def buildCloseContactAtoms(self, percentCutoff, ligand, comment="USER AD> "):
pairDict = self.distanceSelector.select(ligand.allAtoms,
self.macro_atoms, percentCutoff=percentCutoff)
self.pairDict = pairDict
#reset here
lig_close_ats = AtomSet()
macro_close_ats = AtomSet()
cdict = {}
for k,v in list(pairDict.items()):
if len(v):
cdict[k] = 1
for at in v:
if at not in macro_close_ats:
cdict[at] = 1
closeAtoms = AtomSet(list(cdict.keys()))
lig_close_ats = closeAtoms.get(lambda x: x.top==ligand).uniq()
#ligClAtStr = lig_close_ats.full_name()
ligClAtStr = comment + "lig_close_ats: %d\n" %( len(lig_close_ats))
if len(lig_close_ats):
ligClAtStr += comment + "%s\n" %( lig_close_ats.full_name())
macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms).uniq()
macroClAtStr = comment + "macro_close_ats: %d\n" %( len(macro_close_ats))
if len(macro_close_ats):
macroClAtStr += comment + "%s\n" %( macro_close_ats.full_name())
#macroClAtStr = "macro_close_ats: " + len(macro_close_ats)+"\n" +macro_close_ats.full_name()
rdict = self.results
rdict['lig_close_atoms'] = lig_close_ats
rdict['macro_close_atoms'] = macro_close_ats
if self.verbose: print("macroClAtStr=", macroClAtStr)
if self.verbose: print("ligClAtStr=", ligClAtStr)
if self.verbose: print("returning "+ macroClAtStr + '==' + ligClAtStr)
return macroClAtStr , ligClAtStr
def buildCloseContactAtoms(self, percentCutoff, ligand, comment="USER AD> "):
pairDict = self.distanceSelector.select(ligand.allAtoms,
self.macro_atoms, percentCutoff=percentCutoff)
self.pairDict = pairDict
#reset here
lig_close_ats = AtomSet()
macro_close_ats = AtomSet()
cdict = {}
for k,v in pairDict.items():
if len(v):
cdict[k] = 1
for at in v:
if at not in macro_close_ats:
cdict[at] = 1
closeAtoms = AtomSet(cdict.keys())
lig_close_ats = closeAtoms.get(lambda x: x.top==ligand).uniq()
#ligClAtStr = lig_close_ats.full_name()
ligClAtStr = comment + "lig_close_ats: %d\n" %( len(lig_close_ats))
if len(lig_close_ats):
ligClAtStr += comment + "%s\n" %( lig_close_ats.full_name())
macro_close_ats = closeAtoms.get(lambda x: x in self.macro_atoms).uniq()
macroClAtStr = comment + "macro_close_ats: %d\n" %( len(macro_close_ats))
if len(macro_close_ats):
macroClAtStr += comment + "%s\n" %( macro_close_ats.full_name())
#macroClAtStr = "macro_close_ats: " + len(macro_close_ats)+"\n" +macro_close_ats.full_name()
rdict = self.results
rdict['lig_close_atoms'] = lig_close_ats
rdict['macro_close_atoms'] = macro_close_ats
if self.verbose: print "macroClAtStr=", macroClAtStr
if self.verbose: print "ligClAtStr=", ligClAtStr
if self.verbose: print "returning "+ macroClAtStr + '==' + ligClAtStr
return macroClAtStr , ligClAtStr
def setupUndoAfter(self, ats, angle,**kw):
#no atoms, <4 atoms,
aSet = AtomSet(self.atomList)
self.undoMenuString = self.name
if len(self.atomList)==0:
undoCmd = 'self.setTorsionGC.atomList=[]; self.setTorsionGC.update()'
elif len(self.atomList)<4:
#need to step back here
undoCmd = 'self.setTorsionGC.atomList=self.setTorsionGC.atomList[:-1]; self.setTorsionGC.update()'
elif self.origValue==self.oldValue:
return
else:
restoreAngle = self.origValue
self.undoNow = 1
undoCmd = 'self.setTorsionGC(\''+ aSet.full_name()+ '\',' + str(restoreAngle) + ', topCommand=0)'
self.vf.undo.addEntry((undoCmd), (self.name))
def setupUndoAfter(self, ats, angle, **kw):
#no atoms, <4 atoms,
aSet = AtomSet(self.atomList)
self.undoMenuString = self.name
if len(self.atomList) == 0:
undoCmd = 'self.setTorsionGC.atomList=[]; self.setTorsionGC.update()'
