def guiCallback(self):
if len(self.vf.Mols) == 0: return
self.chooser = MoleculeChooser(self.vf,
mode='extended',
title='Choose Molecules to delete')
self.undoableVar = Tkinter.IntVar()
self.undoableVar.set(1)
self.chooser.ipf.append({
'name': 'Undo',
'widgetType': Tkinter.Checkbutton,
'wcfg': {
'text': ' Undoable Delete',
'variable': self.undoableVar
},
'gridcfg': {
'sticky': Tkinter.E + Tkinter.W
}
})
self.chooser.ipf.append({
'name': 'Delete Button',
'widgetType': Tkinter.Button,
'text': 'Delete Molecule',
'wcfg': {
'bd': 6
},
'gridcfg': {
'sticky': Tkinter.E + Tkinter.W
},
'command': self.deleteMolecule_cb
})
self.form = self.chooser.go(modal=0, blocking=0)
def ClosestAtom():
"""ask for 2 molecules, compute for each atom
the distance to the closest atom in the other
molecule. After execution, each atom has a new
attribute 'closest' holding the distance"""
# it would be better to ask for the attribute's name also
from Pmv.guiTools import MoleculeChooser
p = MoleculeChooser(self, 'extended', 'Choose 2 molecules')
mols = p.go(modal=1)
mol1Atoms = mols[0].allAtoms
mol2Atoms = mols[1].allAtoms
def distanceToClosestPoint(point, setOfPoints):
"""computes the shortest distance between point and setOfPoints"""
diff = Numeric.array(point) - Numeric.array(setOfPoints)
diff = diff * diff
len = Numeric.sqrt(Numeric.sum(diff, 1))
return min(len)
for a in mol1Atoms:
a.closest = distanceToClosestPoint(a.coords, mol2Atoms.coords)
for a in mol2Atoms:
a.closest = distanceToClosestPoint(a.coords, mol1Atoms.coords)
def ClosestAtom():
"""ask for 2 molecules, compute for each atom
the distance to the closest atom in the other
molecule. After execution, each atom has a new
attribute 'closest' holding the distance"""
# it would be better to ask for the attribute's name also
from Pmv.guiTools import MoleculeChooser
p = MoleculeChooser(self, 'extended', 'Choose 2 molecules')
mols = p.go(modal=1)
mol1Atoms = mols[0].allAtoms
mol2Atoms = mols[1].allAtoms
def distanceToClosestPoint(point, setOfPoints):
"""computes the shortest distance between point and setOfPoints"""
diff = Numeric.array(point) - Numeric.array(setOfPoints)
diff = diff*diff
len = Numeric.sqrt(Numeric.sum(diff,1))
return min(len)
for a in mol1Atoms:
a.closest = distanceToClosestPoint( a.coords, mol2Atoms.coords)
for a in mol2Atoms:
a.closest = distanceToClosestPoint( a.coords, mol1Atoms.coords)
def sesExposurePercent():
"""Compute the percentage of solvent exposed surface for each amino acide.
After running this macro, each residue has the 2 following members:
ses_area: total surface area for this residue
ses_ratio: percentage of residue surface exposed to solvent
The ratio is the percentage of SES area exposed to the solvent in each
residue, where 100 is the surface of that particular residue when all other
atoms are ignored
"""
import mslib
import numpy.oldnumeric as Numeric
from Pmv.guiTools import MoleculeChooser
mol = MoleculeChooser(self).go(modal=0, blocking=1)
allrads = mol.defaultRadii()
allResidues = mol.chains.residues
allAtoms = mol.allAtoms
# compute the surface
srf = mslib.MSMS(coords=allAtoms.coords, radii=allrads)
srf.compute()
srf.compute_ses_area()
# get surface areas per atom
import swig
ses_areas = []
for i in xrange(srf.nbat):
atm = srf.get_atm(i)
ses_areas.append(swig.getdoublearray(atm.ses_area, (1,))[0])
# get surface areas to each atom
allAtoms.ses_area = ses_areas
# sum up ses areas over resdiues
for r in allResidues:
r.ses_area = Numeric.sum(r.atoms.ses_area)
# compute the surface for each residue independantly
# compute the % of ses
srfList = []
for r in allResidues:
coords = r.atoms.coords
rad = map(lambda x: x.radius, r.atoms)
m = mslib.MSMS(coords=coords, radii=rad)
m.compute()
m.compute_ses_area()
srfList.append(m)
if r.ses_area > 0.0:
r.ses_ratio = (r.ses_area * 100) / m.sesr.fst.a_ses_area
else:
r.ses_ratio = 0.0
def sesExposurePercent():
"""Compute the percentage of solvent exposed surface for each amino acide.
