def createChemModel(neuroCompt, spineCompt, psdCompt):
# Stuff in spine + psd
#psdCa = createPool( psdCompt, 'Ca', 0.0001 )
psdGluR = createPool(psdCompt, 'psdGluR', 1)
headCa = createPool(spineCompt, 'Ca', 1e-4)
headGluR = createPool(spineCompt, 'headGluR', 2)
toPsd = createPool(spineCompt, 'toPsd', 0)
toPsdInact = createPool(spineCompt, 'toPsdInact', 1e-3)
turnOnPsd = moose.Reac(spineCompt.path + '/turnOnPsd')
moose.connect(turnOnPsd, 'sub', headCa, 'reac', 'OneToOne')
moose.connect(turnOnPsd, 'sub', toPsdInact, 'reac', 'OneToOne')
moose.connect(turnOnPsd, 'prd', toPsd, 'reac', 'OneToOne')
turnOnPsd.Kf = 1e3
turnOnPsd.Kb = 1
toPsdEnz = moose.Enz(toPsd.path + '/enz')
toPsdEnzCplx = moose.Pool(toPsdEnz.path + '/cplx')
toPsdEnzCplx.concInit = 0
moose.connect(toPsdEnz, 'enz', toPsd, 'reac', 'OneToOne')
moose.connect(toPsdEnz, 'sub', headGluR, 'reac', 'OneToOne')
moose.connect(toPsdEnz, 'prd', psdGluR, 'reac', 'OneToOne')
moose.connect(toPsdEnz, 'cplx', toPsdEnzCplx, 'reac', 'OneToOne')
toPsdEnz.Km = 1.0e-3
toPsdEnz.kcat = 10.0
fromPsd = moose.Reac(psdCompt.path + '/fromPsd')
moose.connect(fromPsd, 'sub', psdGluR, 'reac', 'OneToOne')
moose.connect(fromPsd, 'prd', headGluR, 'reac', 'OneToOne')
fromPsd.Kf = 0.5
fromPsd.Kb = 0.0
# Stuff in dendrite
dendCa = createPool(neuroCompt, 'Ca', 1e-4)
bufCa = moose.Pool(neuroCompt.path + '/bufCa')
bufCa.concInit = 1e-4
pumpCa = moose.Reac(neuroCompt.path + '/pumpCa')
moose.connect(pumpCa, 'sub', dendCa, 'reac', 'OneToOne')
moose.connect(pumpCa, 'prd', bufCa, 'reac', 'OneToOne')
pumpCa.Kf = 1
pumpCa.Kb = 1
dendKinaseInact = createPool(neuroCompt, 'inact_kinase', 1e-4)
dendKinase = createPool(neuroCompt, 'Ca.kinase', 0.0)
dendTurnOnKinase = moose.Reac(neuroCompt.path + '/turnOnKinase')
moose.connect(dendTurnOnKinase, 'sub', dendCa, 'reac')
moose.connect(dendTurnOnKinase, 'sub', dendKinaseInact, 'reac')
moose.connect(dendTurnOnKinase, 'prd', dendKinase, 'reac')
dendTurnOnKinase.Kf = 50000
dendTurnOnKinase.Kb = 1
dendKinaseEnz = moose.Enz(dendKinase.path + '/enz')
dendKinaseEnzCplx = moose.Pool(dendKinase.path + '/enz/cplx')
kChan = createPool(neuroCompt, 'kChan', 1e-3)
kChan_p = createPool(neuroCompt, 'kChan_p', 0.0)
moose.connect(dendKinaseEnz, 'enz', dendKinase, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'sub', kChan, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'prd', kChan_p, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'cplx', dendKinaseEnzCplx, 'reac', 'OneToOne')
dendKinaseEnz.Km = 1e-4
dendKinaseEnz.kcat = 20
dendPhosphatase = moose.Reac(neuroCompt.path + '/phosphatase')
moose.connect(dendPhosphatase, 'sub', kChan_p, 'reac')
moose.connect(dendPhosphatase, 'prd', kChan, 'reac')
dendPhosphatase.Kf = 1
dendPhosphatase.Kb = 0.0
def makeModel():
""" This function creates a bistable reaction system using explicit
MOOSE calls rather than load from a file.
The reaction is::
a ---b---> 2b # b catalyzes a to form more of b.
2b ---c---> a # c catalyzes b to form a.
a <======> 2b # a interconverts to b.
"""
# create container for model
model = moose.Neutral('model')
compartment = moose.CubeMesh('/model/compartment')
compartment.volume = 1e-15
# the mesh is created automatically by the compartment
mesh = moose.element('/model/compartment/mesh')
# create molecules and reactions
size = 100
for i in range(size):
a = moose.Pool('/model/compartment/a%s' % i)
b = moose.Pool('/model/compartment/b%s' % i)
c = moose.Pool('/model/compartment/c%s' % i)
enz1 = moose.Enz('%s/enz1' % a.path)
enz2 = moose.Enz('%s/enz2' % c.path)
cplx1 = moose.Pool('%s/cplx' % enz1.path)
cplx2 = moose.Pool('%s/cplx' % enz2.path)
reac = moose.Reac('/model/compartment/reac%s' % i)
# connect them up for reactions
moose.connect(enz1, 'sub', a, 'reac')
moose.connect(enz1, 'prd', b, 'reac')
moose.connect(enz1, 'prd', b, 'reac') # Note 2 molecules of b.
