# DUM, DUMP

NAME
DUM, DUMP - dump selected numeric data to the console (standard output) or the the specified file.
SYNOPSIS

SHORT FORM | LONG FORM
DUM HYD DUM HYD filename DUM AVE DUM AVE filename DUM WEI DUM WEI filename DUM F1 DUM F1 filename DUM F2 DUM F2 filename DUM F3 DUM F3 filename DUM F4 DUM F4 filename DUM F5 DUM F5 filename DUM F6 DUM F6 filename DUM F7 DUM F7 filename | DUMP HYDROPHOBICITY DUMP HYDROPHOBICITY filename DUMP AVERAGE DUMP AVERAGE filename DUMP WEIGHTED DUMP WEIGHTED filename DUMP F1 DUMP F1 filename DUMP F2 DUMP F2 filename DUMP F3 DUMP F3 filename DUMP F4 DUMP F4 filename DUMP F5 DUMP F5 filename DUMP F6 DUMP F6 filename DUMP F7 DUMP F7 filename

DESCRIPTION
The command DUM (DUMP) may be used to dump selected numeric data to the console (standard output) or to the specified file. At present (version 1.6), the command DUMP may be used to dump hydrophobicity functions. Note that the selected hydrophobicity function should be calculated first, which is forced by executing the command PLOT (for example, PLOT AVERAGE will force the calculation of the average hydrophobicity). The output consists of two columns: The first column contains the residue serial number (integer) and the second column contains the requested value (floating point value). Sample output:

    # Raw hydrophobicity
           0    -3.63
           1     0.46
           2    -2.80
           3     1.25
           4    -0.46
           5    -1.15
           6    -3.64
           7    -0.50
           8    -1.81
           9     0.67
          10    -1.15

The first line is just a comment.
The simplest hydrophobicity function are the raw hydrophobicity and the average hydrophobicity. The weighted hydrophobicity was introduced in version 1.6. The hydrophobicity functions F1, F2, F3, F4 and F5 were introduced in version 1.4, and functions F6 F7 were introduced in version 1.6. These hydrophobicity functions are described in the following source files:
F1: hyphob_function1.c
F2: hyphob_function2.c
F3: hyphob_function3.c
F4: hyphob_function4.c
F5: hyphob_function5.c
F6: hyphob_function6.c
F7: hyphob_function7.c
KEYWORDS

KEYWORD (SHORT) | KEYWORD (LONG) | DESCRIPTION
HYD | HYDROPHOBICITY | Dump raw hydrophobicity values.
AVE | AVERAGE | Dump average hydrophobicity, using the current sliding window width.
WEI | WEIGHTED | Dump weighted hydrophobicity, defined in the source file weighted_hydrophobicity.c .
F1 | F1 | Dump hydrophobicity function F1.
F2 | F2 | Dump hydrophobicity function F2.
F3 | F3 | Dump hydrophobicity function F3.
F4 | F4 | Dump hydrophobicity function F4.
F5 | F5 | Dump hydrophobicity function F5.
F6 | F6 | Dump hydrophobicity function F6.
F7 | F7 | Dump hydrophobicity function F7.

EXAMPLES

COMMAND | DESCRIPTION
dump ave | Dump average hydrophobicity to the console.
dump hyd raw.data | Dump raw hydrophobicity values to the file called raw.data (file names are case sensitive).

NOTES
(1) A very simple output format was choosen to make it compatible with popular drawing programs.
RELATED COMMANDS
PLOT is used to draw the specified hydrophobicity function. It should be used before the command dump, to force the calculation of the specified hydrophobicity function. The only exception is raw hydrophobicity (keyword HYD) - it is assigned automatically.
WINDOW is used to define the sliding window width, which affects the average hydrophobicity function.