QMF

ModelFile
Overview
The root node of a QMF file.
It's also what you get from QUB.ModelView.currModel.getAsNode(), and what you give to QUB.ModelView.currModel.setAsNode().
Trees such as Results can contain ModelFile subtrees. In this case, the ModelFile node's data can serve as an identifier.
Data
optional QTR_TYPE_STRING: an identifier e.g. "237 Final"
Children
Example: COC.qmf
ModelFile
{
	States
	{
		State
		{
			x =16.4859
			y =63.2054
			Class =0
			Pr =0
			Gr =0
		}
		State
		{
			x =59.0022
			y =63.2054
			Class =1
			Pr =0
			Gr =0
		}
		State
		{
			x =82.4295
			y =24.605
			Class =0
			Pr =0
			Gr =0
		}
	}
	Rates
	{
		Rate
		{
			States =0	1
			k0 =10	10
			k1 =0	0
			dk0 =0	0
			dk1 =0	4.62415e-296
			P =1	0
			Q =0	0
			PNames
			{
				STRING PName =Ligand
				STRING PName =Ligand
			}
			QNames
			{
				STRING QName =Voltage
				STRING QName =Voltage
			}
			PValue =43776604	43776604
			QValue =43776676	43776676
		}
		Rate
		{
			States =2	1
			k0 =800	500
			k1 =0	0
			dk0 =0	0
			dk1 =0	8.19338e-297
			P =0	0
			Q =0	0
			PNames
			{
				STRING PName =Ligand
				STRING PName =Ligand
			}
			QNames
			{
				STRING QName =Voltage
				STRING QName =Voltage
			}
			PValue =43776604	43776604
			QValue =43776676	43776676
		}
	}
	Constraints
	{
		FixRate =0	1
		{
			UNSIGNED HasValue =0
			Value =1
		}
	}
	ConstraintsAmpVar
	ChannelCount =1
	(	Amps	Stds	NAr
		0	0.1	0
		1	0.15	0
		2	0.2	0
		3	0.25	0
		4	0.3	0
		5	0.35	0
		6	0.4	0
		7	0.45	0
		8	0.5	0
		9	0.55	0 )
	Ars
	{
		(	Ar	Ar
			0	0
			0	0
			0	0
			0	0
			0	0
			0	0
			0	0
			0	0
			0	0
			0	0 )
	}
	Properties
	{
		ColorBack =12975867
		ColorLine =0
		ColorRate =0
		ColorSelected =255
		ColorFrame =0
		ColorPanel =0
		StateSize =20
		LineWidth =0
		AlignToGrid =0
		UseGlobalCond =0
		ScrollRates =1
		DiagonalRates =0
		ShowK1 =0
		EnforceConstraints =0
		MarginH =5
		MarginV =5
	}
}
States
Data
none
Children
State
Data
none
Children
x
Data
QTR_TYPE_DOUBLE: the x coordinate of the state, from 0 to 100
y
Data
QTR_TYPE_DOUBLE: the y coordinate of the state, from 0 to 100
Class
Data
QTR_TYPE_INT: the color of the state, from 0 to Amps.DataCount-1
Pr
Data
QTR_TYPE_DOUBLE: Probability of starting in this state, from 0 to 1
Gr
Data
QTR_TYPE_INT: Group of this state
Rates
Data
none
Children
Rate
Data
none
Children
States
Overview
Indices of the two states connected by this rate
Data
2 of QTR_TYPE_INT: zero-based state indices
k0
Overview
the pre-exponential rate constant, both forward and backward
Data
QTR_TYPE_DOUBLE: 2 x 1
k1
Overview
the exponential rate constant, both forward and backward
Data
QTR_TYPE_DOUBLE: 2 x 1
dk0
Overview
Standard error of k0. Usually valid only in Results
Data
QTR_TYPE_DOUBLE: 2 x 1
dk1
Overview
Standard error of k1. Usually valid only in Results
Data
QTR_TYPE_DOUBLE: 2 x 1
P
Overview
Whether the rate is concentration-dependent, both forward and backward.
Data
2 of QTR_TYPE_INT; either 1 (true) or 0 (false)
Q
Overview
Whether the rate is voltage-dependent, both forward and backward.
Data
2 of QTR_TYPE_INT; either 1 or 0
PNames
Overview
Which ligands this rate is sensitive to. The first PName child is for the forward rate. The second is for the backward rate.
Data
none
Children
PName
Overview
The name of a concentration-dependence factor.
Data
QTR_TYPE_STRING; e.g. "Ligand1"
QNames
Overview
Which voltages this rate is sensitive to. The first QName child is for the forward rate. The second is for the backward rate.