elif len(self.atomList) < 4:
#need to step back here
undoCmd = 'self.setTorsionGC.atomList=self.setTorsionGC.atomList[:-1]; self.setTorsionGC.update()'
elif self.origValue == self.oldValue:
return
else:
restoreAngle = self.origValue
self.undoNow = 1
undoCmd = 'self.setTorsionGC(\'' + aSet.full_name() + '\',' + str(
restoreAngle) + ', topCommand=0)'
self.vf.undo.addEntry((undoCmd), (self.name))
class AddBondsGUICommand(MVCommand, MVAtomICOM):
"""
The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them. To use this command you need first to load it into PMV. Then you can find the entry 'addBonds' under the Edit menu. To add bonds you just need to pick on the 2 atoms you want to bind. If you drag select a bunch of atoms, the command will buildBondsByDistance between them.This command is undoable.
\nPackage : Pmv
\nModule : bondsCommands
\nClass : AddBondsGUICommand
\nCommand : addBondsGC
\nSynopsis:\n
None<-addBondsGC(atoms)\n
\nRequired Arguments:\n
atoms : atom(s)\n
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.atomList = AtomSet([])
self.undoAtList = AtomSet([])
self.labelStrs = []
def onRemoveObjectFromViewer(self, obj):
removeAts = AtomSet([])
for at in self.atomList:
if at in obj.allAtoms:
removeAts.append(at)
self.atomList = self.atomList - removeAts
removeAts = AtomSet([])
for at in self.undoAtList:
if at in obj.allAtoms:
removeAts.append(at)
self.undoAtList = self.undoAtList - removeAts
self.update()
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands',
'setICOM',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('addBonds'):
self.vf.loadCommand('bondsCommands',
'addBonds',
'Pmv',
topCommand=0)
if not self.vf.commands.has_key('removeBondsGC'):
self.vf.loadCommand('bondsCommands',
'removeBondsGC',
'Pmv',
topCommand=0)
self.masterGeom = Geom('addBondsGeom',
shape=(0, 0),
pickable=0,
protected=True)
self.masterGeom.isScalable = 0
self.spheres = Spheres(name='addBondsSpheres',
shape=(0, 3),
inheritMaterial=0,
radii=0.2,
quality=15,
materials=((1., 1., 0.), ),
protected=True)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands', [
'labelByExpression',
],
'Pmv',
topCommand=0)
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)
def __call__(self, atoms, **kw):
"""None<-addBondsGC(atoms)
\natoms : atom(s)"""
if type(atoms) is StringType:
self.nodeLogString = "'" + atoms + "'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (ats, ), kw)
def doit(self, ats):
if len(ats) > 2:
if len(self.atomList):
atSet = ats + self.atomList
else:
atSet = ats
parent = atSet[0].parent
parent.buildBondsByDistanceOnAtoms(atSet)
self.atomList = AtomSet([])
self.update(True)
else:
lenAts = len(self.atomList)
last = None
if lenAts:
last = self.atomList[-1]
top = self.atomList[0].top
for at in ats:
#check for repeats of same atom
if lenAts and at == last:
continue
#lenAts = len(self.atomList)
#if lenAts and at==self.atomList[-1]:
# continue
if lenAts and at.top != self.atomList[-1].top:
msg = "intermolecular bond to %s disallowed" % (
at.full_name())
self.warningMsg(msg)
self.atomList.append(at)
self.undoAtList.append(at)
lenAts = len(self.atomList)
self.update(True)
#if only have one atom, there is nothing else to do
if lenAts < 2: return
#now build bonds between pairs of atoms
atSet = self.atomList
if lenAts % 2 != 0:
atSet = atSet[:-1]
#all pairs of atoms will be bonded
#so keep only the last one
self.atomList = atSet[-1:]
lenAts = lenAts - 1
else:
self.vf.labelByExpression(self.atomList,
negate=1,
topCommand=0)