moose.connect(enz1, 'enz', b, 'reac')
moose.connect(enz1, 'cplx', cplx1, 'reac')
moose.connect(enz2, 'sub', b, 'reac')
moose.connect(enz2, 'sub', b, 'reac') # Note 2 molecules of b.
moose.connect(enz2, 'prd', a, 'reac')
moose.connect(enz2, 'enz', c, 'reac')
moose.connect(enz2, 'cplx', cplx2, 'reac')
moose.connect(reac, 'sub', a, 'reac')
moose.connect(reac, 'prd', b, 'reac')
moose.connect(reac, 'prd', b, 'reac') # Note 2 order in b.
add_table(a)
add_table(b)
add_table(c)
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
return compartment
def makeModel():
# create container for model
model = moose.Neutral( 'model' )
compartment = moose.CubeMesh( '/model/compartment' )
compartment.volume = 1e-20
# the mesh is created automatically by the compartment
mesh = moose.element( '/model/compartment/mesh' )
# create molecules and reactions
a = moose.Pool( '/model/compartment/a' )
b = moose.Pool( '/model/compartment/b' )
c = moose.Pool( '/model/compartment/c' )
enz1 = moose.Enz( '/model/compartment/b/enz1' )
enz2 = moose.Enz( '/model/compartment/c/enz2' )
cplx1 = moose.Pool( '/model/compartment/b/enz1/cplx' )
cplx2 = moose.Pool( '/model/compartment/c/enz2/cplx' )
reac = moose.Reac( '/model/compartment/reac' )
# connect them up for reactions
moose.connect( enz1, 'sub', a, 'reac' )
moose.connect( enz1, 'prd', b, 'reac' )
moose.connect( enz1, 'enz', b, 'reac' )
moose.connect( enz1, 'cplx', cplx1, 'reac' )
moose.connect( enz2, 'sub', b, 'reac' )
moose.connect( enz2, 'prd', a, 'reac' )
moose.connect( enz2, 'enz', c, 'reac' )
moose.connect( enz2, 'cplx', cplx2, 'reac' )
moose.connect( reac, 'sub', a, 'reac' )
moose.connect( reac, 'prd', b, 'reac' )
# connect them up to the compartment for volumes
#for x in ( a, b, c, cplx1, cplx2 ):
# moose.connect( x, 'mesh', mesh, 'mesh' )
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
# Create the output tables
graphs = moose.Neutral( '/model/graphs' )
outputA = moose.Table2( '/model/graphs/concA' )
outputB = moose.Table2( '/model/graphs/concB' )
# connect up the tables
moose.connect( outputA, 'requestOut', a, 'getConc' );
moose.connect( outputB, 'requestOut', b, 'getConc' );
'''
def makeModel():
"""This function creates a bistable reaction system using explicit
MOOSE calls rather than load from a file.
The reaction is::
a ---b---> 2b # b catalyzes a to form more of b.
2b ---c---> a # c catalyzes b to form a.
a <======> 2b # a interconverts to b.
"""
# create container for model
model = moose.Neutral("model")
compartment = moose.CubeMesh("/model/compartment")
compartment.volume = 1e-15
# the mesh is created automatically by the compartment
mesh = moose.element("/model/compartment/mesh")
# create molecules and reactions
a = moose.BufPool("/model/compartment/a")
b = moose.Pool("/model/compartment/b")
c = moose.Pool("/model/compartment/c")
enz1 = moose.Enz("/model/compartment/b/enz1")
enz2 = moose.Enz("/model/compartment/c/enz2")
cplx1 = moose.Pool("/model/compartment/b/enz1/cplx")
cplx2 = moose.Pool("/model/compartment/c/enz2/cplx")
reac = moose.Reac("/model/compartment/reac")
# connect them up for reactions
moose.connect(enz1, "sub", a, "reac")
moose.connect(enz1, "prd", b, "reac")
moose.connect(enz1, "prd", b, "reac") # Note 2 molecules of b.
moose.connect(enz1, "enz", b, "reac")
moose.connect(enz1, "cplx", cplx1, "reac")
moose.connect(enz2, "sub", b, "reac")
moose.connect(enz2, "sub", b, "reac") # Note 2 molecules of b.
moose.connect(enz2, "prd", a, "reac")
moose.connect(enz2, "enz", c, "reac")
moose.connect(enz2, "cplx", cplx2, "reac")
moose.connect(reac, "sub", a, "reac")
moose.connect(reac, "prd", b, "reac")
moose.connect(reac, "prd", b, "reac") # Note 2 order in b.
