MDL
Overview
- contains a QuB hidden markov model
- stored as ASCII text
- missing features which are present in QMF format:
- the names of P and Q variables (e.g. Ligand and Voltage)
- constraints on amplitude
- kinetic constraints with a value
- display properties
Specification
<mdl> = {
<nch> Number of Channels
<ncl> Number of Class
Amp Sd Color (conductance info)
<class>*
<nst> Number of states
Pr Color x y (State Info)
<state>*
<nconn> Number of connections
<connection>*
<ncns> Number of Constrain Parameters
itype->0:fix a 1:scale a 2:loop 3:fix b 4:scale b
itype state index
<constraint>*
<ncoeff> Number of Coefficients
<coeffs>
}
<class> = {
<amp> <sd> <color>
}
<state> = {
<start_prob> <color> <x> <y>
}
<connection> = {
<start> <end> <a_there> <b_there> <drug_there> \
<a_back> <b_back> <drug_back>
}
<constraint> = {
<cns_type> <cns_state0> <cns_state1> ... <cns_staten-1>
}
<cns_type>: 0=fix a; 1=scale a; 2=loop; 3=fix b; 4=scale b
<cns_statei>: the first state is 1
<coeffs>: all ten Ars of the first class, followed by the second class, ..., one coeff per line.
Example
1 Number of Channels
2 Number of Classes
Amp Sd Color (conductance info)
0 0.1 0
1 0.15 1
3 Number of States
Pr Color x y (state info)
0 0 16.4 63.14
0 1 59 63.14
0 0 82.4 24.58
2 Number of Connections
1 2 10 0 1 10 0 0
3 2 800 0 0 500 0 0
1 Number of Constraint Parameters
itype->0:fix a 1:scale a 2:loop 3:fix b 4:scale b
itype state index
0 0 1
0 Number of Coefficients
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0