Recent changes to ExternalModelParameters

ExternalModelParameters modified by KKozlov

KKozlov — Wed, 03 Feb 2021 06:28:02 -0000

--- v3
+++ v4
@@ -55,7 +55,7 @@

 ###  parmtypes=1; 0; 0;

- * type of parameters: 1 - integer values to be produced by rounding, 2 - integer values to be produced by sorting, 0 - real values; 4 - integer values to be produced by special rounding. Methods a re described in [ConvertDoubleToInt]
+ * type of parameters: 1 - integer values to be produced by rounding, 2 - integer values to be produced by sorting, 0 - real values; 4 - integer values to be produced by special rounding. Methods are described in [ConvertDoubleToInt]

 ###  maskvals=0; 0; 0;

ExternalModelParameters modified by KKozlov

KKozlov — Wed, 03 Feb 2021 06:27:16 -0000

--- v2
+++ v3
@@ -55,7 +55,7 @@

 ###  parmtypes=1; 0; 0;

- * type of parameters: 1 - integer as rounding, 2 - integer as sorting, 0 - real
+ * type of parameters: 1 - integer values to be produced by rounding, 2 - integer values to be produced by sorting, 0 - real values; 4 - integer values to be produced by special rounding. Methods a re described in [ConvertDoubleToInt]

 ###  maskvals=0; 0; 0;

ExternalModelParameters modified by KKozlov

KKozlov — Wed, 21 Oct 2020 10:27:27 -0000

--- v1
+++ v2
@@ -37,7 +37,53 @@
 ### hbound | valhbound

   * **hbound=0;0;...;0;** is the upper bound for each parameter individually. 
-  * **valhbound=0** is the upper bound for all parameters. 
+  * **valhbound=0** is the upper bound for all parameters.
+
+Another form of definition:
+
+###  partnames=x;beta;MB;
+
+ * names of groups of parameters
+
+###  partsizes=60; 55; 1;
+
+ * number of parameters in each group
+
+###  parmvals=200; 5; 5;
+
+ * initial values for each group
+
+###  parmtypes=1; 0; 0;
+
+ * type of parameters: 1 - integer as rounding, 2 - integer as sorting, 0 - real
+
+###  maskvals=0; 0; 0; 
+
+  * values for masks
+
+###  tweakvals=1; 1; 1; 
+
+ * define if the value can be changed. 
+
+###  dparmvals=200; 5.5; 5;
+
+ * initial values for each group
+
+###  lboundvals=0; -10; 0.01;
+
+ * lower bound for each group
+
+###  hboundvals=1924; 10; 9;
+
+ * upper bound for each group
+
+###  limitvals=1; 1; 1;
+
+ * defines if parameters are limited
+
+###  scalevals=1; 1; 1;
+
+ * scale factor for aparameters

 ### command

@@ -48,10 +94,14 @@
 Defines the parameter's file format. The following formats are supported: 

   * **convert=sdf** for molecules. 
-  * **convert=gemstat** for gemstat program. 
-  * **convert=subset**
-  * **convert=subsubset**
-  * **convert=octave**
+  * **convert=gemstat** for gemstat program: one line in a file, starting with parameter name, parameters are delimited by space
+  * **convert=dgemstat** two lines in a file, starting with parameter name, parameters are delimited by space
+  * **convert=subset** for integer indices
+  * **convert=subsubset** for subset of integer indices
+  * **convert=octave** to use in Octave with source command
+  * **convert=r** to use in R with source command
+  * **convert=ini** ini format to use with Qt framework
+  * if this option is not given parameters are printed to the command line 

