Virtual Computational Chemistry Laboratory

Method description Configuration file Data matrix file Model file Result files


Configuration file

Program operation is controlled by configuration file cfg that is formed by the interface Java applet. Data file (see download filed on the applet) containing the descriptor and activity values and model file (can be only avaialble if mone saved it from previous analysis) are used to provide data and models. Text calculation results are returned in file comp and the data for illustrative plots are output to file graphics. The format of these files is specified below. Sample input and output files are provided with the software.

Configuration file consists of a number of "KEYWORD = VALUE" pairs given in separate lines. This file is available on page with calculated results. The possible keywords and values of parameters are listed in the table below.

Keyword

Type

Default

Description

INPUTS

INTEGER

*

Number of independent variable (descriptor) columns. The next data column is used for activity/property values, if necessary [MIN=1 MAX=32767]

ROWS

INTEGER

*

Number of compound rows [MIN=1 MAX=32767]

NAMES

INTEGER

0

Compound names are listed in the first (additional) column: 0-no 1-yes

VARIABLE_NAMES

INTEGER

0

Variable (descriptor) names are listed in the first (additional) row: 0-no 1-yes

MODE

INTEGER

0

Mode: 0-calibrate (build model); 1-predict; 2-validate prediction. Calibrate and Validate modes require the additional data column for activity/property values

MAX_PLS_FACTORS

INTEGER

10

Maximum number of extracted PLS factors [MIN=1 MAX=50]

RESIDUAL_VARIANCE

FLOAT

0.001

Minimum relative residual variance of PLS factors [MIN=0 MAX=1]

KEEP_PLS_FACTORS

INTEGER

0

Number of PLS factors to keep in saved models; 0-choose model with highest predictivity (Q2) [MIN=0 MAX=20]

CONSTANT

INTEGER

2

Remove low-variable descriptors that have the same (constant) value for most of the compounds in the training set (all but the number specified by this parameter); 0-do not remove [MIN=0 MAX=5]

GENETIC

INTEGER

1

Genetic selection of descriptors (predictivity - guided optimization of descriptor subset by means of the genetic algorithm): 0-no 1-yes

*Mandatory parameters.

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