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DUM, DUMP
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DUM, DUMP
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NAME
<br>
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DUM, DUMP - dump selected numeric data to the console (standard output)
or the the specified file.
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SYNOPSIS
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SHORT FORM
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LONG FORM
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DUM AVE
<br>
DUM AVE filename
<br>
DUM HYD
<br>
DUM HYD filename
<br>
DUM F1
<br>
DUM F1 filename
<br>
DUM F2
<br>
DUM F2 filename
<br>
DUM F3
<br>
DUM F3 filename
<br>
DUM F4
<br>
DUM F4 filename
<br>
DUM F5
<br>
DUM F5 filename
<br>
DUM F6
<br>
DUM F6 filename
<br>
DUM F7
<br>
DUM F7 filename
</td>
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DUMP AVERAGE
<br>
DUMP AVERAGE filename
<br>
DUMP HYDROPHOBICITY
<br>
DUMP HYDROPHOBICITY filename
<br>
DUMP F1
<br>
DUMP F1 filename
<br>
DUMP F2
<br>
DUMP F2 filename
<br>
DUMP F3
<br>
DUMP F3 filename
<br>
DUMP F4
<br>
DUMP F4 filename
<br>
DUMP F5
<br>
DUMP F5 filename
<br>
DUMP F6
<br>
DUMP F6 filename
<br>
DUMP F7
<br>
DUMP F7 filename
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DESCRIPTION
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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) andthe second
column contains the requested value (floating point value). Example:
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<pre>
# 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
</pre>
The first line is just a comment.
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The simplest hydrophobicity function is the average hydrophobicity.
The hydrophobicity functions F1, F2, F3, F4 and F5 were introduced in
version 1.4, and functions F6 and F7 were introduced in version 1.6.
Hydrophobicity functions are described in the following source files:
<br>
F1: hyphob_function1.c
<br>
F2: hyphob_function2.c
<br>
F3: hyphob_function3.c
<br>
F4: hyphob_function4.c
<br>
F5: hyphob_function5.c
<br>
F6: hyphob_function6.c
<br>
F7: hyphob_function7.c
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KEYWORDS
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KEYWORD
<br>
(SHORT)
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KEYWORD
<br>
(LONG)
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DESCRIPTION
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HYD
</td>
<td align="left">
HYDROPHOBICITY
</td>
<td align="left">
Dump raw hydrophobicity values.
</td>
<tr>
<td align="left">
AVE
</td>
<td align="left">
AVERAGE
</td>
<td align="left">
Dump average hydrophobicity, using
<br>
the current sliding window width.
</td>
<tr>
<td align="left">
F1
</td>
<td align="left">
F1
</td>
<td align="left">
Dump hydrophobicity function F1.
</td>
<tr>
<td align="left">
F2
</td>
<td align="left">
F2
</td>
<td align="left">
Dump hydrophobicity function F2.
</td>
<tr>
<td align="left">
F3
</td>
<td align="left">
F3
</td>
<td align="left">
Dump hydrophobicity function F3.
</td>
<tr>
<td align="left">
F4
</td>
<td align="left">
F4
</td>
<td align="left">
Dump hydrophobicity function F4.
</td>
<tr>
<td align="left">
F5
</td>
<td align="left">
F5
</td>
<td align="left">
Dump hydrophobicity function F5.
</td>
<tr>
<td align="left">
F6
</td>
<td align="left">
F6
</td>
<td align="left">
Dump hydrophobicity function F6.
</td>
<tr>
<td align="left">
F7
</td>
<td align="left">
F7
</td>
<td align="left">
Dump hydrophobicity function F7.
</td>
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EXAMPLES
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COMMAND
</td>
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DESCRIPTION
</td>
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dump ave
</td>
<td align="left">
Dump average hydrophobicity to the console.
</td>
<tr>
<td align="left">
dump hyd raw.data
</td>
<td align="left">
Dump raw hydrophobicity values to the file
<br>
called raw.data (file names are case sensitive).
</td>
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NOTES
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(1) A very simple output format was choosen to make it compatible with
popular drawing programs.
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RELATED COMMANDS
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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.
<br>
WINDOW is used to define the sliding window width, which affects the
average hydrophobicity function.
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