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Jan 9, 2020
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while writting genesis file compartment is added as a group #381

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while writting genesis file compartment is added as a group
hrani Jan 8, 2020
e08492b
kkit: channel's permeability converted from uM to mM, writeSBML: chan…
hrani Jan 8, 2020
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150 changes: 144 additions & 6 deletions python/moose/SBML/writeSBML.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,13 @@
** copyright (C) 2003-2017 Upinder S. Bhalla. and NCBS
Created : Friday May 27 12:19:00 2016(+0530)
Version
Last-Updated: Thr 18 July 15:15:10 2019(+0530)
Last-Updated: Wed 8 Jan 14:15:10 2020(+0530)
By: HarshaRani
**********************************************************************/
/****************************
2020
Jan 08: added function to write Concchannel in form of MMenz
Km in the kinetic law for MMenz is written to the power based on the number of substrate
2019
July 18: added a call for autolayout, this was required for cspace model while trying to write from cmd line
while writting file, the filepath is checked
Expand Down Expand Up @@ -164,15 +167,17 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
if modelAnno:
cremodel_.setAnnotation(modelAnno)
groupInfo = {}
reacGroup = {}
compterrors =""
compartexist, groupInfo,compterrors = writeCompt(modelpath, cremodel_)

if compartexist == True:
species = writeSpecies( modelpath,cremodel_,sbmlDoc,sceneitems,groupInfo)
if species:
writeFunc(modelpath, cremodel_)
reacGroup = {}

writeChannel(modelpath,cremodel_,sceneitems,groupInfo)

writeReac(modelpath, cremodel_, sceneitems,groupInfo)

writeEnz(modelpath, cremodel_, sceneitems,groupInfo)
Expand Down Expand Up @@ -245,7 +250,102 @@ def mooseWriteSBML(modelpath, filename, sceneitems={}):
return False, compterrors
else:
return False,"Atleast one compartment should exist to write SBML"


def writeChannel(modelpath, cremodel_, sceneitems,groupInfo):
for chan in moose.wildcardFind(modelpath + '/##[0][ISA=ConcChan]'):
chanannoexist = False
chanGpnCorCol = " "
cleanChanname = convertSpecialChar(chan.name)
compt = ""
notesE = ""
groupName = moose.element("/")

if moose.exists(chan.path + '/info'):
Anno = moose.Annotator(chan.path + '/info')
notesE = Anno.notes
element = moose.element(chan)
ele = getGroupinfo(element)
ele = findGroup_compt(element)
chanAnno = " "
if ele.className == "Neutral" or sceneitems or Anno.x or Anno.y:
chanannoexist = True
if chanannoexist:
chanAnno = "<moose:ModelAnnotation>\n"
if ele.className == "Neutral":
groupName = ele
if sceneitems:
#Saved from GUI, then scene co-ordinates are passed
chanGpnCorCol = chanGpnCorCol + "<moose:xCord>" + \
str(sceneitems[chan]['x']) + "</moose:xCord>\n" + \
"<moose:yCord>" + \
str(sceneitems[chan]['y'])+ "</moose:yCord>\n"
else:
#Saved from cmdline,genesis coordinates are kept as its
# SBML, cspace, python, then auto-coordinates are done
#and coordinates are updated in moose Annotation field
chanGpnCorCol = chanGpnCorCol + "<moose:xCord>" + \
str(Anno.x) + "</moose:xCord>\n" + \
"<moose:yCord>" + \
str(Anno.y)+ "</moose:yCord>\n"
chanGpnCorCol = chanGpnCorCol+"<moose:Permeability>"+str(chan.permeability)+"</moose:Permeability>\n"
chanSub = chan.neighbors["in"]
chanPrd = chan.neighbors["out"]
if (len(chanSub) != 0 and len(chanPrd) != 0):
chanCompt = findCompartment(chan)
if not isinstance(moose.element(chanCompt), moose.ChemCompt):
return -2
else:
compt = chanCompt.name + "_" + \
str(chanCompt.getId().value) + "_" + \
str(chanCompt.getDataIndex()) + "_"

channel = cremodel_.createReaction()
if notesE != "":
cleanNotesE = convertNotesSpecialChar(notesE)
notesStringE = "<body xmlns=\"http://www.w3.org/1999/xhtml\">\n \t \t" + \
cleanNotesE + "\n\t </body>"
channel.setNotes(notesStringE)

chansetId = str(idBeginWith(cleanChanname +
"_" +
str(chan.getId().value) +
"_" +
str(chan.getDataIndex()) +
"_"))
channel.setId(chansetId)

if groupName != moose.element('/'):
if groupName not in groupInfo:
groupInfo[groupName]=[chansetId]
else:
groupInfo[groupName].append(chansetId)

channel.setName(str(idBeginWith(convertSpecialCharshot(chan.name))))
channel.setReversible(True)
channel.setFast(False)
if chanannoexist:
canAnno = chanAnno + chanGpnCorCol
chanAnno = "<moose:ConcChannel>\n" + \
chanGpnCorCol + "</moose:ConcChannel>"
channel.setAnnotation(chanAnno)
noofSub, sRateLawS = getSubprd(cremodel_, False, "sub", chanSub)
# Modifier
chanMod = chan.neighbors["setNumChan"]
noofMod, sRateLawM = getSubprd(cremodel_, False, "enz", chanMod)

noofPrd, sRateLawP = getSubprd(cremodel_, False, "prd", chanPrd)