self.atomList = AtomSet([])
for i in range(0, lenAts, 2):
at1 = atSet[i]
at2 = atSet[i + 1]
self.vf.addBonds(at1, at2, origin='UserDefined', topCommand=0)
self.update(True)
def applyTransformation(self, pt, mat):
pth = [pt[0], pt[1], pt[2], 1.0]
return Numeric.dot(mat, pth)[:3]
def getTransformedCoords(self, atom):
if not atom.top.geomContainer:
return atom.coords
g = atom.top.geomContainer.geoms['master']
c = self.applyTransformation(atom.coords, g.GetMatrix(g))
return c.astype('f')
def update(self, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[], tagModified=False)
self.vf.labelByExpression(self.atomList, negate=1, topCommand=0)
if self.vf.hasGui:
self.vf.GUI.VIEWER.Redraw()
return
self.lineVertices = []
#each time have to recalculate lineVertices
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
if event:
self.spheres.Set(vertices=self.lineVertices, tagModified=False)
self.vf.labelByExpression(self.atomList,
function='lambda x: x.full_name()',
lambdaFunc=1,
textcolor='yellow',
format='',
negate=0,
location='Last',
log=0,
font='arial1.glf',
only=1,
topCommand=0)
#setting spheres doesn't trigger redraw so do it explicitly
if self.vf.hasGui:
self.vf.GUI.VIEWER.Redraw()
def guiCallback(self, event=None):
self.save = self.vf.ICmdCaller.commands.value["Shift_L"]
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
def setupUndoAfter(self, ats, **kw):
lenUndoAts = len(self.undoAtList)
lenAts = len(ats)
if lenAts == 1:
#after adding 1 self.atomList would be 1 or 0
if len(self.atomList) == 1:
s = '0'
ustr = '"c=self.addBondsGC; self.labelByExpression(c.atomList, negate=1, topCommand=0);c.atomList=c.atomList[:' + s + '];c.undoAtList=c.undoAtList[:-1];c.update()"'
else:
self.vf.undoCmdStack.remove(self.prev_undoCmds)
ind = str(lenUndoAts - 2)
ustr = '"c=self.addBondsGC;nodes=self.expandNodes(' + '\'' + self.undoAtList[
-2:].full_name(
) + '\'' + '); bonds=nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.atomList=nodes[:1];c.undoAtList=c.undoAtList[:' + ind + '];c.update()"'
elif lenUndoAts > lenAts:
ustr = '"c=self.addBondsGC;nodes=self.expandNodes(' + '\'' + ats.full_name(
) + '\'' + ');bonds = nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.undoAtList=c.undoAtList[:' + str(
lenAts) + ']"'
else:
ustr = '"c=self.addBondsGC;nodes=self.expandNodes(' + '\'' + ats.full_name(
) + '\'' + ');bonds = nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.undoAtList=c.undoAtList[:0]"'
if len(self.atomList) and lenAts > 1:
atStr = self.atomList.full_name()
estr = ';nodes=self.expandNodes(' + '\'' + self.atomList.full_name(
) + '\'' + ');c.atomList=nodes;c.update()"'
ustr = ustr + estr
self.undoCmds = "exec(" + ustr + ")"
self.prev_undoCmds = (self.undoCmds, "addBondsGC")
def startICOM(self):
self.vf.setIcomLevel(Atom, topCommand=0)
def stopICOM(self):
if len(self.atomList) != 0:
self.vf.labelByExpression(self.atomList, negate=1, topCommand=0)
del self.atomList[:]
self.labelStrs = []
self.spheres.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
self.save = None
class AddBondsGUICommand(MVCommand, MVAtomICOM):
"""
The AddBondGUICommand provides an interactive way of creating bonds between two given atoms by picking on them. To use this command you need first to load it into PMV. Then you can find the entry 'addBonds' under the Edit menu. To add bonds you just need to pick on the 2 atoms you want to bind. If you drag select a bunch of atoms, the command will buildBondsByDistance between them.This command is undoable.