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
return compartment
def createChemModel(neuroCompt):
dendCa = createPool(neuroCompt, 'Ca', 1e-4)
dendKinaseInact = createPool(neuroCompt, 'inact_kinase', 1e-4)
dendKinase = createPool(neuroCompt, 'Ca.kinase', 0.0)
dendTurnOnKinase = moose.Reac(neuroCompt.path + '/turnOnKinase')
moose.connect(dendTurnOnKinase, 'sub', dendCa, 'reac')
moose.connect(dendTurnOnKinase, 'sub', dendKinaseInact, 'reac')
moose.connect(dendTurnOnKinase, 'prd', dendKinase, 'reac')
dendTurnOnKinase.Kf = 50000
dendTurnOnKinase.Kb = 1
dendKinaseEnz = moose.Enz(dendKinase.path + '/enz')
dendKinaseEnzCplx = moose.Pool(dendKinase.path + '/enz/cplx')
kChan = createPool(neuroCompt, 'kChan', 1e-3)
kChan_p = createPool(neuroCompt, 'kChan_p', 0.0)
moose.connect(dendKinaseEnz, 'enz', dendKinase, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'sub', kChan, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'prd', kChan_p, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'cplx', dendKinaseEnzCplx, 'reac', 'OneToOne')
dendKinaseEnz.Km = 1e-4
dendKinaseEnz.kcat = 20
dendPhosphatase = moose.Reac(neuroCompt.path + '/phosphatase')
moose.connect(dendPhosphatase, 'sub', kChan_p, 'reac')
moose.connect(dendPhosphatase, 'prd', kChan, 'reac')
dendPhosphatase.Kf = 1
dendPhosphatase.Kb = 0.0
def setupEnzymaticReaction(enz, groupName, enzName, specInfoMap,
modelAnnotaInfo):
enzPool = (modelAnnotaInfo[groupName]["enzyme"])
enzPool = str(idBeginWith(enzPool))
enzParent = specInfoMap[enzPool]["Mpath"]
cplx = (modelAnnotaInfo[groupName]["complex"])
cplx = str(idBeginWith(cplx))
complx = moose.element(specInfoMap[cplx]["Mpath"].path)
enzyme_ = moose.Enz(enzParent.path + '/' + enzName)
moose.move(complx, enzyme_)
moose.connect(enzyme_, "cplx", complx, "reac")
moose.connect(enzyme_, "enz", enzParent, "reac")
sublist = (modelAnnotaInfo[groupName]["substrate"])
prdlist = (modelAnnotaInfo[groupName]["product"])
for si in range(0, len(sublist)):
sl = sublist[si]
sl = str(idBeginWith(sl))
mSId = specInfoMap[sl]["Mpath"]
moose.connect(enzyme_, "sub", mSId, "reac")
for pi in range(0, len(prdlist)):
pl = prdlist[pi]
pl = str(idBeginWith(pl))
mPId = specInfoMap[pl]["Mpath"]
moose.connect(enzyme_, "prd", mPId, "reac")
if (enz.isSetNotes):
pullnotes(enz, enzyme_)
return enzyme_, True
def makeModel():
# create container for model
model = moose.Neutral('model')
compartment = moose.CubeMesh('/model/compartment')
compartment.volume = 1e-20
# the mesh is created automatically by the compartment
mesh = moose.element('/model/compartment/mesh')
# create molecules and reactions
a = moose.Pool('/model/compartment/a')
b = moose.Pool('/model/compartment/b')
c = moose.Pool('/model/compartment/c')
enz1 = moose.Enz('/model/compartment/b/enz1')
enz2 = moose.Enz('/model/compartment/c/enz2')
cplx1 = moose.Pool('/model/compartment/b/enz1/cplx')
cplx2 = moose.Pool('/model/compartment/c/enz2/cplx')
reac = moose.Reac('/model/compartment/reac')
# connect them up for reactions
moose.connect(enz1, 'sub', a, 'reac')
moose.connect(enz1, 'prd', b, 'reac')
moose.connect(enz1, 'enz', b, 'reac')
moose.connect(enz1, 'cplx', cplx1, 'reac')
moose.connect(enz2, 'sub', b, 'reac')
moose.connect(enz2, 'prd', a, 'reac')
moose.connect(enz2, 'enz', c, 'reac')
moose.connect(enz2, 'cplx', cplx2, 'reac')
moose.connect(reac, 'sub', a, 'reac')
moose.connect(reac, 'prd', b, 'reac')
# connect them up to the compartment for volumes
#for x in ( a, b, c, cplx1, cplx2 ):
# moose.connect( x, 'mesh', mesh, 'mesh' )
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
# Create the output tables
graphs = moose.Neutral('/model/graphs')
outputA = moose.Table('/model/graphs/concA')
outputB = moose.Table('/model/graphs/concB')
# connect up the tables
moose.connect(outputA, 'requestOut', a, 'getConc')
moose.connect(outputB, 'requestOut', b, 'getConc')