After running this macro, each residue has the 2 following members:
ses_area: total surface area for this residue
ses_ratio: percentage of residue surface exposed to solvent
The ratio is the percentage of SES area exposed to the solvent in each
residue, where 100 is the surface of that particular residue when all other
atoms are ignored
"""
import mslib
import numpy.oldnumeric as Numeric
from Pmv.guiTools import MoleculeChooser
mol = MoleculeChooser(self).go(modal=0, blocking=1)
allrads = mol.defaultRadii()
allResidues = mol.chains.residues
allAtoms = mol.allAtoms
# compute the surface
srf = mslib.MSMS(coords=allAtoms.coords, radii=allrads)
srf.compute()
srf.compute_ses_area()
# get surface areas per atom
ses_areas = []
for i in xrange(srf.nbat):
atm = srf.get_atm(i)
ses_areas.append(atm.get_ses_area(0))
# get surface areas to each atom
allAtoms.ses_area = ses_areas
# sum up ses areas over resdiues
for r in allResidues:
r.ses_area = Numeric.sum(r.atoms.ses_area)
# compute the surface for each residue independantly
# compute the % of ses
srfList = []
for r in allResidues:
coords = r.atoms.coords
rad = map(lambda x: x.radius, r.atoms)
m = mslib.MSMS(coords=coords, radii=rad)
m.compute()
m.compute_ses_area()
srfList.append(m)
if r.ses_area > 0.0:
r.ses_ratio = (r.ses_area * 100) / m.sesr.fst.a_ses_area
else:
r.ses_ratio = 0.0
def guiCallback(self):
if len(self.vf.Mols) == 0: return
self.chooser = MoleculeChooser(self.vf,mode = 'extended',
title='Choose Molecules to delete' )
self.chooser.ipf.append({'name':'Delete Button',
'widgetType':Tkinter.Button,
'text':'Delete Molecule',
'wcfg':{'bd':6},
'gridcfg':{'sticky':Tkinter.E+Tkinter.W},
'command': self.deleteMolecule_cb})
self.form = self.chooser.go(modal=0, blocking=0)
def selectObject():
"""Bind trackball to a user specified object.
Only geometries related to this object move, scaling
is disabled"""
from Pmv.guiTools import MoleculeChooser
mol = MoleculeChooser(self).go(modal=0, blocking=1)
vi = self.GUI.VIEWER
vi.TransformRootOnly(yesno=0)
obj = mol.geomContainer.geoms['master']
vi.SetCurrentObject(obj)
vi.BindTrackballToObject(obj)
vi.currentTransfMode = 'Object'
def setMobSequence(self):
molName = MoleculeChooser(self.vf).go().name
self.vf.alnEditor.master.lift()
if molName not in self.vf.alignment.seqNames:
return
#recolor the previous reference sequence, if it exists
if hasattr(self,'mobMolName'):
uniqtag = self.mobMolName+'_name'
item = self.vf.alnEditor.canvas.find_withtag(uniqtag)
color = self.vf.alnEditor.colors['default']
self.vf.alnEditor.canvas.itemconfig(item,fill=color)
uniqtag = molName+'_name'
self.vf.alnEditor.colors['special'][uniqtag]='green'
item = self.vf.alnEditor.canvas.find_withtag(uniqtag)
self.vf.alnEditor.canvas.itemconfig(item,fill='green')
self.mobMolName = molName
def getSequence(self,mol=None):
if not mol:
mol = MoleculeChooser(self.vf).go()
if not mol:
return
self.vf.alnEditor.master.lift()
#for extracting sequence(s) from molecules
chains = mol.children
seqList = []
numbers = []
for chain in chains:
seqList = seqList+chain.children.type+['-','|','-']
for residue in chain.children:
numbers.append(chain.name + residue.type + residue.number)
molSequence = Sequence(sequence=seqList,numbers=numbers,name=mol.name)
seqName = mol.name
if seqName in self.vf.alignment.seqNames:
# if sequence with this molecule name is already in the alignment,
# only need to update the numbers
sequence = self.vf.alignment.sequences[seqName]
sequence.applyNumbers(numbers)
return
self.vf.alignment.addSequence(molSequence)
self.vf.alnEditor.redraw()
def guiCallback(self):
if not hasattr(self.vf, "SL"):
self.warningMsg(
"This command requires 'SLCommands' module. Load the module.")
