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Hi Bob,
I've looked at the JavaScripts for the documentation, and the XML was not well
formed... also, I the process of fixing the JavaScript code.js, I found two
database errors...
The diff is:
diff -u jmoldoc.orig/cmds.js jmoldoc/cmds.js
- --- jmoldoc.orig/cmds.js 2004-10-18 02:41:44.000000000 +0200
+++ jmoldoc/cmds.js 2004-11-05 10:44:22.254546000 +0100
@@ -59,7 +59,7 @@
newCmd('.loop','','anim','Causes the script to restart at the beginning, with
an optional time delay.','1','.on','','')
newCmd('','','','','1','._time_delay','','')
newCmd('.move','','anim','The move command provides powerful animation
capabilities. It allows you to specify rotations, zooming, and translations
to be performed in a specified period of time. xRot, yRot, and zRot are
rotations about the cartesian axes in degrees. Zoom specifies a zoom factor
(there is a good chance this is not currently implemented properly) xTrans,
yTrans, and zTrans are translations in the range -100 to 100. If you do not
know what slab is, just put in a zero. see the slab command for more
information.
','11','._drotx','._droty','._drotz','._dzoom','._dtransx','._dtransy','._dtransz','._dSlab','._floatSecondsTotal','._move_fps{30}','._move_maxAccel{5}')
- -newCmd('.moveto','','anim','<img align="right" src="examples/moveto.gif">The
moveto command rotates the molecule to a predefined orientation. The first
parameter specifies the number of seconds during which the molecule should
rotate smoothly from the current orientation to the new orientation. A 0 for
this first parameter specifies an instantaneous reorientation. The next three
parameters (x, y, and z) define the axis relative to the default orientation
about which the molecule should be rotated. The fifth parameter defines the
counterclockwise (right-hand) rotation in degrees about this axis. "moveto 0
0 0 0 0" rotates the model to the default orientation (equivalent to
"reset"). If the fifth parameter is 0 but any one of x, y, or z is nonzero,
then no reorientation occurs (because the axis has been specified, but the
rotation is 0 degrees). In conjunction with "show orientation" this command
allows reading and restoring specific user-specified
orientations.','5','._inttime','._coordinate','._coordinate','._coordinate','._cwrotation','','','','','','')
+newCmd('.moveto','','anim','<img align="right"
src="examples/moveto.gif" />The moveto command rotates the molecule to a
predefined orientation. The first parameter specifies the number of seconds
during which the molecule should rotate smoothly from the current orientation
to the new orientation. A 0 for this first parameter specifies an
instantaneous reorientation. The next three parameters (x, y, and z) define
the axis relative to the default orientation about which the molecule should
be rotated. The fifth parameter defines the counterclockwise (right-hand)
rotation in degrees about this axis. "moveto 0 0 0 0 0" rotates the model to
the default orientation (equivalent to "reset"). If the fifth parameter is 0
but any one of x, y, or z is nonzero, then no reorientation occurs (because
the axis has been specified, but the rotation is 0 degrees). In conjunction
with "show orientation" this command allows reading and restoring specific
user-specified
orientations.','5','._inttime','._coordinate','._coordinate','._coordinate','._cwrotation','','','','','','')