# Schedule the whole lot
moose.setClock(4, 0.01) # for the computational objects
moose.setClock(8, 1.0) # for the plots
# The wildcard uses # for single level, and ## for recursive.
moose.useClock(4, '/model/compartment/##', 'process')
moose.useClock(8, '/model/graphs/#', 'process')
def checkCreate(scene, view, modelpath, mobj, string, ret_string, num,
event_pos, layoutPt):
# The variable 'compt' will be empty when dropping cubeMesh,cyclMesh, but rest it shd be
# compartment
# if modelpath.find('/',1) > -1:
# modelRoot = modelpath[0:modelpath.find('/',1)]
# else:
# modelRoot = modelpath
print "28 ", modelpath
if moose.exists(modelpath + '/info'):
mType = moose.Annotator((moose.element(modelpath + '/info'))).modeltype
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))
pos = view.mapToScene(event_pos)
modelpath = moose.element(modelpath)
if num:
string_num = ret_string + str(num)
else:
string_num = ret_string
if string == "CubeMesh" or string == "CylMesh":
if string == "CylMesh":
mobj = moose.CylMesh(modelpath.path + '/' + string_num)
else:
mobj = moose.CubeMesh(modelpath.path + '/' + string_num)
mobj.volume = 1e-15
mesh = moose.element(mobj.path + '/mesh')
qGItem = ComptItem(scene,
pos.toPoint().x(),
pos.toPoint().y(), 100, 100, mobj)
qGItem.setPen(
QtGui.QPen(Qt.QColor(66, 66, 66, 100), 1, Qt.Qt.SolidLine,
Qt.Qt.RoundCap, Qt.Qt.RoundJoin))
view.sceneContainerPt.addItem(qGItem)
qGItem.cmptEmitter.connect(
qGItem.cmptEmitter,
QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),
layoutPt.positionChange1)
qGItem.cmptEmitter.connect(
qGItem.cmptEmitter,
QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),
layoutPt.objectEditSlot)
compartment = qGItem
layoutPt.qGraCompt[mobj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), mobj)
elif string == "Pool" or string == "BufPool":
#getting pos with respect to compartment otherwise if compartment is moved then pos would be wrong
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
if string == "Pool":
poolObj = moose.Pool(mobj.path + '/' + string_num)
else:
poolObj = moose.BufPool(mobj.path + '/' + string_num)
poolinfo = moose.Annotator(poolObj.path + '/info')
#Compartment's one Pool object is picked to get the font size
qGItem = PoolItem(poolObj, itemAtView)
layoutPt.mooseId_GObj[poolObj] = qGItem
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('green'), bgcolor)
poolinfo.color = str(bgcolor.getRgb())
view.emit(QtCore.SIGNAL("dropped"), poolObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
x, y = roundoff(qGItem.scenePos(), layoutPt)
poolinfo.x = x
poolinfo.y = y
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
elif string == "Reac":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
reacObj = moose.Reac(mobj.path + '/' + string_num)
reacinfo = moose.Annotator(reacObj.path + '/info')
qGItem = ReacItem(reacObj, itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), "white",
"white")
#if mType == "new_kkit":
# reacinfo.x = posWrtComp.x()
# reacinfo.y = posWrtComp.y()
layoutPt.mooseId_GObj[reacObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), reacObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
reacinfo.x = x
reacinfo.y = y
elif string == "StimulusTable":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
tabObj = moose.StimulusTable(mobj.path + '/' + string_num)
tabinfo = moose.Annotator(tabObj.path + '/info')
qGItem = TableItem(tabObj, itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('white'),
QtGui.QColor('white'))
#if mType == "new_kkit":
#tabinfo.x = posWrtComp.x()
#tabinfo.y = posWrtComp.y()
layoutPt.mooseId_GObj[tabObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), tabObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
tabinfo.x = x
tabinfo.y = y
elif string == "Function":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
funcObj = moose.Function(mobj.path + '/' + string_num)
funcinfo = moose.Annotator(funcObj.path + '/info')
#moose.connect( funcObj, 'valueOut', mobj ,'setN' )
poolclass = ["ZombieBufPool", "BufPool"]
comptclass = ["CubeMesh", "cyclMesh"]
if mobj.className in poolclass:
funcParent = layoutPt.mooseId_GObj[element(mobj.path)]
elif mobj.className in comptclass:
funcParent = layoutPt.qGraCompt[moose.element(mobj)]
posWrtComp = funcParent.mapFromScene(pos).toPoint()
#posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
qGItem = FuncItem(funcObj, funcParent)
#print " function ", posWrtComp.x(),posWrtComp.y()
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('red'), QtGui.QColor('green'))
layoutPt.mooseId_GObj[funcObj] = qGItem
#if mType == "new_kkit":
#funcinfo.x = posWrtComp.x()
#funcinfo.y = posWrtComp.y()
view.emit(QtCore.SIGNAL("dropped"), funcObj)
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
mooseCmpt = findCompartment(mobj)
if isinstance(mooseCmpt, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mooseCmpt)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
funcinfo.x = x
funcinfo.y = y
elif string == "Enz" or string == "MMenz":
#If 2 enz has same pool parent, then pos of the 2nd enz shd be displaced by some position, need to check how to deal with it
posWrtComp = pos
enzPool = layoutPt.mooseId_GObj[mobj]
if ((mobj.parent).className == "Enz"):
QtGui.QMessageBox.information(
None, 'Drop Not possible',
'\'{newString}\' has to have Pool as its parent and not Enzyme Complex'
.format(newString=string), QtGui.QMessageBox.Ok)
return
else:
enzparent = findCompartment(mobj)
parentcompt = layoutPt.qGraCompt[enzparent]
if string == "Enz":
enzObj = moose.Enz(moose.element(mobj).path + '/' + string_num)
enzinfo = moose.Annotator(enzObj.path + '/info')
moose.connect(enzObj, 'enz', mobj, 'reac')
qGItem = EnzItem(enzObj, parentcompt)
layoutPt.mooseId_GObj[enzObj] = qGItem
posWrtComp = pos
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),
posWrtComp.y() - 40,
QtGui.QColor('green'), bgcolor)
x, y = roundoff(qGItem.scenePos(), layoutPt)
enzinfo.x = x
enzinfo.y = y
enzinfo.color = str(bgcolor.name())
enzinfo.textColor = str(QtGui.QColor('green').name())
#if mType == "new_kkit":
#enzinfo.x = posWrtComp.x()
#enzinfo.y = posWrtComp.y()
#enzinfo.color = str(bgcolor.name())
e = moose.Annotator(enzinfo)
#e.x = posWrtComp.x()
#e.y = posWrtComp.y()
Enz_cplx = enzObj.path + '/' + string_num + '_cplx'
cplxItem = moose.Pool(Enz_cplx)
cplxinfo = moose.Annotator(cplxItem.path + '/info')
qGEnz = layoutPt.mooseId_GObj[enzObj]
qGItem = CplxItem(cplxItem, qGEnz)
layoutPt.mooseId_GObj[cplxItem] = qGItem
enzboundingRect = qGEnz.boundingRect()
moose.connect(enzObj, 'cplx', cplxItem, 'reac')
qGItem.setDisplayProperties(enzboundingRect.height() / 2,
enzboundingRect.height() - 40,
QtGui.QColor('white'),
QtGui.QColor('white'))
#cplxinfo.x = enzboundingRect.height()/2
#cplxinfo.y = enzboundingRect.height()-60
view.emit(QtCore.SIGNAL("dropped"), enzObj)
else:
enzObj = moose.MMenz(mobj.path + '/' + string_num)
enzinfo = moose.Annotator(enzObj.path + '/info')
moose.connect(mobj, "nOut", enzObj, "enzDest")
qGItem = MMEnzItem(enzObj, parentcompt)
posWrtComp = pos
bgcolor = getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),
posWrtComp.y() - 30,
QtGui.QColor('green'), bgcolor)
#enzinfo.x = posWrtComp.x()
#enzinfo.y = posWrtComp.y()
enzinfo.color = str(bgcolor.name())
layoutPt.mooseId_GObj[enzObj] = qGItem
view.emit(QtCore.SIGNAL("dropped"), enzObj)
x, y = roundoff(qGItem.scenePos(), layoutPt)
enzinfo.x = x
enzinfo.y = y
setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(enzparent, moose.ChemCompt):
updateCompartmentSize(parentcompt)
if view.iconScale != 1:
view.updateScale(view.iconScale)
def createChemModel(neuroCompt, spineCompt, psdCompt):
# Stuff in spine + psd
# The psdCa pool is an unfortunate necessity because of limitations in
# the solver setup that require molecules to diffuse through all
# compartments, at least as of the July 2013 version.
psdCa = createPool(psdCompt, 'Ca', 0.0001)
psdGluR = createPool(psdCompt, 'psdGluR', 1)
headCa = createPool(spineCompt, 'Ca', 1e-4)
headGluR = createPool(spineCompt, 'headGluR', 2)
toPsd = createPool(spineCompt, 'toPsd', 0)
toPsdInact = createPool(spineCompt, 'toPsdInact', 1e-3)
turnOnPsd = moose.Reac(spineCompt.path + '/turnOnPsd')
moose.connect(turnOnPsd, 'sub', headCa, 'reac', 'OneToOne')
moose.connect(turnOnPsd, 'sub', toPsdInact, 'reac', 'OneToOne')
moose.connect(turnOnPsd, 'prd', toPsd, 'reac', 'OneToOne')