 ### delimiters

@@ -65,17 +115,23 @@

   * defines the reordering of keys 

+Example:
+    
     [default_model]
-    parts=hb;2;Kr;2;gt;2;kni;2;bcd;2;cad;2;tll;2;basal_transcription =;1;hb hb;1;Kr Kr;1;gt gt;1;kni kni;1;bcd bcd;1;cad cad;1;tll tll;1;
-    mask=1;0;0;0;0;0;0;0;0;0;0;0;0;0;1;1;0;0;0;0;0;0;
-    parms=0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;
-    dparms=0.964910;1.011700;1.056578;1.099454;0.154759;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.257495;0.705276;1.858218;0.566396;1.420308;0.660813;0.356575;0.014055;
-    tweak=1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;
-    lbound=0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.0001;
-    hbound=100;100;100;100;100;100;100;100;100;100;100;100;100;100;500;500;500;500;500;500;500;0.1;
-    command=./script
-    convert=gemstat
-    delimiters= ,\n\t\s
-    keys=23;
-    mapping=0;
-    
+    partnames=x;beta;MB;
+    partsizes=60; 55; 1;
+    parmvals=200; 5; 5; 
+    parmtypes=1; 0; 0;
+    maskvals=0; 0; 0;
+    tweakvals=1; 1; 1;
+    dparmvals=200; 5.5; 5; 
+    lboundvals=0; -10; 0.01;
+    hboundvals=1924; 10; 9; 
+    limitvals=1; 1; 1;
+    scalevals=1; 1; 1;
+    command=script 
+    delimiters=\n=
+    keys=0;1;2;
+    convert=ini
+    mapping=0;0;1;2;
+    type=command

ExternalModelParameters modified by KKozlov

KKozlov — Wed, 11 Feb 2015 12:39:36 -0000

Last modified 4 weeks ago

Parameters for External Model

Section xmmodel defines external model. No consistency checks are performed for parameters. The order of parameters should be as below.

parts

is the list of headers in par file with the number of parameters in each line

mask | nummask

mask=1;0;...;0; is an array of 0 and 1 of the length that is the number of parameters (not used).
nummask=31 specifies the number of 1 in the array.

parms | numparms

parms=2;3;1;...;5; are the values of the parameters as integers (not used).
numparms=40 number of parameters.

dparms | numdparms

dparms=0.1;0.2;...;0.9 are the values of parameters as doubles (in case of convert=gemstat in par file in the left-to-right up-to-bottom order).
numdparms=40 number of parameters.

tweak | numtweak | valnottweak

tweak=1;0;1;...;1; define if the value can be changed.
numtweak=16 number of parameters to tweak. 1 will be inserted in first numtweak places, all others will be set to 0.
valnottweak=1;34;15; is the list of indices to be set to 0, all others will be set to 1;

lbound | vallbound

lbound=0;0;...;0; is the lower bound for each parameter individually.
vallbound=0 is the lower bound for all parameters.

hbound | valhbound

hbound=0;0;...;0; is the upper bound for each parameter individually.
valhbound=0 is the upper bound for all parameters.

command

is run to get the score. The par file is simply appended to this string.

convert

Defines the parameter's file format. The following formats are supported:

convert=sdf for molecules.
convert=gemstat for gemstat program.
convert=subset
convert=subsubset
convert=octave

delimiters

are used to parse the output of the command

keys

defines the indices of the elements of the parsed output that we need

mapping

defines the reordering of keys

[default_model]
parts=hb;2;Kr;2;gt;2;kni;2;bcd;2;cad;2;tll;2;basal_transcription =;1;hb hb;1;Kr Kr;1;gt gt;1;kni kni;1;bcd bcd;1;cad cad;1;tll tll;1;
mask=1;0;0;0;0;0;0;0;0;0;0;0;0;0;1;1;0;0;0;0;0;0;
parms=0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;
dparms=0.964910;1.011700;1.056578;1.099454;0.154759;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.699184;1.257495;0.705276;1.858218;0.566396;1.420308;0.660813;0.356575;0.014055;
tweak=1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;
lbound=0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.01;0.0001;
hbound=100;100;100;100;100;100;100;100;100;100;100;100;100;100;500;500;500;500;500;500;500;0.1;
command=./script
convert=gemstat
delimiters= ,\n\t\s
keys=23;
mapping=0;