newCmd('.slab','','slabdepth',' Slab and Depth together control the
percentage of the molecule to be displayed based on clipping planes. "slab
on" turns slab/depth on. "slab 50" shows the back 50% of the molecule. "slab
25" show the back 25% of the molecule.','1','._on_off','','')
diff -u jmoldoc.orig/code.js jmoldoc/code.js
- --- jmoldoc.orig/code.js 2004-10-28 17:00:27.000000000 +0200
+++ jmoldoc/code.js 2004-11-05 10:42:42.882644000 +0100
@@ -182,28 +182,29 @@
if(!dowritexml)shead+="<tr xml=hr><td colspan=\"5\"><hr /></td></tr
xml=/hr></table xml=/headlist>"
s=shead+s
}
if(dowritexml){
s=s.replace(/ valign\=\"top\"/g,"")
s=s.replace(/\<table\>/g," ")
s=s.replace(/\<td\>/g," ")
s=s.replace(/\<tr\>/g," ")
s=s.replace(/\<blockquote\>/g," ")
s=s.replace(/\<\/table\>/g," ")
s=s.replace(/\<\/td\>/g," ")
s=s.replace(/\<\/tr\>/g," ")
s=s.replace(/\<\/blockquote\>/g," ")
s=s.replace(/td xml\=/g,"")
s=s.replace(/tr xml\=/g,"")
s=s.replace(/table xml\=/g,"")
s=s.replace(/i xml\=/g,"")
s=s.replace(/b xml\=/g,"")
s=s.replace(/\<\/\//g,"</")
s=s.replace(/\</g,"<")
+ s=s.replace(/\[\<\;/g,"\[\&\;lt\;")
s=s.replace(/\<\;cmd/g,"<br /><cmd")
s=s.replace(/\<\;\/cmd/g,"<br /></cmd")
s=s.replace(/\<\;jmol/g,"<br /><br /><jmol")
s=s.replace(/\<\;\/jmol/g,"<br /></jmol")
}
document.write(s)
}
@@ -383,15 +384,15 @@
var scr=Examples[swhat].script
if(scr){
if(scr.indexOf("||")<0)scr=scr.replace(/\;/g,"||")
scr=" "+scr.replace(/\|\|/g,"<br /> ")
if(dowritexml)scr="<cmdscript><br />"+scr+"</cmdscript>"
s+=(dowritexml?scr:"<tr><td class=example>"+scr+"</td></tr>")
}
if(Examples[swhat].html){
s+=(dowritexml?"<cmdhtml>":"<tr><td> See ")
S=Examples[swhat].html.split(",")
for(var i=0;i<S.length;i++){
- - s+="<a target=_blank href=examples/"+S[i]+">"+S[i]+"</a> "
+ s+="<a target=\"_blank\" href=\"examples/"+S[i]+"\">"+S[i]+"</a> "
}
s+=(dowritexml?"</cmdhtml>":"</td></tr>")
}
diff -u jmoldoc.orig/defs.js jmoldoc/defs.js
- --- jmoldoc.orig/defs.js 2004-10-16 15:11:08.000000000 +0200
+++ jmoldoc/defs.js 2004-11-05 10:44:34.314767000 +0100
@@ -74,7 +74,7 @@
newDef('._xoffset','(integer)','x-offset','the x-offset')
newDef('._xyz','.x,.y,.z','"x" or "y" or "z"','')
newDef('._yoffset','(integer)','y-offset','the y-offset')
- -newDef('._backbone_radius','(decimal)[<=4.0]','backbond-radius','the radius
of the backbone')
+newDef('._backbone_radius','(decimal)[<=4.0]','backbone-radius','the radius
of the backbone')
newDef('._trace_radius','(decimal)[<=4.0]','trace-radius','the radius of the
trace')
newDef('._mesh_radius','(decimal)[<=4.0]','mesh-radius','the overall radius
of the mesh')
newDef('._cartoon_radius','(decimal)[<=4.0]','cartoon-radius','the radius of
the cartoon elements')
In other words; the two db errors:
- -moveto did not have the close tag for the <img> element.
- -typo: backbond instead of backbone
The problem with the XML wellformedness:
1. s+="<a target=\"_blank\" href=\"examples/"+S[i]+"\">"+S[i]+"</a> "
which licked the quotes...
2. [<=4.0], as in the def _backbone, needs to be escaped with the added line:
s=s.replace(/\[\<\;/g,"\[\&\;lt\;")
Bob, these files are not yet in CVS, right?
Ok, my next step will be to convert this XML output to DocBook XML...
Egon
- --
[EMAIL PROTECTED]
- ---------------------------------------
CDK: http://cdk.sf.net/
JChemPaint: http://jchempaint.sf.net/
Jmol: http://www.jmol.org/
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