chanAnalysis.hoc

// func sum_g_chan() { local Gsum
// // meang_KD_ca3( Dt )
// 
// 	Gsum=0
// 	sprint( strtmp, "Gsum += g_%s*area(0.5)", $s1)
// 	forsec $o2 {
// 		execute(strtmp)
// // 		Gsum += g_hcn*area(0.5)	// S/cm2*µm2 ≠ S
// 	}
// 	return Gsum
// }

// 11 July 2017 - RBD - fixed units, so values match description and fixed bug wasted calculations

// ***** hAnalysis
begintemplate hAnalysis
public gh, nh, hSA, hGM, ih, SL, update, setGtot, remove
external HList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {

	if (numarg()) {
		if (argtype(1)==1) {		// input 1 is SectionList obj
			SL = $o1
		} else if (argtype(1)==2) {		// input 1 is char array naming sections
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = HList
	} else SL = HList		// no input uses default SectionList
	
	forsec SL hSA += area(0.5)		// total surface area µm2
	// to get the average conductance density within sections containing the channel the
	// 	 HList should be limited to sections with the channel. For the average conductance 
	//   density across the entire cell then HList should contain all sections
	
	setGtot()
	update()
	AddToStep(this)
}

proc setGtot() {
	forsec SL {
		if (ismembrane("h")) {
			hGM += gmax_h*area(0.5)*1e-2		// maximum total conductance µS
		} else SL.remove()
	}
}

proc update() { local Gsum, Isum, gtmp

	Gsum=0
	Isum=0
	if (hGM == 0)	return
	forsec SL {
		gtmp = g_h(0.5)*area(0.5)*1e-2	// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-e_h)		// total current in (nA) µS*10^-3(V/mV)
	}
	nh = Gsum/hGM		// % channel activation
	gh = Gsum/hSA*1e2	// conductance density S/cm2
	ih = Isum			// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate hAnalysis


// ***** hcnAnalysis
begintemplate hcnAnalysis
public gh, nh, hSA, hGM, ih, SL, update, remove, setGtot
external HList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {

	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = HList
	} else SL = HList

	forsec SL hSA += area(0.5)		// total surface area µm2
	// to get the average conductance density within sections containing the channel the
	// 	 HList should be limited to sections with the channel. For the average conductance 
	//   density across the entire cell then HList should contain all sections

	setGtot()
	update()
	SN=AddToStep(this)
	SN=SN-1
}

proc setGtot() {
	forsec SL {
		if (ismembrane("hcn")) {
			hGM += gmax_hcn*area(0.5)*1e-2		// maximum total conductance µS
		} else SL.remove()
	}
}

proc update() { local Gsum, Isum, gtmp

	Gsum=0
	Isum=0
	if (hGM == 0) return
	forsec SL {
		gtmp = g_hcn(0.5)*area(0.5)*1e-2	// section conductance in µS
		Gsum += gtmp						// total conductance (µS)
		Isum += gtmp*(v(0.5)-e_hcn)			// total current in (nA) µS*mV
	}
	nh = Gsum/hGM		// % channel activation
	gh = Gsum/hSA*1e2	// conductance density S/cm2
	ih = Isum			// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate hcnAnalysis


// ***** MAnalysis
begintemplate MAnalysis
public gM, nM, MSA, MGM, iM, SL, update, remove, setGtot
external MList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {

	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = MList
	} else SL = MList

	forsec SL MSA += area(0.5)

	setGtot()
	update()
	AddToStep(this)
}

proc setGtot() {
	forsec SL {
		if (ismembrane("M")) {
			MGM += gmax_M*area(0.5)*1e-2	// maximum total conductance µS
		} else SL.remove()
	}
}

proc update() { local Gsum, Isum, gtmp
	Gsum=0
	Isum=0
	if (MGM == 0) return
	forsec SL {
		gtmp = g_M(0.5)*area(0.5)*1e-2	// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-ek)		// total current in (nA) µS*mV
	}
	nM = Gsum/MGM		// % channel activation
	gM = Gsum/MSA*1e2	// conductance density S/cm2
	iM = Isum			// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}

