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1/09/2008
Starting a "new branche" of SketchEl called WIMSchem.
Because it is likely that some of the functionality and fileformat
will be altered, I've chosen not to relate in terms of "package name" to
the mother program SketchEl.
4/09/2008
Quitting...this is too difficult
5/09/2008
Well, nothing permanent...
A reasonable working compromise...does not yet give feedback.
6/09/2008
Checking now goes fine...
Will try to incorporate in WIMS module and see if there are still problems.
7/09/2008
Parameter configurable tool-button-bar [lefthand]
Parameter configurable menu [top]
8/09/2008
Aplication program only:
Exporting a single molecule into a Javascript string,
suitable for wims_variable substitution in "dynamic javascript".
Just experimenting with "easy" assembly of a "database of chemicals"
Adding calulation of molmass
16/09/2008
Added "crippled" Smiles output (as alternative to Brutto-Formula)
The problem of showing/representing the "correct answer" remains troublesome,
if we want to avoid a huge image database linked to a WIMSchem/SketchEl native format dataset.
[so of every molecule we must produce a name.jpg ...]
Some ideas:
1) To solve this partially , I've added -very primitive and not always very correct- Smiles output for "correct answer"
and "student reply" in function CompareNative(). This is not really usefull for stereochemistry...etc...
2) We can show in the applet the correct answer together with the student reply ,
just before sending the appletreply to WIMS using AppendMoleculeNative().
However this can sometimes be a very unclear cluttering of molecules...
3) Another [WIMS] possibility to show the student the correct answers, is ofcourse using the applet as "image" with all params to "no"
in the answer.phtml.
This could mean up to 10 instances of the applet in "my modules".
4) Automatically produce an image of the molecules with the applet ...?
Technically this could be implemented in java/applet. But I see a lot of WIMS trouble.
Corrected number_format trouble in "MoleculeStream.java" on my WinXP installation...
Other Locales can give wrong conversions [a decimal point into a "decimal comma" ].
Now internal standard "US".
On Linux/FreeBSD no trouble , ofcourse :)
17/09/2008
Changed the order of applet-answer, to avoid problems with WIMS and backslashes in LaTeX
18/09/2008
Fixed error in calculating Molecule weights [implicite/explicit Hydrogen]
1/10/2008
Cleaning up a bit...
14/11/2008
Input molecules [the correct molecule as javascript strings] may now also be in MDLMol format.
The MDLMol format is converted to a Native-format string and is used comparing with the student drawing & scoring.
The applet detects Native and MDLMol format: no need to specify.
The application program will now also export a drawing as MDLMol data javascript string.
[Native export to javascript string was already supported]
Added support for "file" and "url" loading [both Native and MDMol].
<param name="file" value="file:test.mol">
or
<param name="file" value="file:$wims_home/public_html/modules/H4/mymodule/data/molecule1.mol">
or
<param name="file" value="http://this_server/123.mol"> -->
note: applets can only load files from the originating server.
note: only signed applets can load files from filesystem
15/11/2008
Added param triggered atom menulist.
<param name="atoms" value="H,P,O,C,Zn,S">
<param name="atoms" value="H:P:O:C:Zn:S">
<param name="atoms" value="H;P;O;C;Zn;S">
<param name="atoms" value="H P O C Zn S">
<param name="atoms" value=""> will give default list
No "atoms" param will give default list.
28/11/2008
Added param
<param name="showfile" value="yes">
If set to "YES" or "1" the file given with param <param name="file" value="$wims_refname/etc"> will be shown on startup.
To be used as imageviewer or as question_molecule to be modified by the student ?
If this param is not present or set to anything but 1,yes...
it will load the "file" into the variable "Correct_answer" and it can be used for
comparing of the student drawing withing the applet [using CompareNative()].
Note: I did not succeed in compiling the Latest version of SketchEl-1.21
Even a precompiled SketchEl-1.21.jar did not run on my java version "1.5.0"
Java(TM) 2 Runtime Environment, Standard Edition (build diablo-1.5.0-b01)
Java HotSpot(TM) Client VM (build diablo-1.5.0_07-b01, mixed mode)
However on "Java 1.6.0/07" [WinXP] it runs fine [but I did not try to compile...]
18/12/2008
Improved java version_check mechanism.
Version is now exported as "150" instead of "1.5.0"
Makes parsing in javascript easier.