return
file = self.vf.askFileOpen(types=[('BSPT file', '*.bsp')],
title="Read .bsp")
if file:
root = Tkinter.Toplevel()
root.withdraw()
from SimpleDialog import SimpleDialog
ans = SimpleDialog(root,
text="Bind object to molecule?",
buttons=["Yes", "No", "Cancel"],
default=0,
title="new data dialog").go()
root.destroy()
mol = None
if ans == 0:
from Pmv.guiTools import MoleculeChooser
ans = MoleculeChooser(self.vf).go()
if ans:
mol = ans.name
apply(self.doitWrapper, (file, mol), {})
class DeleteMolecule(MVCommand):
"""Command to delete a molecule from the MoleculeViewer
\nPackage : Pmv
\nModule : deleteCommands
\nClass : DeleteMolecule
\nCommand : deleteMolecule
\nSynopsis:\n
None<---deleteMol(nodes, **kw)
\nRequired Arguments:\n
nodes --- TreeNodeSet holding the current selection
It resets the undo stack automatically.\n
"""
def onAddCmdToViewer(self):
self.vf._deletedLevels = []
if not self.vf.commands.has_key('select'):
self.vf.loadCommand("selectionCommands", "select", "Pmv",
topCommand=0)
if not self.vf.commands.has_key('clearSelection'):
self.vf.loadCommand("selectionCommands", "clearSelection", "Pmv",
topCommand=0)
def onAddObjectToViewer(self, obj):
if hasattr(self, 'chooser')\
and self.chooser is not None \
and self.form.root.winfo_exists():
w = self.chooser.form.descr.entryByName['Molecule']['widget']
molParser = obj.parser
molStr = molParser.getMoleculeInformation()
w.add((obj.name, molStr))
def deleteMolecule_cb(self):
"""called each time the 'Delete Molecule' button is pressed"""
mols = self.chooser.getMolSet()
if mols is not None and len(mols):
if self.vf.undoCmdStack == []:
self.doitWrapper(mols, redraw=0)
else:
text = """WARNING: This command cannot be undone.
if you choose to continue the undo list will be reset.
The hide Button will make the molecule disappear without
resetting the Undo list. Do you want to continue?"""
if not hasattr(self, 'idf'):
self.idf = InputFormDescr(title="WARNING")
self.idf.append({'widgetType':Tkinter.Label,
'wcfg':{'text':text},
'gridcfg':{'columnspan':3,'sticky':'w'}})
self.idf.append({'name': 'Continue Button',
'widgetType':Tkinter.Button,
'wcfg':{'text':'CONTINUE',
'command':self.continue_cb},
'gridcfg':{'sticky':'we'}})
self.idf.append({'name': 'Cancel Button',
'widgetType':Tkinter.Button,
'wcfg':{'text':'CANCEL',
'command':self.cancel_cb},
'gridcfg':{'row':-1,'sticky':'we'}})
self.idf.append({'name': 'Hide Button',
'widgetType':Tkinter.Button,
'wcfg':{'text':'HIDE',
'command':self.hide_cb},
'gridcfg':{'row':-1,'sticky':'we'}})
form = self.vf.getUserInput(self.idf, okcancel=0)
self.form.root.protocol('WM_DELETE_WINDOW',self.cancel_cb)
def hide_cb(self):
if hasattr(self, 'chooser'):
if self.chooser.ipf.form is not None:
mols = self.chooser.getMolSet()
self.vf.showMolecules(mols.name, negate=1, topCommand=0)
self.chooser.done_cb()
self.idf.form.destroy()
def continue_cb(self):
if hasattr(self, 'chooser'):
if self.chooser.ipf.form is not None:
mols = self.chooser.getMolSet()
self.vf.resetUndo(topCommand=0)
self.doitWrapper(mols, redraw=0)
self.idf.form.destroy()
def cancel_cb(self):
self.idf.form.destroy()
def guiCallback(self):
if len(self.vf.Mols) == 0: return
self.chooser = MoleculeChooser(self.vf,mode = 'extended',
title='Choose Molecules to delete' )
self.chooser.ipf.append({'name':'Delete Button',
'widgetType':Tkinter.Button,
'text':'Delete Molecule',
'wcfg':{'bd':6},
'gridcfg':{'sticky':Tkinter.E+Tkinter.W},
'command': self.deleteMolecule_cb})
self.form = self.chooser.go(modal=0, blocking=0)
def deleteMol(self, mol):
""" Function to delete all the references to each elements of a
molecule and then these elements and the molecule to free the
memory space."""