turnOnPsd.Kf = 1e3
turnOnPsd.Kb = 1
toPsdEnz = moose.Enz(toPsd.path + '/enz')
toPsdEnzCplx = moose.Pool(toPsdEnz.path + '/cplx')
mesh = moose.element(spineCompt.path + '/mesh')
moose.connect(toPsdEnzCplx, 'mesh', mesh, 'mesh')
toPsdEnzCplx.concInit = 0
moose.connect(toPsdEnz, 'enz', toPsd, 'reac', 'OneToOne')
moose.connect(toPsdEnz, 'sub', headGluR, 'reac', 'OneToOne')
moose.connect(toPsdEnz, 'prd', psdGluR, 'reac', 'OneToOne')
moose.connect(toPsdEnz, 'cplx', toPsdEnzCplx, 'reac', 'OneToOne')
toPsdEnz.Km = 1.0e-3
toPsdEnz.kcat = 10.0
fromPsd = moose.Reac(psdCompt.path + '/fromPsd')
moose.connect(fromPsd, 'sub', psdGluR, 'reac', 'OneToOne')
moose.connect(fromPsd, 'prd', headGluR, 'reac', 'OneToOne')
fromPsd.Kf = 0.5
fromPsd.Kb = 0.0
# Stuff in dendrite
dendCa = createPool(neuroCompt, 'Ca', 1e-4)
bufCa = moose.Pool(neuroCompt.path + '/bufCa')
mesh = moose.element(neuroCompt.path + '/mesh')
moose.connect(mesh, 'mesh', bufCa, 'mesh', 'Single')
bufCa.concInit = 1e-4
pumpCa = moose.Reac(neuroCompt.path + '/pumpCa')
moose.connect(pumpCa, 'sub', dendCa, 'reac', 'OneToOne')
moose.connect(pumpCa, 'prd', bufCa, 'reac', 'OneToOne')
pumpCa.Kf = 1
pumpCa.Kb = 1
dendKinaseInact = createPool(neuroCompt, 'inact_kinase', 1e-4)
dendKinase = createPool(neuroCompt, 'Ca.kinase', 0.0)
dendTurnOnKinase = moose.Reac(neuroCompt.path + '/turnOnKinase')
moose.connect(dendTurnOnKinase, 'sub', dendCa, 'reac')
moose.connect(dendTurnOnKinase, 'sub', dendKinaseInact, 'reac')
moose.connect(dendTurnOnKinase, 'prd', dendKinase, 'reac')
dendTurnOnKinase.Kf = 50000
dendTurnOnKinase.Kb = 1
dendKinaseEnz = moose.Enz(dendKinase.path + '/enz')
dendKinaseEnzCplx = moose.Pool(dendKinase.path + '/enz/cplx')
moose.connect(dendKinaseEnzCplx, 'mesh', mesh, 'mesh')
kChan = createPool(neuroCompt, 'kChan', 1e-3)
kChan_p = createPool(neuroCompt, 'kChan_p', 0.0)
moose.connect(dendKinaseEnz, 'enz', dendKinase, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'sub', kChan, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'prd', kChan_p, 'reac', 'OneToOne')
moose.connect(dendKinaseEnz, 'cplx', dendKinaseEnzCplx, 'reac', 'OneToOne')
dendKinaseEnz.Km = 1e-4
dendKinaseEnz.kcat = 20
dendPhosphatase = moose.Reac(neuroCompt.path + '/phosphatase')
moose.connect(dendPhosphatase, 'sub', kChan_p, 'reac')
moose.connect(dendPhosphatase, 'prd', kChan, 'reac')
dendPhosphatase.Kf = 1
dendPhosphatase.Kb = 0.0
def makeModel():
# create container for model
model = moose.Neutral('model')
compartment = moose.CubeMesh('/model/compartment')
compartment.volume = 1e-15
# the mesh is created automatically by the compartment
moose.le('/model/compartment')
mesh = moose.element('/model/compartment/mesh')
# create molecules and reactions
a = moose.Pool('/model/compartment/a')
b = moose.Pool('/model/compartment/b')
c = moose.Pool('/model/compartment/c')
enz1 = moose.Enz('/model/compartment/b/enz1')
enz2 = moose.Enz('/model/compartment/c/enz2')
cplx1 = moose.Pool('/model/compartment/b/enz1/cplx')
cplx2 = moose.Pool('/model/compartment/c/enz2/cplx')
reac = moose.Reac('/model/compartment/reac')
# connect them up for reactions
moose.connect(enz1, 'sub', a, 'reac')
moose.connect(enz1, 'prd', b, 'reac')
moose.connect(enz1, 'enz', b, 'reac')
moose.connect(enz1, 'cplx', cplx1, 'reac')
moose.connect(enz2, 'sub', b, 'reac')
moose.connect(enz2, 'prd', a, 'reac')
moose.connect(enz2, 'enz', c, 'reac')
moose.connect(enz2, 'cplx', cplx2, 'reac')
moose.connect(reac, 'sub', a, 'reac')
moose.connect(reac, 'prd', b, 'reac')
# connect them up to the compartment for volumes
#for x in ( a, b, c, cplx1, cplx2 ):
# moose.connect( x, 'mesh', mesh, 'mesh' )
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
# Create the output tables
graphs = moose.Neutral('/model/graphs')
outputA = moose.Table2('/model/graphs/concA')
outputB = moose.Table2('/model/graphs/concB')
# connect up the tables
moose.connect(outputA, 'requestOut', a, 'getConc')
moose.connect(outputB, 'requestOut', b, 'getConc')
# We need a finer timestep than the default 0.1 seconds,
# in order to get numerical accuracy.
for i in range(11, 15):
moose.setClock(i, 0.001) # for computational objects
QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),