Note: use javascript example from CheckVersion.java
Tested javascript molecule-string / molecule-url loading on WinXP on several browsers [latest versions]:
[java 1.6.0_6 version]
Browser URL JS-String VERSIONCHECK
Google chrome OK OK OK
Safari OK OK [very fast] OK
Firefox OK OK OK
IExplore OK OK OK
OPERA 9.3 OK OK [very fast] OK
OPERA 9.7 OK? NOK NOK [null]
OPERA 10a OK? NOK NOK [null]
It seems that OPERA > 9.3 has some problems with Java-Javascript.
I've added an javascript alert_comment:
"It seems your browser does not support Java - Javascript communication.\n Continue at own risk..."
27/12/2008
Introduced param <param name="show_hydrogen" value="no"> to trigger the viewing of [carbon] H's
example: CH3-CH2-CH3 -> C-C-C
Introduced param <param name="show_carbon" value="no"> to trigger the viewing of C's
example:
CH3-CH2-SH -> -- -- SH
Defaults [or if param not present] for both params are "yes"
28/12/2008
Added param for tailoring the templates. Ofcourse only in the applet.
The standalone application will use the templates from the jar.
If the Applet param is not present or "empty" the templates from the jar will be used.
File format of the template molecules [Native or MDLMol] is autodetected.
example:
<param name="template1" value="$wims_ref_name?session=$session&cmd=getfile&special_parm=1.mol">
<param name="template2" value="$wims_ref_name?session=$session&cmd=getfile&special_parm=2.el">
...
<param name="template_n" value="$wims_ref_name?session=$session&cmd=getfile&special_parm=n.mol">
29/12/2008
Successfully tested the template-param usage in combination with WIMS !filewrite in the "getfile" directory.
TO DO: make it work for "Native / MDLmol molecules" as javascript-strings.
29/12/2008
In MoleculeStream.java there was reintroduced one wrong decimal_number_format:
Producing errors on all Microsoft based browsers.
Now all DecimaFormat's are: DecimalFormat fmt=new DecimalFormat("0.0000",new DecimalFormatSymbols(Locale.US));
30/12/2008
Forgotten an extra validity check on param "template" ...
if( parm != null && parm.length()!=0 ){}
Now things like <param name="template1" value=" "> will no longer give a fatal error.
9/2/2009
Added "editor.NormaliseBondLengths();" to a few functions in MainPanel.java
Every time a molecule gets loaded, it will first be run through the function NormaliseBondLengths();
from EditorPane.java
So now externally generated MDLmol-files will show "normal" bondlength.
[todo: clean up demonstation 1.html file...it's a bit of a mess right now.]
13/1/2010
THIS IS AN INTERMEDIATE VERSION: SELECTING BONDS IS NOT YET IMPLEMENTED
[and may contain bugs...]
Added params for colouring atoms:
<param name="select_atoms" value="1,3,5,7,8,10,15"> line numbers in loaded MDLmol file
<param name="select_color1" value="10,7,250">
<param name="select_color10" value="255,0,0">
If "select_color[x]" param is not set, the default colour for a selected atom is red [alpha 100]
Alpha can be changed with param:
<param name="select_alpha" value="130"><!-- optional : default 100 -->
Standalone version works normal
13/1/2010
If no "select_color[x]" is set : red will be used for atom x
If default_select_color is set, this will be the default color for all selected atoms without dedicated color.
If no select_alpha , the value 100 is used
Rotation is in degrees
Adapted 1.html
<param name="default_select_color" value="0,255,0"><!-- optional : default 255,0,0 [red] -->
<param name="rotation" value="-123.12345"> <!-- optional : angle in degrees -->
17/1/2010
Right_mouse_click selects bonds & atoms.
Functions
ReadAtomSelection();
ReadBondSelection();
read these date [comma separated list] from applet. see 1.html
Slight change in applet param syntax:
<param name="default_atom_select_color" value="255,255,0">
<param name="default_bond_select_color" value="255,255,0">
<param name="color_alpha" value="250">
17/1/2010
Added extra param to disable the filling array with userclicks
Changed from expensive int[] to cheap boolean[] to store clicks.
[drawback: no information on type of bonds is stored]
<param name="user_selection" value="1">-->
<!-- optional: default no .
If set to yes/1 user atom/bond selection will be coloured/marked and stored --->
18/1/2010
Added iconbutton & menuitem "unselect" for clearing the userbased right_mouse_click_selection of atoms & bonds
<param name="TOOL_UNSELECT" value="yes">
The same functionality in the menubar subitem "select" --> "Unselect all your..."
18/1/2010
Corrected selecting invisible C's