# Call the removeObject function for all the command having an
# onRemoveMol function
self.vf.removeObject(mol)
# Maybe do that in moleculeViewer ???
# also need to clean up selector.selection:
nodes = self.vf.getSelection()
mol.__class__._numberOfDeletedNodes = 0
node = mol
while len(node.children):
node = node.children
# Initialize the variable _numberOfDeletedNodes at 0
node[0].__class__._numberOfDeletedNodes = 0
sslevels = [Coil, Helix, Strand, Turn]
# Initialize the variable _numberOfDeletedNodes for each secondary
# structure to 0.
for sl in sslevels:
# Initialize the variable _numberOfDeletedNodes at 0
sl._numberOfDeletedNodes = 0
# but only change selection if there is any
if nodes is not None and len(nodes)>0:
setClass = nodes.__class__
thisMolNodes = setClass(nodes.get(lambda x, mol=mol: x.top==mol))
#only change selection if this molecule has any nodes in it
if len(thisMolNodes)>0:
nodes = nodes-thisMolNodes
self.vf.clearSelection(topCommand=0)
if nodes is not None:
self.vf.select(nodes)
#self.vf.selector.select(nodes)
if hasattr(self, 'chooser') and self.form.root.winfo_exists():
# update the listChooser
lc = self.chooser.ipf.entryByName['Molecule']['widget']
lc.remove(mol.name)
#lc.clearComments()
#check for any possible reference in self.vf.GUI.VIEWER.lastPick
if self.vf.hasGui and self.vf.GUI.VIEWER.lastPick:
for key in self.vf.GUI.VIEWER.lastPick.hits.keys():
if hasattr(key,'mol'):
if mol==key.mol:
del self.vf.GUI.VIEWER.lastPick.hits[key]
# Remove the atoms of the molecule you are deleting from the
# the AtomSet self.vf.allAtoms
self.vf.allAtoms = self.vf.allAtoms - mol.allAtoms
# Delete all the reference to the atoms you want to delete
if hasattr(mol.allAtoms, 'bonds'):
bnds = mol.allAtoms.bonds[0]
for b in bnds:
b.__dict__.clear()
del(b)
mol.allAtoms.__dict__.clear()
del mol.allAtoms
if self.vf.hasGui and hasattr(mol, 'geomContainer'):
for g in mol.geomContainer.geoms.values():
if hasattr(g, 'mol'):
delattr(g, 'mol')
mol.geomContainer.geoms.clear()
mol.geomContainer.atoms.clear()
delattr(mol.geomContainer, 'mol')
del mol.geomContainer
if hasattr(mol, 'atmNum'):
mol.atmNum.clear()
del mol.atmNum
if hasattr(mol, 'childByName'):
mol.childByName.clear()
del mol.childByName
if hasattr(mol, 'parser') and hasattr(mol.parser, 'mol'):
delattr(mol.parser,'mol')
del mol.parser
# delete molecule from Vision, if Vision is running
if self.vf.visionAPI:
self.vf.visionAPI.remove(mol)
if len(mol.children):
deletedLevels = mol.deleteSubTree()
else:
deletedLevels = []
# then delete all the refences to the molecule
del mol.top
# Then delete the molecule
deletedLevels.insert(0, mol.__class__)
mol.__dict__.clear()
del mol
self.vf._deletedLevels = deletedLevels
if len(self.vf.Mols) == 0 and hasattr(self, 'chooser') \
and self.form.root.winfo_exists():
self.chooser.done_cb()
def getFreeMemoryInformation(self):
"""Store how many TreeNodes have been actually free'ed during the
last delete operation in a dictionary"""
memoryInformation = {}
#print 'self.vf._deletedLevels=', self.vf._deletedLevels
for d in self.vf._deletedLevels:
#print 'checking ', d, ' for deletedNodes'
memoryInformation[d.__name__] = d._numberOfDeletedNodes
sslevels = [Coil, Helix, Strand, Turn]
## geomslevels = [IndexedPolylines, IndexedPolygons]
# Have to loop on the known secondarystructure because our
# Data structure doesn't support multiple children and parents.
for sl in sslevels:
if sl._numberOfDeletedNodes!=0:
memoryInformation[sl.__name__] = sl._numberOfDeletedNodes
## for sg in geomslevels:
## if sl._numberOfDeletedNodes!=0:
## memoryInformation[sl.__name__] = sl._numberOfDeletedNodes
return memoryInformation
def doit(self, nodes):
#if called with no selection, just return
molecules, nodeSets = self.vf.getNodesByMolecule(nodes)
for mol in molecules: self.deleteMol(mol)
def __call__(self, nodes, **kw):
"""None <- deleteMol(nodes, **kw)
\nnodes: TreeNodeSet holding the current selection.
