Egon,
OK, I get it. Well, at least I had well-defined XML, just not DOCBOOK
XML, I think!
Questions:
1. Is HTML allowed within <xxx> and </xxx>? Or does this format not
allow for HTML?
2. Looks to me like the <table></table> information (as in color HBONDS)
had to be removed. Is that correct? Was that necessary? (Is there any
way to show tables in a docbook?)
3. What else besides <table></table> information did you have to delete?
Looks like all <a> tags are out as well?
Bob
Maybe you can send me that Perl script.
Egon Willighagen wrote:
On Thursday 01 December 2005 23:50, Bob Hanson wrote:
Egon, can you just send me privately the final output you would like
to have? I'll see how close I can get.
The full DocBook XML-ized version is at [1].
An item looks sort of like:
<section id="animation" xreflabel="animation or anim">
<title>animation or anim</title>
<para>
Sets selected animation parameters or turns animation on or
off. Note that there are four distinct animation types that can
be employed using Jmol: (1) files may contain multiple stuctures
that are "played" sequencially, (2) Gaussian output files may
contain vibrational modes that can be animated, (3) scripts may
be run through with delays and loops, and (4) the model may spin
or move in a predefined way. The "animation" command only refers
to method (1).
</para>
<variablelist>
<title>Syntax</title>
<varlistentry>
<term>
<command>animation ON/OFF{default: ON}</command>
</term>
<listitem>
<para>Turns on or off animation.</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<command>animation direction -1</command>
</term>
<listitem>
<para>Sets the animation direction to be from last frame to
first frame.</para>
</listitem>
</varlistentry>
</variablelist>
<variablelist>
<title>Definitions</title>
<varlistentry>
<term>
<option>[frames-per-second]</option>
</term>
<listitem>
<para>is the animation rate -- (integer)</para>
</listitem>
</varlistentry>
<varlistentry>
<term>
<option>[time-delay1]</option>
</term>
<listitem>
<para>is the time in seconds to pause on the first frame --
(integer|decimal, >=0)</para>
</listitem>
</varlistentry>
</variablelist>
<para>
See also:
<xref linkend="delay" />,
<xref linkend="exit" />,
<xref linkend="frame" />,
<xref linkend="loop" />,
<xref linkend="zoom" />
</para>
</section>
<section id="atomexpressions" xreflabel="atom expressions">
<title>atom expressions</title>
<para>
The Jmol commands select, restrict, define, center, and
polyhedra take for parameters expressions that represent
collections of atoms in one or more models. While this
documentation does not attempt to define these expressions
completely, several examples are given here. Note that the
substructure() function takes a quoted smiles string for its
argument. The first parameter of the within() function can be a
decimal distance in Angstroms or one of the words group, chain,
or model.
</para>
<para>Examples:</para>
<programlisting>
select atomno=1;color purple; spacefill 600
select nitrogen;color yellow select [PRO]; color green select
within(5.0,[PRO]62) and not [PRO]62; color white select
within(group,within(5.0,[PRO])); color yellow select
substructure("[Fe][S]"); wireframe 1.0
</programlisting>
</section>
I have removed some contant that did not provide new markup.
If you want to add comments, or thoughts, on the output format, please
include them as:
<!-- some comment on why I used element X here (or so) -->
Thanx for doing this! This will make it much easier for me (or one of the
others) to keep the docs in Jmol releases up to date with your website.
Egon
1.http://cvs.sourceforge.net/viewcvs.py/jmol/Jmol/doc/source/guide/scriptCommands.docbook.xml?rev=1.7&view=log
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