self.mobj)
if change == QGraphicsItem.ItemSelectedChange and value == True:
self.qgtextPositionChange.emit(self.mobj)
# self.cmptEmitter.emit(
# QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),
# self.mobj)
return QGraphicsItem.itemChange(self, change, value)
if __name__ == '__main__':
import sys
from PyQt5.QtWidgets import QApplication, QGraphicsView, QGraphicsScene
app = QApplication(sys.argv)
a = moose.Pool('pool')
b = moose.Reac('reac')
c = moose.Enz('enzyme')
gview = QGraphicsView()
scene = QGraphicsScene(gview)
reacItem = ReacItem(b)
reacItem.setDisplayProperties(50, 5, QtGui.QColor('yellow'),
QtGui.QColor('green'))
enzItem = EnzItem(c)
enzItem.setDisplayProperties(100, 10, QtGui.QColor('blue'),
QtGui.QColor('yellow'))
scene.addItem(reacItem)
scene.addItem(enzItem)
gview.setScene(scene)
gview.show()
sys.exit(app.exec_())
def makeModel():
""" This function creates a bistable reaction system using explicit
MOOSE calls rather than load from a file
"""
# create container for model
model = moose.Neutral( 'model' )
compartment = moose.CubeMesh( '/model/compartment' )
compartment.volume = 1e-15
# the mesh is created automatically by the compartment
mesh = moose.element( '/model/compartment/mesh' )
# create molecules and reactions
a = moose.Pool( '/model/compartment/a' )
b = moose.Pool( '/model/compartment/b' )
c = moose.Pool( '/model/compartment/c' )
enz1 = moose.Enz( '/model/compartment/b/enz1' )
enz2 = moose.Enz( '/model/compartment/c/enz2' )
cplx1 = moose.Pool( '/model/compartment/b/enz1/cplx' )
cplx2 = moose.Pool( '/model/compartment/c/enz2/cplx' )
reac = moose.Reac( '/model/compartment/reac' )
# connect them up for reactions
moose.connect( enz1, 'sub', a, 'reac' )
moose.connect( enz1, 'prd', b, 'reac' )
moose.connect( enz1, 'enz', b, 'reac' )
moose.connect( enz1, 'cplx', cplx1, 'reac' )
moose.connect( enz2, 'sub', b, 'reac' )
moose.connect( enz2, 'prd', a, 'reac' )
moose.connect( enz2, 'enz', c, 'reac' )
moose.connect( enz2, 'cplx', cplx2, 'reac' )
moose.connect( reac, 'sub', a, 'reac' )
moose.connect( reac, 'prd', b, 'reac' )
# Assign parameters
a.concInit = 1
b.concInit = 0
c.concInit = 0.01
enz1.kcat = 0.4
enz1.Km = 4
enz2.kcat = 0.6
enz2.Km = 0.01
reac.Kf = 0.001
reac.Kb = 0.01
# Create the output tables
graphs = moose.Neutral( '/model/graphs' )
outputA = moose.Table ( '/model/graphs/concA' )
outputB = moose.Table ( '/model/graphs/concB' )
outputC = moose.Table ( '/model/graphs/concC' )
outputCplx1 = moose.Table ( '/model/graphs/concCplx1' )
outputCplx2 = moose.Table ( '/model/graphs/concCplx2' )
# connect up the tables
moose.connect( outputA, 'requestOut', a, 'getConc' );
moose.connect( outputB, 'requestOut', b, 'getConc' );
moose.connect( outputC, 'requestOut', c, 'getConc' );
moose.connect( outputCplx1, 'requestOut', cplx1, 'getConc' );
moose.connect( outputCplx2, 'requestOut', cplx2, 'getConc' );
return compartment
def checkCreate(scene, view, modelpath, mobj, string, ret_string, num,
event_pos, layoutPt):
# The variable 'compt' will be empty when dropping cubeMesh,cyclMesh,
# but rest it shd be compartment
logger_.debug( "checkCreate is called")
if moose.exists(modelpath + '/info'):
moose.Annotator((moose.element(modelpath + '/info'))).modeltype
itemAtView = view.sceneContainerPt.itemAt(view.mapToScene(event_pos))
pos = view.mapToScene(event_pos)
modelpath = moose.element(modelpath)
if num:
string_num = ret_string + str(num)
else:
string_num = ret_string
if string == "CubeMesh" or string == "CylMesh":
if string == "CylMesh":
mobj = moose.CylMesh(modelpath.path + '/' + string_num)
else:
mobj = moose.CubeMesh(modelpath.path + '/' + string_num)
mobj.volume = 1e-15
qGItem = kkitQGraphics.ComptItem(scene,
pos.toPoint().x(),
pos.toPoint().y(), 100, 100, mobj)
qGItem.setPen(
QtGui.QPen(Qt.QColor(66, 66, 66, 100), 1, Qt.Qt.SolidLine,
Qt.Qt.RoundCap, Qt.Qt.RoundJoin))
view.sceneContainerPt.addItem(qGItem)
qGItem.cmptEmitter.connect(
qGItem.cmptEmitter,
QtCore.SIGNAL("qgtextPositionChange(PyQt_PyObject)"),
layoutPt.positionChange1)
qGItem.cmptEmitter.connect(
qGItem.cmptEmitter,
QtCore.SIGNAL("qgtextItemSelectedChange(PyQt_PyObject)"),
layoutPt.objectEditSlot)
