srd


SYNOPSIS

srd  [pc=<number of PCs; defaults to the number of PCs of the current PLS model>]  \
    [type={WEIGHTS | LOADINGS; defaults to WEIGHTS}]  \
    [seeds=<number of seeds to be extracted; defaults to the smallest  \
    among the following three parameters:
    1) 1/10 of the total number of X variables;
    2) 1/2 of the number of active X variables;
    3) 3000 >  \
    [critical_distance=<distance in Å below which variables are assigned to the nearest seed>; defaults to 1.0 Å]  \
    [collapse={YES | NO; defaults to YES}]  \
    [collapse_distance=<distance in Å between two seeds below which the respective groups are collapsed into one>; defaults to 2.0 Å]


DESCRIPTION

The srd keyword is used to carry out a variable grouping procedure called Smart Region Definition by Pastor et al. who originally implemented it in GOLPE [1]. While a brief explanation of the meaning of the different keywords is reported below, full details about the methodology can be found in the original literature.

    1. 1/10 of the total number of X variables
    2. 1/2 of the number of active X variables
    3. 3000

EXAMPLES

# the following commands perform a Smart Region Definition variable grouping, operating the initial D-optimal selection to identify the default number of seeds in the space of PLS partial weights; 3 principal components are taken into account, using the default critical distance (1.0 Å). No collapsing is carried out after assigning variables to the respective seeds
srd  pc=3  type=WEIGHTS  collapse=NO

# the following commands performs a Smart Region Definition variable grouping, operating the initial D-optimal selection to identify 1500 seeds in the space of PLS loadings; 5 principal components are taken into account, using the default critical distance (1.0 Å). Collapsing is carried out using a 2.5 Å collapse distance
srd  pc=5  type=LOADINGS  seeds=1500  collapse=YES  \
    collapse_distance=2.5


REFERENCES

  1. Pastor, M.; Cruciani, G.; Clementi, S. J. Med. Chem. 1997, 40, 1455-1464.   DOI

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Last update:
May 31. 2015 20:39:42

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