ExternalModelParameters

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.

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 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;

• 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

• 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: 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

• 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

Example:

[default_model]
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