layoutPt.qGraCompt[mobj] = qGItem
# Attach a drop signal.
qGItem.dropped.emit()
elif string == "Pool" or string == "BufPool":
#getting pos with respect to compartment otherwise if compartment is moved then pos would be wrong
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
if string == "Pool":
poolObj = moose.Pool(mobj.path + '/' + string_num)
else:
poolObj = moose.BufPool(mobj.path + '/' + string_num)
poolinfo = moose.Annotator(poolObj.path + '/info')
qGItem = kkitQGraphics.PoolItem(poolObj, itemAtView)
layoutPt.mooseId_GObj[poolObj] = qGItem
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
bgcolor = kkitUtil.getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('green'), bgcolor)
poolinfo.color = str(bgcolor.getRgb())
qGItem.dropped.emit()
kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
x, y = roundoff(qGItem.scenePos(), layoutPt)
poolinfo.x = x
poolinfo.y = y
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
elif string == "Reac":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
reacObj = moose.Reac(mobj.path + '/' + string_num)
reacinfo = moose.Annotator(reacObj.path + '/info')
qGItem = kkitQGraphics.ReacItem(reacObj, itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(), "white",
"white")
layoutPt.mooseId_GObj[reacObj] = qGItem
qGItem.dopped.emit()
# view.emit(QtCore.SIGNAL("dropped"), reacObj)
kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
reacinfo.x = x
reacinfo.y = y
elif string == "StimulusTable":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
tabObj = moose.StimulusTable(mobj.path + '/' + string_num)
tabinfo = moose.Annotator(tabObj.path + '/info')
qGItem = kkitQGraphics.TableItem(tabObj, itemAtView)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('white'),
QtGui.QColor('white'))
layoutPt.mooseId_GObj[tabObj] = qGItem
qGItem.dropped.emit()
# view.emit(QtCore.SIGNAL("dropped"), tabObj)
kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
# Dropping is on compartment then update Compart size
if isinstance(mobj, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mobj)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
tabinfo.x = x
tabinfo.y = y
elif string == "Function":
posWrtComp = (itemAtView.mapFromScene(pos)).toPoint()
funcObj = moose.Function(mobj.path + '/' + string_num)
funcinfo = moose.Annotator(funcObj.path + '/info')
#moose.connect( funcObj, 'valueOut', mobj ,'setN' )
poolclass = ["ZombieBufPool", "BufPool"]
comptclass = ["CubeMesh", "cyclMesh"]
if mobj.className in poolclass:
funcParent = layoutPt.mooseId_GObj[moose.element(mobj.path)]
elif mobj.className in comptclass:
funcParent = layoutPt.qGraCompt[moose.element(mobj)]
posWrtComp = funcParent.mapFromScene(pos).toPoint()
elif mobj.className in "Neutral":
funcParent = layoutPt.qGraGrp[moose.element(mobj)]
qGItem = kkitQGraphics.FuncItem(funcObj, funcParent)
qGItem.setDisplayProperties(posWrtComp.x(), posWrtComp.y(),
QtGui.QColor('red'), QtGui.QColor('green'))
layoutPt.mooseId_GObj[funcObj] = qGItem
qGItem.dropped.emit()
# view.emit(QtCore.SIGNAL("dropped"), funcObj)
kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
#Dropping is on compartment then update Compart size
mooseCmpt = findCompartment(mobj)
if isinstance(mooseCmpt, moose.ChemCompt):
compt = layoutPt.qGraCompt[moose.element(mooseCmpt)]
updateCompartmentSize(compt)
x, y = roundoff(qGItem.scenePos(), layoutPt)
funcinfo.x = x
funcinfo.y = y
elif string == "Enz" or string == "MMenz":
# FIXME: If 2 enz has same pool parent, then pos of the 2nd enz shd be
# displaced by some position, need to check how to deal with it
posWrtComp = pos
if ((mobj.parent).className == "Enz"):
QMessageBox.information(
None, "Drop Not possible",
"'{}' has to have Pool as its parent and not Enzyme Complex".
format(string), QMessageBox.Ok)
return None
else:
enzparent = findCompartment(mobj)
parentcompt = layoutPt.qGraCompt[enzparent]
if string == "Enz":
enzObj = moose.Enz(moose.element(mobj).path + '/' + string_num)
enzinfo = moose.Annotator(enzObj.path + '/info')
moose.connect(enzObj, 'enz', mobj, 'reac')
qGItem = kkitQGraphics.EnzItem(enzObj, parentcompt)
layoutPt.mooseId_GObj[enzObj] = qGItem
posWrtComp = pos
bgcolor = kkitUtil.getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),
posWrtComp.y() - 40,
QtGui.QColor('green'), bgcolor)
x, y = roundoff(qGItem.scenePos(), layoutPt)
enzinfo.x = x
enzinfo.y = y
enzinfo.color = str(bgcolor.name())
enzinfo.textColor = str(QtGui.QColor('green').name())
moose.Annotator(enzinfo)
Enz_cplx = enzObj.path + '/' + string_num + '_cplx'
cplxItem = moose.Pool(Enz_cplx)
moose.Annotator(cplxItem.path + '/info')
qGEnz = layoutPt.mooseId_GObj[enzObj]
kkitQGraphics.CplxItem(cplxItem, qGEnz)
layoutPt.mooseId_GObj[cplxItem] = qGItem
enzboundingRect = qGEnz.boundingRect()
moose.connect(enzObj, 'cplx', cplxItem, 'reac')
qGItem.setDisplayProperties(int(enzboundingRect.height() / 2),
enzboundingRect.height() - 40,
QtGui.QColor('white'),
QtGui.QColor('white'))
qGItem.dropped.emit()
# view.emit(QtCore.SIGNAL("dropped"), enzObj)
else:
enzObj = moose.MMenz(mobj.path + '/' + string_num)
enzinfo = moose.Annotator(enzObj.path + '/info')
moose.connect(mobj, "nOut", enzObj, "enzDest")
qGItem = kkitQGraphics.MMEnzItem(enzObj, parentcompt)
posWrtComp = pos
bgcolor = kkitUtil.getRandColor()
qGItem.setDisplayProperties(posWrtComp.x(),
posWrtComp.y() - 30,
QtGui.QColor('green'), bgcolor)
enzinfo.color = str(bgcolor.name())
layoutPt.mooseId_GObj[enzObj] = qGItem
qGItem.dropped.emit()
# view.emit(QtCore.SIGNAL("dropped"), enzObj)
x, y = roundoff(qGItem.scenePos(), layoutPt)
enzinfo.x = x
enzinfo.y = y
kkitUtil.setupItem(modelpath.path, layoutPt.srcdesConnection)
layoutPt.drawLine_arrow(False)
# Dropping is on compartment then update Compart size
if isinstance(enzparent, moose.ChemCompt):
updateCompartmentSize(parentcompt)
if view.iconScale != 1:
view.updateScale(view.iconScale)