\nPackage : Pmv
\nModule : bondsCommands
\nClass : AddBondsGUICommand
\nCommand : addBondsGC
\nSynopsis:\n
None<-addBondsGC(atoms)\n
\nRequired Arguments:\n
atoms : atom(s)\n
"""
def __init__(self, func=None):
MVCommand.__init__(self, func)
MVAtomICOM.__init__(self)
self.atomList = AtomSet([])
self.undoAtList = AtomSet([])
self.labelStrs = []
def onRemoveObjectFromViewer(self, obj):
removeAts = AtomSet([])
for at in self.atomList:
if at in obj.allAtoms:
removeAts.append(at)
self.atomList = self.atomList - removeAts
removeAts = AtomSet([])
for at in self.undoAtList:
if at in obj.allAtoms:
removeAts.append(at)
self.undoAtList = self.undoAtList - removeAts
self.update()
def onAddCmdToViewer(self):
if not self.vf.commands.has_key('setICOM'):
self.vf.loadCommand('interactiveCommands', 'setICOM', 'Pmv',
topCommand=0)
if not self.vf.commands.has_key('addBonds'):
self.vf.loadCommand('bondsCommands', 'addBonds', 'Pmv',
topCommand=0)
if not self.vf.commands.has_key('removeBondsGC'):
self.vf.loadCommand('bondsCommands', 'removeBondsGC', 'Pmv',
topCommand=0)
self.masterGeom = Geom('addBondsGeom',shape=(0,0),
pickable=0, protected=True)
self.masterGeom.isScalable = 0
self.spheres = Spheres(name='addBondsSpheres', shape=(0,3),
inheritMaterial=0,
radii=0.2, quality=15,
materials = ((1.,1.,0.),), protected=True)
if not self.vf.commands.has_key('labelByExpression'):
self.vf.loadCommand('labelCommands',
['labelByExpression',], 'Pmv', topCommand=0)
if self.vf.hasGui:
miscGeom = self.vf.GUI.miscGeom
self.vf.GUI.VIEWER.AddObject(self.masterGeom, parent=miscGeom)
self.vf.GUI.VIEWER.AddObject(self.spheres, parent=self.masterGeom)
def __call__(self, atoms, **kw):
"""None<-addBondsGC(atoms)
\natoms : atom(s)"""
if type(atoms) is StringType:
self.nodeLogString = "'"+atoms+"'"
ats = self.vf.expandNodes(atoms)
if not len(ats): return 'ERROR'
return apply(self.doitWrapper, (ats,), kw)
def doit(self, ats):
if len(ats)>2:
if len(self.atomList):
atSet = ats + self.atomList
else: atSet = ats
parent = atSet[0].parent
parent.buildBondsByDistanceOnAtoms(atSet)
self.atomList = AtomSet([])
self.update(True)
else:
lenAts = len(self.atomList)
last = None
if lenAts:
last = self.atomList[-1]
top = self.atomList[0].top
for at in ats:
#check for repeats of same atom
if lenAts and at==last:
continue
#lenAts = len(self.atomList)
#if lenAts and at==self.atomList[-1]:
# continue
if lenAts and at.top!=self.atomList[-1].top:
msg = "intermolecular bond to %s disallowed"%(at.full_name())
self.warningMsg(msg)
self.atomList.append(at)
self.undoAtList.append(at)
lenAts = len(self.atomList)
self.update(True)
#if only have one atom, there is nothing else to do
if lenAts<2: return
#now build bonds between pairs of atoms
atSet = self.atomList
if lenAts%2!=0:
atSet = atSet[:-1]
#all pairs of atoms will be bonded
#so keep only the last one
self.atomList = atSet[-1:]
lenAts = lenAts -1
else:
self.vf.labelByExpression(self.atomList, negate=1, topCommand=0)
self.atomList = AtomSet([])
for i in range(0, lenAts, 2):