\nIt resets the undo stack automatically.
"""
if type(nodes) is types.StringType:
self.nodeLogString = "'"+nodes+"'"
self.vf.resetUndo(topCommand=0)
apply ( self.doitWrapper, (nodes,), kw )
class DeleteMolecule(MVCommand):
"""Command to delete a molecule from the MoleculeViewer
\nPackage : Pmv
\nModule :
deleteCommands
\nClass : DeleteMolecule
\nCommand : deleteMolecule
\nSynopsis:\n
None<---deleteMol(nodes, **kw)
\nRequired Arguments:\n
nodes --- TreeNodeSet holding the current selection
It resets the undo stack automatically.\n
"""
def onAddCmdToViewer(self):
self.vf._deletedLevels = []
if not self.vf.commands.has_key('select'):
self.vf.loadCommand("selectionCommands",
"select",
"Pmv",
topCommand=0)
if not self.vf.commands.has_key('clearSelection'):
self.vf.loadCommand("selectionCommands",
"clearSelection",
"Pmv",
topCommand=0)
def onAddObjectToViewer(self, obj):
if hasattr(self, 'chooser')\
and self.chooser is not None \
and self.form.root.winfo_exists():
w = self.chooser.form.descr.entryByName['Molecule']['widget']
molParser = obj.parser
molStr = molParser.getMoleculeInformation()
w.add((obj.name, molStr))
def deleteMolecule_cb(self):
"""called each time the 'Delete Molecule' button is pressed"""
mols = self.chooser.getMolSet()
if mols is not None and len(mols):
if self.vf.undoCmdStack == []:
undoable = self.undoableVar.get()
for mol in mols:
self.doitWrapper(mol, redraw=0, undoable=undoable)
else:
self.continue_cb()
def hide_cb(self):
if hasattr(self, 'chooser'):
if self.chooser.ipf.form is not None:
mols = self.chooser.getMolSet()
self.vf.showMolecules(mols.name, negate=1, topCommand=0)
self.chooser.done_cb()
self.idf.form.destroy()
def continue_cb(self):
if hasattr(self, 'chooser'):
if self.chooser.ipf.form is not None:
mols = self.chooser.getMolSet()
undoable = self.undoableVar.get()
if not undoable:
self.vf.resetUndo(topCommand=0)
for mol in mols:
self.doitWrapper(mol, redraw=0, undoable=undoable)
#self.idf.form.destroy()
def cancel_cb(self):
self.idf.form.destroy()
def guiCallback(self):
if len(self.vf.Mols) == 0: return
self.chooser = MoleculeChooser(self.vf,
mode='extended',
title='Choose Molecules to delete')
self.undoableVar = Tkinter.IntVar()
self.undoableVar.set(1)
self.chooser.ipf.append({
'name': 'Undo',
'widgetType': Tkinter.Checkbutton,
'wcfg': {
'text': ' Undoable Delete',
'variable': self.undoableVar
},
'gridcfg': {
'sticky': Tkinter.E + Tkinter.W
}
})
self.chooser.ipf.append({
'name': 'Delete Button',
'widgetType': Tkinter.Button,
'text': 'Delete Molecule',
'wcfg': {
'bd': 6
},
'gridcfg': {
'sticky': Tkinter.E + Tkinter.W
},
'command': self.deleteMolecule_cb
})
self.form = self.chooser.go(modal=0, blocking=0)
def deleteMol(self, mol, undoable=False):
""" Function to delete all the references to each elements of a
molecule and then these elements and the molecule to free the
memory space."""
