk, grouplist = readmmp(assy, filename, isInsert=True)
# WARNING: ok_junk is not a boolean; see readmmp doc for details
if not grouplist:
raise Exception(
"Trouble with output file: " + filename
) ###@@@ predict NameError: Exception (good enough for now)
viewdata, mainpart, shelf = grouplist
if len(mainpart.members) == 1:
thing = mainpart.members[0]
else:
thing = mainpart # won't happen for now
del viewdata #k or kill?
thing.name = name
shelf.kill()
# wware 060704 - fix valence problems on the ends
while True:
found_one = False
for atm in thing.atoms.values():
if atm.element.symbol == 'C' and len(atm.realNeighbors()) == 1:
atm.kill()
found_one = True
if not found_one:
break
for atm in thing.atoms.values():
if atm.element.symbol == 'C' and len(atm.realNeighbors()) == 2:
atm.set_atomtype('sp2', always_remake_bondpoints=True)
# problem: for some kinds of errors, the only indication is that we're inserting a 0-atom mol, not a many-atom mol. hmm.
####@@@@
return thing # doesn't actually insert it, GBC does that
def insert_output(self, outfiles, params, name):
## return self.create_methane_test(params, name)
if debug_run():
print "inserting output from",outfiles ###@@@
# modified from dna generator's local function insertmmp(filename, tfm)
assert len(outfiles) == 1 # for now
filename = outfiles[0]
assert filename.endswith('.mmp') # for now; in future, also permit .pdb or anything else we know how to read
assy = self.win.assy #k
from files.mmp.files_mmp import readmmp
ok_junk, grouplist = readmmp(assy, filename, isInsert = True)
# WARNING: ok_junk is not a boolean; see readmmp doc for details
if not grouplist:
raise Exception("Trouble with output file: " + filename)###@@@ predict NameError: Exception (good enough for now)
viewdata, mainpart, shelf = grouplist
if len(mainpart.members) == 1:
thing = mainpart.members[0]
else:
thing = mainpart # won't happen for now
del viewdata #k or kill?
thing.name = name
shelf.kill()
# wware 060704 - fix valence problems on the ends
while True:
found_one = False
for atm in thing.atoms.values():
if atm.element.symbol == 'C' and len(atm.realNeighbors()) == 1:
atm.kill()
found_one = True
if not found_one:
break
for atm in thing.atoms.values():
if atm.element.symbol == 'C' and len(atm.realNeighbors()) == 2:
atm.set_atomtype('sp2', always_remake_bondpoints = True)
# problem: for some kinds of errors, the only indication is that we're inserting a 0-atom mol, not a many-atom mol. hmm.
####@@@@
return thing # doesn't actually insert it, GBC does that