Data
none
Children
QName
Overview
The name of a voltage-dependence constant
Data
QTR_TYPE_STRING; e.g. "Voltage1"
PValue
Overview
While QUB is running, it uses this field to link to the actual value of P. You should ignore it.
Data
QTR_TYPE_POINTER: 2 x 1
QValue
Overview
While QUB is running, it uses this field to link to the actual value of Q. You should ignore it.
Data
QTR_TYPE_POINTER: 2 x 1
Constraints
Overview
Each child of Constraints represents one constraint; e.g. fix the rate from state 1 -> 2
Data
none
Children
FixRate
Overview
Exempts a preexponential rate constant from optimization
Data
QTR_TYPE_INT: two 0-based state indices
Children
FixExp
Overview
Exempts an exponential rate constant from optimization
Data
QTR_TYPE_INT: two 0-based state indices
Children
ScaleRate
Overview
Constrains one preexponential rate constant to scale with another.
Data
QTR_TYPE_INT: four 0-based state indices
Children
ScaleExp
Overview
Constrains one exponential rate constant to scale with another.
Data
QTR_TYPE_INT: four 0-based state indices
Children
LoopBal
Overview
Constrains a (connected) cycle of three or more states to stay in detailed balance
Data
QTR_TYPE_INT: three or more 0-based state indices, in the order they are connected.
Children
LoopImbal
Overview
Constrains a (connected) cycle of three or more states to stay out of detailed balance by its present ratio
Data
QTR_TYPE_INT: three or more 0-based state indices, in the order they are connected.
Children
HasValue
Overview
unknown
Data
QTR_TYPE_UCHAR: 1 x 1
Value
Overview
unknown
Data
QTR_TYPE_DOUBLE: 1 x 1
ConstraintsAmpVar
Overview
unknown
Data
none
Children
ChannelCount
Overview
How many simultaneous channels are in the patch
Data
QTR_TYPE_INT: 1 x 1
Amps
Overview
Amps.Data[i] is the amplitude in pA of color i
Data
at least 10 of QTR_TYPE_DOUBLE;
if State["Cls"].Data == i, Amps needs at least i+1 elements.
Amps should have the same number of elements as Stds and NAr.
Stds
Overview
Stds.Data[i] is the standard deviation of the amplitude of color i.
Data
at least 10 of QTR_TYPE_DOUBLE;
if State["Cls"].Data == i, Stds needs at least i+1 elements.
Stds should have the same number of elements as Amps and NAr.
NAr
Overview
NAr.Data[i] is the number of autoregressive noise coefficients for color i.
Data
at least 10 of QTR_TYPE_DOUBLE;
if State["Cls"].Data == i, NAr needs at least i+1 elements.
NAr should have the same number of elements as Amps and Stds.
Ars
Overview
A container for the autoregressive noise coefficients. The actual coefficients are in its children.
Ars[i].Data[j] is the jth coefficient for color i.
Data
none
Children
Ar
Overview
The autoregressive noise coefficients for one color (class). There are always 10, but only the first NAr will be used.
Data
QTR_TYPE_DOUBLE: 10 x 1
Properties
Data
none
Children
ColorBack
Data
QTR_TYPE_INT: the RGB color of the background
ColorLine
Data
QTR_TYPE_INT: the RGB color of the lines
ColorRate
Data
QTR_TYPE_INT: the RGB color of the rate numbers
ColorSelected
Data
QTR_TYPE_INT: the RGB color of the selected rate number
ColorFrame
Data
QTR_TYPE_INT: the RGB color of the dashed line around the model
ColorPanel
Data
QTR_TYPE_INT: the RGB color of ?
StateSize
Data
QTR_TYPE_INT: size in pixels of a state box
LineWidth
Data
QTR_TYPE_INT: width in pixels of the lines between states
AlignToGrid
Data
QTR_TYPE_INT: nonzero if states should snap to a grid
UseGlobalCond
Data
QTR_TYPE_INT: nonzero if the rates etc should be calculated using the global conditions; zero to use conditions from the current file
ScrollRates
Data
QTR_TYPE_INT: nonzero if the rates can be changed by pointing at them and spinning the scroll wheel
DiagonalRates
Data
QTR_TYPE_INT: nonzero if the rate captions should be drawn parallel to the lines
ShowK1
Data
QTR_TYPE_INT: nonzero if the rate captions should show k0 and k1 separately. Honored only if DiagonalRates is also true.
EnforceConstraints
Data
QTR_TYPE_INT: nonzero if the constraints should be re-applied after every edit
Data
QTR_TYPE_INT: left and right margin, in pixels
MarginV
Data
QTR_TYPE_INT: top and bottom margin, in pixels