endtemplate MAnalysis


// ***** KD3Analysis
begintemplate KD3Analysis
public gKD, lKD, nKD, KDSA, KDGM, iKD, SL, update, remove
external KDList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {
	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = KDList
	} else SL = KDList
	forsec SL KDSA += area(0.5)		// total area µm2
	forsec SL {
		if (ismembrane("KD_ca3")) {
			KDGM += gmax_KD_ca3*area(0.5)*1e-2	// maximum total conductance µS
		} else SL.remove()
	}
	update()
	AddToStep(this)
}

proc update() { local Gsum, lsum, nsum, gtmp, am
	Gsum=0
	Isum=0
	lsum=0
	nsum=0
	if (KDGM == 0) return
	forsec SL {
		am = area(0.5)*1e-2
		gtmp = g_KD_ca3(0.5)*am			// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-ek)		// total current in (nA) µS*mV
		lsum += l_KD_ca3(0.5)*gmax_KD_ca3*am
		nsum += n_KD_ca3(0.5)*gmax_KD_ca3*am
	}
	gKD = Gsum/KDSA*1e2	// conductance density (S/cm2)
	lKD = lsum/KDGM		// % channel inactivation
	nKD = nsum/KDGM		// % channel activation
	iKD = Isum			// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate KD3Analysis


// ***** KDAnalysis
begintemplate KDAnalysis
public gKD, lKD, nKD, KDSA, KDGM, iKD, SL, update, remove, setGtot
external KDList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {

	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = KDList
	} else SL = KDList
	
	forsec SL KDSA += area(0.5)		// total surface area µm2
	// to get the average conductance density within sections containing the channel the
	// 	 HList should be limited to sections with the channel. For the average conductance 
	//   density across the entire cell then HList should contain all sections

	setGtot()
	update()
	AddToStep(this)
}

proc update() { local Gsum, lsum, nsum, gtmp, am
	Gsum=0
	Isum=0
	lsum=0
	nsum=0
	if (KDGM == 0) return
	forsec SL {
		am = area(0.5)*1e-2
		gtmp = g_KD(0.5)*am			// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-ek)		// total current in (nA) µS*mV
		lsum += l_KD(0.5)*gmax_KD*am
		nsum += n_KD(0.5)*gmax_KD*am
	}
	gKD = Gsum/KDSA*1e2	// conductance density (S/cm2)
	lKD = lsum/KDGM		// % channel inactivation
	nKD = nsum/KDGM		// % channel activation
	iKD = Isum			// total membrane current (nA)
}

proc setGtot() {
	forsec SL {
		if (ismembrane("KD")) {
			KDGM += gmax_KD*area(0.5)*1e-2		// maximum total conductance µS
		} else SL.remove()
	}
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate KDAnalysis


begintemplate KAAnalysis
public gKA, lKA, nKA, KASA, KAGM, iKA, SL, update, remove, setGtot
external KAList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {

	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = KAList
	} else SL = KAList
	
	forsec SL KASA += area(0.5)		// total surface area µm2
	// to get the average conductance density within sections containing the channel the
	// 	 HList should be limited to sections with the channel. For the average conductance 
	//   density across the entire cell then HList should contain all sections

	setGtot()
	update()
	AddToStep(this)
}

proc update() { local Gsum, lsum, nsum, gtmp, am
	Gsum=0
	Isum=0
	lsum=0
	nsum=0
	if (KAGM == 0) return
	forsec SL {
		am = area(0.5)*1e-2
		gtmp = g_KA(0.5)*am			// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-ek)		// total current in (nA) µS*mV
		lsum += l_KA(0.5)*gmax_KA*am
		nsum += n_KA(0.5)*gmax_KA*am
	}
	gKA = Gsum/KASA*1e2	// conductance density (S/cm2)
	lKA = lsum/KAGM		// % channel inactivation
	nKA = nsum/KAGM		// % channel activation
	iKA = Isum			// total membrane current (nA)
}

proc setGtot() {
	forsec SL {
		if (ismembrane("KA")) {
			KAGM += gmax_KA*area(0.5)*1e-2		// maximum total conductance µS
		} else SL.remove()
	}
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate KAAnalysis


