<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"> <HTML> <HEAD> <META NAME="GENERATOR" CONTENT="SGML-Tools 1.0.9"> <TITLE>The KMovisto Handbook: File Formats</TITLE> <LINK HREF="index-6.html" REL=next> <LINK HREF="index-4.html" REL=previous> <LINK HREF="index.html#toc5" REL=contents> </HEAD> <BODY> <A HREF="index-6.html">Next</A> <A HREF="index-4.html">Previous</A> <A HREF="index.html#toc5">Contents</A> <HR> <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 BondRadius= 0.05 #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> <HR> <A HREF="index-6.html">Next</A> <A HREF="index-4.html">Previous</A> <A HREF="index.html#toc5">Contents</A> </BODY> </HTML>