kl = channel.createKineticLaw()

fRate_law = compt + " * ( Permeability) * " + sRateLawM + " * (" + sRateLawS+ " - " + sRateLawP +")"
kl.setFormula(fRate_law)
kl.setNotes(
"<body xmlns=\"http://www.w3.org/1999/xhtml\">\n\t\t" +
fRate_law +
"\n \t </body>")

channelUnit = permeablUnit(cremodel_)
printParameters(kl, "Permeability", chan.permeability, channelUnit)
def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
for enz in moose.wildcardFind(modelpath + '/##[0][ISA=EnzBase]'):
enzannoexist = False
Expand Down Expand Up @@ -535,8 +635,14 @@ def writeEnz(modelpath, cremodel_, sceneitems,groupInfo):
enzPrd = enz.neighbors["prd"]
noofPrd, sRateLawP = getSubprd(cremodel_, False, "prd", enzPrd)
kl = enzyme.createKineticLaw()
fRate_law = compt + " * ( kcat * " + sRateLawS + " * " + sRateLawM + \
" / ( Km" + " + " + sRateLawS + "))"
#rate_law = clean_name + "^" + str(count)
fRate_law = compt + " * ( kcat * " + sRateLawS + " * " + sRateLawM + "/(Km"

if len(enzSub) > 1:
fRate_law = fRate_law +"^" +str(len(enzSub))
print("enzyme ",enzyme.name, "number of substrate is greater than 1, kinetics Law Km is written to the power of substrate assumed that km value is factored")
fRate_law = fRate_law +" + " + sRateLawS + "))"

kl.setFormula(fRate_law)
kl.setNotes(
"<body xmlns=\"http://www.w3.org/1999/xhtml\">\n\t\t" +
Expand All @@ -554,6 +660,38 @@ def printParameters(kl, k, kvalue, unit):
para.setValue(kvalue)
para.setUnits(unit)

def permeablUnit(cremodel_):
unit_stream = "litre_per_mmole_per_second"
lud = cremodel_.getListOfUnitDefinitions()
flag = False
for i in range(0, len(lud)):
ud = lud.get(i)
if (ud.getId() == unit_stream):
flag = True
break
if (not flag):
unitdef = cremodel_.createUnitDefinition()
unitdef.setId(unit_stream)

unit = unitdef.createUnit()
unit.setKind(UNIT_KIND_LITRE)
unit.setExponent(1)
unit.setMultiplier(1)
unit.setScale(0)

unit = unitdef.createUnit()
unit.setKind(UNIT_KIND_MOLE)
unit.setExponent(-1)
unit.setMultiplier(1)
unit.setScale(-3)

unit = unitdef.createUnit()
unit.setKind(UNIT_KIND_SECOND)
unit.setExponent(-1)
unit.setMultiplier(1)
unit.setScale(0)
return unit_stream

def KmUnit(cremodel_):
unit_stream = "mmole_per_litre"
lud = cremodel_.getListOfUnitDefinitions()
Expand Down Expand Up @@ -647,7 +785,7 @@ def getSubprd(cremodel_, mobjEnz, type, neighborslist):
rate_law = processRateLaw(
reacPrdCou, cremodel_, noofPrd, "prd", mobjEnz)
return len(reacPrd), rate_law
elif type == "enz":
elif type == "enz" or type == "chan":
enzModifier = neighborslist
enzModCou = Counter(enzModifier)
noofMod = len(enzModCou)
Expand Down
12 changes: 7 additions & 5 deletions python/moose/genesis/writeKkit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,10 @@
__maintainer__ = "Harsha Rani"
__email__ = "[email protected]"
__status__ = "Development"
__updated__ = "Dec 08 2018"

__updated__ = "Jan 08 2020"
#Jan 8: added a line to add compartment info
# permeability from moose is in uM which to be converted to mM for genesis
#2020
# 2018
# Dec 08: using restoreXreacs from fixXreacs
# Nov 22: searched for _xfer_ instead of xfer
Expand Down Expand Up @@ -274,7 +276,7 @@ def writeConcChan(modelpath,f,sceneitems):
color = getRandomColor()
if textcolor == "" or textcolor == " ":
textcolor = getRandomColor()
f.write("simundump kchan /kinetics/" + trimPath(cChan)+ " " + str(int(1)) + " " + str(cChan.permeability)+ " " +
f.write("simundump kchan /kinetics/" + trimPath(cChan)+ " " + str(int(1)) + " " + str(cChan.permeability/1000.0 )+ " " +
str(int(0)) + " " +
str(int(0)) + " " +
str(int(0)) + " " +
Expand Down Expand Up @@ -692,8 +694,8 @@ def writeCompartment(modelpath,compts,f):
if compt.name != "kinetics":
x = xmin+6
y = ymax+1
#f.write("simundump group /kinetics/" + compt.name + " 0 " + "blue" + " " + "green" + " x 0 0 \"\" defaultfile \\\n" )
#f.write( " defaultfile.g 0 0 0 " + str(int(x)) + " " + str(int(y)) + " 0\n")
f.write("simundump group /kinetics/" + compt.name + " 0 " + "blue" + " " + "green" + " x 0 0 \"\" defaultfile \\\n" )
f.write( " defaultfile.g 0 0 0 " + str(int(x)) + " " + str(int(y)) + " 0\n")
i = 0
l = len(compts)
geometry = ""
Expand Down