Sophie: kmovisto-0.4.0-4mdk ppc

kmovisto-0.4.0-4mdk.ppc.rpm

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<H2><A NAME="s5">5. File Formats</A></H2>
<P>
<H2><A NAME="ss5.1">5.1 XYZ Format</A>
</H2>
<P>
The XYZ file format is as simple as it could be to define molecules. The following is an example file
for a thiophosphonic acid derivate:
<P>
<BLOCKQUOTE><CODE>
<PRE>
10
thiophosphonic acid derivate
S      0.871683  -1.247827   1.315619
P     -0.210646   0.079218   0.056609
S      1.267992   1.117124  -1.061959
H      1.713511  -0.321066   1.771431
H      1.094058   0.398580  -2.167606
S     -1.674556  -0.788521  -1.013276
C     -0.748754   1.404111   1.222142
H     -1.405618   0.984684   1.974960
H     -1.291765   2.167737   0.677912
H      0.100135   1.864717   1.715164
</PRE>
</BLOCKQUOTE></CODE>
<P>
The first row describes the number of atoms. The second row allows to define a title, it can be empty.
All following rows defines the atom positions: The first column defines for atom symbols, the second to fourth
column defines the cartesian coordinates. You will find sample files in the <I>samples</I> subdirectory
of your distribution.
<P>
<H2><A NAME="ss5.2">5.2 MVT Format</A>
</H2>
<P>
The MVT file format is made for use with KMovisto. This file format allows to save more information as the
XYZ format does. It contains separate sections: You will found <I>MAIN SECTIONS</I>, which are required for
reading this files correctly and <I>OPTIONAL SECTIONS</I>, which are not nessesary but usefull because
otherwise KMovisto will use the current program settings instead. The following is an example of the
MVT format:
<P>
<BLOCKQUOTE><CODE>
<PRE>
#MAIN SECTION: ATOMS
#BEGIN
1    16    1.228192  -1.499652  -0.538837  220  220    0  1.020000
2    15   -0.136865  -0.039240   0.183249  200    0    0  1.060000
3    16    0.689132   1.830803  -0.395957  220  220    0  1.020000
4    1     2.311310  -0.913281  -0.030557  220  220  220  0.320000
5    1    -0.134101   2.000157  -1.426792  220  220  220  0.320000
6    16   -2.052683  -0.353575  -0.337801  220  220    0  1.020000
7    6     0.206299  -0.016744   1.995733   50   50   50  0.770000
8    1    -0.022600  -0.985578   2.423625  220  220  220  0.320000
9    1    -0.418978   0.727672   2.474319  220  220  220  0.320000
10   1     1.245284   0.218880   2.197804  220  220  220  0.320000
#END
#MAIN SECTION: BONDS
#BEGIN
1    1,2
2    1,4
3    2,3
4    2,6
5    2,7
6    3,5
7    7,8
8    7,9
9    7,10
#END
#OPTIONAL SECTION: TITLE
#BEGIN
thiophosphonic acid derivate
#END
#OPTIONAL SECTION: MATRIX
#BEGIN
 0.844079   0.275356  -0.460120
 0.148588   0.704370   0.694107
 0.515221  -0.654249   0.553629
#END
#OPTIONAL SECTION: TRANSLATION
#BEGIN
 0.000000
 0.000000
 0.000000
#END
#OPTIONAL SECTION: SETTINGS
#BEGIN
Label=  NOLABEL
Perspective=  2.5
RadiusReduction=  0.5
BondColor=  2105376
BondFudge=  1.12
#END
</PRE>
</BLOCKQUOTE></CODE>
<P>
Of course the <I>ATOMS</I> and <I>BONDS</I> section are required to define molecules completely. Further
sections are optional. Comment lines start with //, sections and other keywords start with #.
<P>
The first section describes the atoms of the molecule. Each row is composed of nine columns. After an index
number the ordinal number follows. The next three columns are for defining the cartesian coordinates.
Column six to eight are red green blue values (0 to 255 are allowed) to define the atom color. The last
column contains the atom radii.
<P>
The <I>BONDS</I> section describes all connections between the atoms. Each row begins with an index. The
next colum defines the connection.
<P>
The next four sections are optional. Within the <I>MATRIX</I> or <I>TRANSLATION</I> section you have the
ability to specify the rotational matrix or a translation vector of the molecule in separate sections.
So the origin atom coordinates and the view changings done by the user are stored independently in this file format.
<P>
The <I>TITLE</I> or <I>SETTINGS</I> part is to save the file title and special program settings used for this file.
If not defined here KMovisto uses the current program settings.
<P>
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