1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<!--Converted with LaTeX2HTML 2002-2-1 (1.71)
original version by: Nikos Drakos, CBLU, University of Leeds
* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
* with significant contributions from:
Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
<HTML>
<HEAD>
<TITLE>General information</TITLE>
<META NAME="description" CONTENT="General information">
<META NAME="keywords" CONTENT="DeveloppersGuide">
<META NAME="resource-type" CONTENT="document">
<META NAME="distribution" CONTENT="global">
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="LaTeX2HTML v2002-2-1">
<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
<LINK REL="STYLESHEET" HREF="DeveloppersGuide.css">
<LINK REL="next" HREF="node21.html">
<LINK REL="previous" HREF="node19.html">
<LINK REL="up" HREF="node19.html">
<LINK REL="next" HREF="node21.html">
</HEAD>
<BODY >
<DIV CLASS="navigation"><!--Navigation Panel-->
<A NAME="tex2html302"
HREF="node21.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
SRC="/usr/share/latex2html/icons/next.png"></A>
<A NAME="tex2html298"
HREF="node19.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
SRC="/usr/share/latex2html/icons/up.png"></A>
<A NAME="tex2html292"
HREF="node19.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
SRC="/usr/share/latex2html/icons/prev.png"></A>
<A NAME="tex2html300"
HREF="node1.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents"
SRC="/usr/share/latex2html/icons/contents.png"></A>
<BR>
<B> Next:</B> <A NAME="tex2html303"
HREF="node21.html">List of existing nodes</A>
<B> Up:</B> <A NAME="tex2html299"
HREF="node19.html">XML Files</A>
<B> Previous:</B> <A NAME="tex2html293"
HREF="node19.html">XML Files</A>
<B> <A NAME="tex2html301"
HREF="node1.html">Contents</A></B>
<BR>
<BR></DIV>
<!--End of Navigation Panel-->
<H2><A NAME="SECTION000111000000000000000">
General information</A>
</H2>
<P>
All the XML files containing the thermodynamic parameters are in the Data folder. In each
file, I put the data set of a scientific article or I collected the complementary data set
of several articles.
<BR>
<BR>
I have used the name <SPAN CLASS="textit">data</SPAN> for the main node of each XML file. The name of a <SPAN CLASS="textit">data</SPAN>
subnode is choosen depending on the structure and the model they are made for. You can see the different
existing subnode and existing attributes in the following section.
The enthalpy and entropy value are in cal/mol and are put as character of the subsubnodes enthalpy
and entropy. (see the following example)
<P>
<PRE>
<data type="crick">
<neighbor sequence="AA/TT">
<enthalpy>-7900.0</enthalpy>
<entropy>-22.2</entropy>
</neighbor>
<neighbor sequence="AC/TG">
<enthalpy>-8400.0</enthalpy>
<entropy>-22.4</entropy>
</neighbor>
[...]
<initiation type="per-G/C">
<enthalpy>100.0</enthalpy>
<entropy>-2.8</entropy>
</initiation>
<symmetry>
<enthalpy>0.0</enthalpy>
<entropy>-1.4</entropy>
</symmetry>
</data>
</PRE>
<P>
Each enthalpy and entropy value are stocked into a Thermodynamics object. (see the Javadoc for the
Thermodynamics class from melting package)
<P>
<BR><HR>
<ADDRESS>
Computational Neurobiology
2009-08-24
</ADDRESS>
</BODY>
</HTML>
|