# Call the removeObject function for all the command having an
# onRemoveMol function
self.vf.removeObject(mol, undoable=undoable)
# Maybe do that in moleculeViewer ???
# also need to clean up selector.selection:
nodes = self.vf.getSelection()
mol.__class__._numberOfDeletedNodes = 0
node = mol
while len(node.children):
node = node.children
# Initialize the variable _numberOfDeletedNodes at 0
node[0].__class__._numberOfDeletedNodes = 0
sslevels = [Coil, Helix, Strand, Turn]
# Initialize the variable _numberOfDeletedNodes for each secondary
# structure to 0.
for sl in sslevels:
# Initialize the variable _numberOfDeletedNodes at 0
sl._numberOfDeletedNodes = 0
# but only change selection if there is any
if nodes is not None and len(nodes) > 0:
setClass = nodes.__class__
thisMolNodes = setClass(nodes.get(lambda x, mol=mol: x.top == mol))
#only change selection if this molecule has any nodes in it
if len(thisMolNodes) > 0:
nodes = nodes - thisMolNodes
self.vf.clearSelection(topCommand=0)
if nodes is not None:
self.vf.select(nodes)
#self.vf.selector.select(nodes)
if hasattr(self, 'chooser') and self.form.root.winfo_exists():
# update the listChooser
lc = self.chooser.ipf.entryByName['Molecule']['widget']
lc.remove(mol.name)
#lc.clearComments()
#check for any possible reference in self.vf.GUI.VIEWER.lastPick
if self.vf.hasGui and self.vf.GUI.VIEWER.lastPick:
for key in self.vf.GUI.VIEWER.lastPick.hits.keys():
if hasattr(key, 'mol'):
if mol == key.mol:
del self.vf.GUI.VIEWER.lastPick.hits[key]
# Remove the atoms of the molecule you are deleting from the
# the AtomSet self.vf.allAtoms
self.vf.allAtoms = self.vf.allAtoms - mol.allAtoms
if not undoable:
# Delete all the reference to the atoms you want to delete
if hasattr(mol.allAtoms, 'bonds'):
bnds = mol.allAtoms.bonds[0]
for b in bnds:
b.__dict__.clear()
del (b)
mol.allAtoms.__dict__.clear()
del mol.allAtoms
if self.vf.hasGui and hasattr(mol, 'geomContainer'):
for g in mol.geomContainer.geoms.values():
if hasattr(g, 'mol'):
delattr(g, 'mol')
mol.geomContainer.geoms.clear()
mol.geomContainer.atoms.clear()
delattr(mol.geomContainer, 'mol')
del mol.geomContainer
if hasattr(mol, 'atmNum'):
mol.atmNum.clear()
del mol.atmNum
if hasattr(mol, 'childByName'):
mol.childByName.clear()
del mol.childByName
if hasattr(mol, 'parser') and hasattr(mol.parser, 'mol'):
delattr(mol.parser, 'mol')
del mol.parser
# delete molecule from Vision, if Vision is running
if self.vf.visionAPI:
self.vf.visionAPI.remove(mol)
if not undoable:
if len(mol.children):
deletedLevels = mol.deleteSubTree()
else:
deletedLevels = []
# then delete all the refences to the molecule
del mol.top
# Then delete the molecule
deletedLevels.insert(0, mol.__class__)
mol.__dict__.clear()
del mol
self.vf._deletedLevels = deletedLevels
if len(self.vf.Mols) == 0 and hasattr(self, 'chooser') \
and self.form.root.winfo_exists():
self.chooser.done_cb()
def getFreeMemoryInformation(self):
"""Store how many TreeNodes have been actually free'ed during the
last delete operation in a dictionary"""
memoryInformation = {}
#print 'self.vf._deletedLevels=', self.vf._deletedLevels
for d in self.vf._deletedLevels:
#print 'checking ', d, ' for deletedNodes'
memoryInformation[d.__name__] = d._numberOfDeletedNodes
sslevels = [Coil, Helix, Strand, Turn]
## geomslevels = [IndexedPolylines, IndexedPolygons]
# Have to loop on the known secondarystructure because our
# Data structure doesn't support multiple children and parents.
for sl in sslevels:
if sl._numberOfDeletedNodes != 0:
memoryInformation[sl.__name__] = sl._numberOfDeletedNodes
## for sg in geomslevels:
## if sl._numberOfDeletedNodes!=0:
## memoryInformation[sl.__name__] = sl._numberOfDeletedNodes
return memoryInformation
def doit(self, nodes, undoable=False):
#if called with no selection, just return
molecules, nodeSets = self.vf.getNodesByMolecule(nodes)
event = BeforeDeleteMoleculesEvent(molecules)
self.vf.dispatchEvent(event)
for mol in molecules:
self.deleteMol(mol, undoable)
if self.vf.hasGui:
self.vf.GUI.VIEWER.SetCurrentObject(self.vf.GUI.VIEWER.rootObject)
if not undoable:
self.vf.resetUndo(topCommand=0)
def __call__(self, nodes, undoable=False, **kw):
"""None <- deleteMol(nodes, **kw)
\nnodes: TreeNodeSet holding the current selection.