begintemplate KD2Analysis
public gKD, lKD, nKD, KDSA, KDGM, iKD, SL, update, remove
external KDList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL
// strdef gstr, lstr, nstr, maxstr

proc init() {
	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = KDList
	} else SL = KDList
	forsec SL KDSA += area(0.5)
	forsec SL {
		if (ismembrane("KD2")) {
			KDGM += gmax_KD2*area(0.5)*1e-2
		} else SL.remove()
	}
	update()
	AddToStep(this)
}

proc update() { local Gsum, lsum, nsum, gtmp, am
	Gsum=0
	Isum=0
	lsum=0
	nsum=0
	if (KDGM == 0) return
	forsec SL {
		am = area(0.5)*1e-2
		gtmp = g_KD2(0.5)*am			// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-ek)		// total current in (nA) µS*mV
		lsum += l_KD2(0.5)*gmax_KD2*am
		nsum += n_KD2(0.5)*gmax_KD2*am
	}
	gKD = Gsum/KDSA*1e2	// conductance density (S/cm2)
	lKD = lsum/KDGM		// % channel inactivation
	nKD = nsum/KDGM		// % channel activation
	iKD = Isum			// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate KD2Analysis


begintemplate CaTAnalysis
public gCaT, sCaT, hCaT, CaTSA, CaTGM, iCaT, SL, update, remove
external CaTList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {
	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = CaTList
	} else SL = CaTList
	forsec SL CaTSA += area(0.5)	// (µm2)
	// to get the average conductance density within sections containing the channel the
	// 	 SectionList should be limited to sections with the channel. For the average conductance 
	//   density across the entire cell the SectionList should contain all sections
	forsec SL {
		if (ismembrane("CaT")) {
			CaTGM += gmax_CaT*area(0.5)*1e-2	// max total conductance in µS
		} else SL.remove()
	}
	update()
	AddToStep(this)
}

proc update() { local Gsum, lsum, nsum, gtmp, am
	Gsum=0
	Isum=0
	ssum=0
	hsum=0
	if (CaTGM == 0) return
	forsec SL {
		am = area(0.5)*1e-2
		gtmp = g_CaT(0.5)*am			// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-eca)		// total current in (nA) µS*mV
		ssum += s_CaT(0.5)*gmax_CaT*am
		hsum += h_CaT(0.5)*gmax_CaT*am
	}
	gCaT = Gsum/CaTSA*1e2	// conductance density (S/cm2)
	sCaT = ssum/CaTGM		// % channel inactivation
	hCaT = hsum/CaTGM		// % channel activation
	iCaT = Isum				// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate CaTAnalysis


begintemplate KCaAnalysis
public gKCa, nKCa, KCaSA, KCaGM, iKCa, SL, update, remove
external CaTList, AddToStep, RemoveFromStep, StepEvents_
objref this, SL

proc init() {
	if (numarg()) {
		if (argtype(1)==1) {
			SL = $o1
		} else if (argtype(1)==2) {
			SL = new SectionList()
			forall ifsec $s1 SL.append()
		} else SL = CaTList
	} else SL = CaTList
	forsec SL KCaSA += area(0.5)
	// to get the average conductance density within sections containing the channel the
	// 	 SectionList should be limited to sections with the channel. For the average conductance 
	//   density across the entire cell the SectionList should contain all sections
	forsec SL {
		if (ismembrane("KCa")) {
			KCaGM += gmax_KCa*area(0.5)*1e-2 	// max total conductance in µS
		} else SL.remove()
	}
	update()
	AddToStep(this)
}

proc update() { local Gsum, Isum, gtmp
	Gsum=0
	Isum=0
	if (KCaGM == 0) return
	forsec SL {
		gtmp = g_KCa(0.5)*area(0.5)*1e-2// section conductance in µS
		Gsum += gtmp					// total conductance (µS)
		Isum += gtmp*(v(0.5)-ek)		// total current in (nA) µS*10^-3(V/mV)
	}
	gKCa = Gsum/KCaSA*1e2	// conductance density (S/cm2)
	nKCa = Gsum/KCaGM		// % channel activation
	iKCa = Isum				// total membrane current (nA)
}

proc remove() {
	RemoveFromStep(this)
}
endtemplate KCaAnalysis