at1 = atSet[i]
at2 = atSet[i+1]
self.vf.addBonds(at1, at2, origin='UserDefined', topCommand=0)
self.update(True)
def applyTransformation(self, pt, mat):
pth = [pt[0], pt[1], pt[2], 1.0]
return Numeric.dot(mat, pth)[:3]
def getTransformedCoords(self, atom):
if not atom.top.geomContainer:
return atom.coords
g = atom.top.geomContainer.geoms['master']
c = self.applyTransformation(atom.coords, g.GetMatrix(g))
return c.astype('f')
def update(self, event=None):
if not len(self.atomList):
self.spheres.Set(vertices=[], tagModified=False)
self.vf.labelByExpression(self.atomList, negate=1, topCommand=0)
if self.vf.hasGui:
self.vf.GUI.VIEWER.Redraw()
return
self.lineVertices=[]
#each time have to recalculate lineVertices
for at in self.atomList:
c1 = self.getTransformedCoords(at)
self.lineVertices.append(tuple(c1))
if event:
self.spheres.Set(vertices=self.lineVertices, tagModified=False)
self.vf.labelByExpression(self.atomList,
function = 'lambda x: x.full_name()',
lambdaFunc = 1,
textcolor = 'yellow',
format = '', negate = 0,
location = 'Last', log = 0,
font = 'arial1.glf', only = 1,
topCommand=0)
#setting spheres doesn't trigger redraw so do it explicitly
if self.vf.hasGui:
self.vf.GUI.VIEWER.Redraw()
def guiCallback(self, event=None):
self.save = self.vf.ICmdCaller.commands.value["Shift_L"]
self.vf.setICOM(self, modifier="Shift_L", topCommand=0)
def setupUndoAfter(self, ats, **kw):
lenUndoAts = len(self.undoAtList)
lenAts = len(ats)
if lenAts==1:
#after adding 1 self.atomList would be 1 or 0
if len(self.atomList)==1:
s = '0'
ustr='"c=self.addBondsGC; self.labelByExpression(c.atomList, negate=1, topCommand=0);c.atomList=c.atomList[:'+s+'];c.undoAtList=c.undoAtList[:-1];c.update()"'
else:
self.vf.undoCmdStack.remove(self.prev_undoCmds)
ind = str(lenUndoAts - 2)
ustr = '"c=self.addBondsGC;nodes=self.expandNodes('+'\''+self.undoAtList[-2:].full_name()+'\''+'); bonds=nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.atomList=nodes[:1];c.undoAtList=c.undoAtList[:'+ind+'];c.update()"'
elif lenUndoAts>lenAts:
ustr='"c=self.addBondsGC;nodes=self.expandNodes('+'\''+ats.full_name()+'\''+');bonds = nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.undoAtList=c.undoAtList[:'+str(lenAts)+']"'
else:
ustr='"c=self.addBondsGC;nodes=self.expandNodes('+'\''+ats.full_name()+'\''+');bonds = nodes.bonds[0];self.removeBondsGC(bonds, topCommand=0);c.undoAtList=c.undoAtList[:0]"'
if len(self.atomList) and lenAts>1:
atStr = self.atomList.full_name()
estr = ';nodes=self.expandNodes('+'\''+self.atomList.full_name()+'\''+');c.atomList=nodes;c.update()"'
ustr = ustr + estr
self.undoCmds = "exec("+ustr+")"
self.prev_undoCmds = (self.undoCmds, "addBondsGC")
def startICOM(self):
self.vf.setIcomLevel( Atom, topCommand=0)
def stopICOM(self):
if len(self.atomList)!=0:
self.vf.labelByExpression(self.atomList, negate=1, topCommand = 0)
del self.atomList[:]
self.labelStrs = []
self.spheres.Set(vertices=[], tagModified=False)
self.vf.GUI.VIEWER.Redraw()
self.save = None