"""
if type(nodes) is types.StringType:
self.nodeLogString = "'" + nodes + "'"
kw['undoable'] = undoable
self.doitWrapper(*(nodes, ), **kw)
def setupUndoBefore(self, molecule, undoable=False):
if undoable:
if type(molecule) is types.StringType:
molecules, nodeSets = self.vf.getNodesByMolecule(molecule)
if not len(molecules): return
molecule = molecules[0]
molecule.code = self.vf.getStateCodeForMolecule(molecule)
self.addUndoCall([molecule], {}, self.name)
def undo(self):
"""Undo for DeleteMolecule:
We use self.vf.getStateCodeForMolecule from setupUndoBefore to restore the state of the molecule.
"""
mol = self.undoStack.pop()
mol = mol[0][0]
self.vf.addMolecule(mol)
exec(mol.code, {'self': self.vf})
def doSetOperation(self, name1, name2, opname, res_name, bindToMol):
""" Performs Bspt set operations. """
ex = 0.5
expon = 1.0
bspt_set1 = None
bspt_set2 = None
if name1 in self.setdict.keys():
#check if we need to recompute the Bspt for the object
if self.recomputeBSPT1.get():
if hasattr(self.obj_dict[name1]['obj'], "SLnewobj"):
# this object had been created by SL :
# do not recompute
bspt_set1 = self.setdict[name1]
else:
#remove the computed Bspt from self.setdict
# remove a copy of the object from
# self.obj_dict so that the function could use
# updated arrays of vertices and faces.
del (self.setdict[name1])
if self.obj_dict[name1].has_key('copy_obj'):
del (self.obj_dict[name1]['copy_obj'])
else:
bspt_set1 = self.setdict[name1]
if not geometrylib.Size_of_Set(bspt_set1):
bspt_set1 = None
if not bspt_set1:
if self.obj_dict[name1].has_key('copy_obj'):
object1 = self.obj_dict[name1]['copy_obj']
else:
## if isinstance(self.obj_dict[name1]['obj'], GleObject):
## object1 = self.obj_dict[name1]['obj']
## else:
object1 = self.obj_dict[name1]['obj'].asIndexedPolygons(
run=1, removeDupVerts=0)
self.obj_dict[name1]['copy_obj'] = object1
v1 = object1.vertexSet.vertices.array
#print "object1: ", object1
## if isinstance(object1, GleObject):
## f1 = self.triangulate_strips(object1.faceSet.faces.array)
## else:
f1 = object1.faceSet.faces.array
#print "obj1, verts: ", len(v1), "faces: ", len(f1)
brep_set1 = sl.buildBrepSet(v1, f1)
t1 = time()
bspt_set1 = sl.Brep_To_Bspt(brep_set1, expense=ex, exponent=expon)
t2 = time()
print "time to build bspt_set1(%s) is %.5f " % (name1, (t2 - t1))
if name2 in self.setdict.keys():
if self.recomputeBSPT2.get():
if hasattr(self.obj_dict[name2]['obj'], "SLnewobj"):
bspt_set2 = self.setdict[name2]
else:
del (self.setdict[name2])
if self.obj_dict[name2].has_key('copy_obj'):
del (self.obj_dict[name2]['copy_obj'])
else:
bspt_set2 = self.setdict[name2]
if not geometrylib.Size_of_Set(bspt_set2):
bspt_set2 = None
if not bspt_set2:
if self.obj_dict[name2].has_key('copy_obj'):
object2 = self.obj_dict[name2]['copy_obj']
else:
object2 = self.obj_dict[name2]['obj'].asIndexedPolygons(
run=1, removeDupVerts=0)
self.obj_dict[name2]['copy_obj'] = object2
#print "object2: ", object2
v2 = object2.vertexSet.vertices.array
## if isinstance(object2, GleObject):
## f2 = self.triangulate_strips(object2.faceSet.faces.array)
## else:
f2 = object2.faceSet.faces.array
brep_set2 = sl.buildBrepSet(v2, f2)
t1 = time()
bspt_set2 = sl.Brep_To_Bspt(brep_set2, expense=ex, exponent=expon)
t2 = time()
print "time to build bspt_set2(%s) is %.5f " % (name2, (t2 - t1))
rset = sl.operateBsptSets(bspt_set1,
bspt_set2,
opname,
expense=ex,
copy="duplicate")
brep_set = sl.convert_to_Brep(rset, expense=ex, duplicate=1)
verts, faces, vnorms, fnorms = sl.getBoundaries(brep_set,
has_vnormals=0,
has_fnormals=1)
vs, fs, vns, fns = sl.indexedFromArr(verts, faces, fnorms=fnorms)
#sl.discardSet(brep_set)
#brep_set = None
if find(res_name, "_"): #name should not contain "_"
res_name = replace(res_name, "_", "-")
## if vs:
## length = map( len, fs)
## mlength = max(length)
## for i in range(len(fs)):
## d = mlength-len(fs[i])
## if d:
## for j in range(d):
## fs[i].append(-1)
vi = self.vf.GUI.VIEWER
mol = None
res_fullname = 'root|' + res_name
if bindToMol:
from Pmv.guiTools import MoleculeChooser
mol = MoleculeChooser(self.vf).go()
if mol:
#mol_geom = self.vf.Mols.NodesFromName( molname )[0].geomContainer.masterGeom
mol_geom = mol.geomContainer.masterGeom
res_fullname = mol_geom.fullName + '|' + res_name
#find if an object with the same name already exists:
obj_fullnames = self.obj_dict.keys()
objnames = map(lambda x: split(x, '|')[-1], obj_fullnames)
overwrite = False
if res_name in objnames:
ind = objnames.index(res_name)
if res_fullname in obj_fullnames:
ipg = self.obj_dict[res_fullname]['obj']
if hasattr(ipg, "SLnewobj"): # the object is a result
# of SL operation
if ipg.SLnewobj:
overwrite = True # will overwrite the object's
# vertices and faces arrays
## if not overwrite:
## ipg = self.obj_dict[ obj_fullnames[ind] ]['obj']
## if isinstance(ipg, IndexedPolygons):
## #ask the user :
## root = Tkinter.Toplevel()
## root.withdraw()
## from SimpleDialog import SimpleDialog
## ans = SimpleDialog(root, text="Object %s exists. Overwrite it?"% (obj_fullnames[ind],),
## buttons=["Yes", "No"],
## default=0,
## title="overwrite dialog").go()
## root.destroy()
## if ans == 0:
## overwrite = True
if overwrite:
ipg.Set(vertices=vs,
faces=fs,
fnormals=fns,
freshape=True,
tagModified=False)
if mol:
cl_atoms = self.vf.bindGeomToMolecularFragment(ipg,
mol.name,
log=0)
#addToViewer=False, log=0)
if cl_atoms:
#self.vf.bindGeomToMolecule.data[res_name]['fns']=fns
self.vf.bindGeomToMolecularFragment.data[
ipg.fullName]['fns'] = fns
else:
ipg = IndexedPolygons(
res_name,
vertices=vs,
faces=fs, #fnormals=fns,
#materials=col2,
visible=1,
inheritMaterial=0,
protected=True,
)
if self.vf.userpref['Sharp Color Boundaries for MSMS'][
'value'] == 'blur':
ipg.Set(
inheritSharpColorBoundaries=False,
sharpColorBoundaries=False,
)
if mol:
cl_atoms = self.vf.bindGeomToMolecularFragment(ipg,
mol.name,
log=0)
if cl_atoms:
#self.vf.bindGeomToMolecule.data[res_name]['fns']=fns
self.vf.bindGeomToMolecularFragment.data[
ipg.fullName]['fns'] = fns
else:
vi.AddObject(ipg)
else:
vi.AddObject(ipg)
ipg.Set(frontPolyMode=GL.GL_FILL, shading=GL.GL_FLAT)
ipg.Set(fnormals=fns, tagModified=False)
self.setdict[ipg.fullName] = rset
ipg.SLnewobj = True
print "size of bspt_set1:", geometrylib.Size_of_Set(bspt_set1)
print "size of bspt_set2:", geometrylib.Size_of_Set(bspt_set2)
print "size of rset:", geometrylib.Size_of_Set(rset)
else:
print "Number of vertices of the resultant object is 0."
if name1 not in self.setdict.keys():
self.setdict[name1] = bspt_set1
if name2 not in self.setdict.keys():
self.setdict[name2] = bspt_set2