Re: [Jmol-users] JmolSmilesApplet.jar

[Otis Rothenberger]

Alas, it's unfortunate that the wheel has to be reinvented, but as one 
of my favorite authors says, "So it goes."


Having said this, I'll mention that I adopted JME as an educational tool 
years ago for two main reasons: 1) It had the functionality that I 
needed; 2) It was light weight.


With respect to functionality, JME has a limited ability to generate 
unique SMILES for student testing. This feature has been enhanced by 
Bob's recent work on the find method (applet). Recently also, the 
addition of UFF to Jmol allowed for a 2D to 3D connection of JME and 
Jmol. This also has been enhanced through Bob's efforts. In the best of 
worlds, JME would go open source and become an integral part of Jmol. 
Since that's not going to happen, I definitely support reinventing the 
wheel.


I've stated above in general terms the functionality that I think is 
important in a drawing component connection to Jmol: SMILES 
communication and 2D to 3D capability. While there may be a number of 
specific features that fall under this umbrella, I would urge developers 
to resist the temptation to make the Jmol drawing component a full 
featured drawing application. Marvin is neat, but it's also clunky as 
all get out!


My wish list:

1) SMILES communication for educational testing
2) 2D to 3D capability
3) As slick as JME!

Otis



On 5/13/2010 9:15 AM, Robert Hanson wrote:
1. Education. I'm definitely interested in something VERY simple -- 
just JME-type capability plus the option to extend as open-source 
ideas arise. For me, the audience is education. JME is perfect EXCEPT 
that it is not open source and never will be. MarvinSketch is 
beautiful, but it comes at a price of 2MB of download. Same for 
JChemPaint. We know that JME is only 39K, so the task CAN be 
accomplished in roughly that amount of space.


2. I like the idea of extending the capabilities of JME to inorganic 
chemists. Nothing really that fancy in that, other than being able to 
indicate the full range of stereochemistry


3. Graphically, just a basic interface -- as simple as possible. 
Programmatically, as rich as possible.


Bob

On Thu, May 13, 2010 at 6:27 AM, Philip Bays > wrote:


Boy, you are an eager beaver.   And on a sleep cycle much
different from mine:-)

I would ask several questions about the goals of such a project:
1. What would be the audience?  Primarily teaching situations or a
more general, even commercial setting?
2. How much of the periodic table do you want to use? Is this for
organikers, or all brands of chemists?
3. How flexible an interface?

I have previously made a couple of comments about MarvinSketch on
the list.  There are things I like about that interface better
than JME and others that I like better in JME.  For example:
   The ability to arrange the icons in the interface
differently, omitting some if necessary (Marvin)
   You can choose a ChemDraw, Isis, or Marvin style
interface. and rearrange the icons to your hearts delight.
   The ability to use the standard select, copy, paste, erase,
keyboard shortcuts (Marvin)
   The option to separate the single bond, wedge up, wedge
down, double and triple bond in the interface, or use them all in
a single popup, or use the click method that JME uses.   I have
not fully decided which I like better here.  For a beginning
student, seeing them all as separate entities might be easiest. On
the other hand, simply clicking on a wedge to make it up or down
is convenient for the more experienced user as in JME.
   The applet layout size (JME).  MarvinSketch seems designed
to be the central focus of the page.  For my use, I want to be
able to have a sketching applet, a visualization applet (Jmol),
and a teacher/student interaction space all on the same page.
 MarvinSketch is more difficult to work around for that purpose in
my experience.  Of course that may be the product of interface
flexibility.

Just a few early morning thoughts.

Phil

On May 12, 2010, at 11:12 PM, Robert Hanson wrote:

> Probably what we should do is write a simple open-source version
of JME to provide a frame to JmolSmilesApplet. It's too bad that
Peter's work is not extensible in that regard. Peter, you sure you
don't want to do this? But it would be a nice project - either to
use a streamlined version of JChemPaint or just start from
scratch. I mostly like Peter's interface, but there are some very
good ideas in JChemPaint as well. Suggestions? What we are looking
for is a very small, simple interface. Nothing fancy. If it comes
from CDK it will need to be VERY highly streamlined.
Interestingly, my first version was 120K, then I refactored Jmol
and got it down to 43K, then I did a clean build and discovered it
was only 39K. Interesting process.

J. Philip Bays

Re: [Jmol-users] JmolSmilesApplet.jar

[Philip Bays]

On May 13, 2010, at 9:15 AM, Robert Hanson wrote:

> Graphically, just a basic interface -- as simple as possible. 
> Programmatically, as rich as possible.

OK.   I am looking at the JChemPaint applet.  I like the layout of the 
interface.  However, there are things I could do without:
The templates -- we do not need all of those structures.   However, the 
JME implementation of functional groups by MolInsipiration is very useful.
Also the ability to display the smiles string from an icon as in JME.
The rotation is nice; not sure I need the flip horizontal or vertical.
Not sure about copy and past to and from the clipboard.  
Not sure I need the zoom and shrink features.
I do not need all the options under the file menu.  I am not using this 
as a drawing program for documents.
In fact, for my purposes, I do not need to display all of those options 
along the top.   Most of those are evident in the icons surrounding the drawing 
window, or can be invoked in parameter tags.
I would either use a periodic table icon to select additional (beyond 
the most frequently used) elements, or us some sort of popup like is used in 
the menu bar -- not both.  Further, for educational use, I would simple have a 
parameter that allows the teacher to specify the elements to be used for that 
particular assignment.  Those would then be the ones that appear along the 
bottom.

These are just my thoughts.   But perhaps they will get the conversation 
started on what a minimal applet would look like.  

J. Philip Bays
Professor of Chemistry
Science Hall 172
Saint Mary's College
Notre Dame  IN  46556
(574) 284-4663

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Re: [Jmol-users] JmolSmilesApplet.jar

[Robert Hanson]

1. Education. I'm definitely interested in something VERY simple -- just
JME-type capability plus the option to extend as open-source ideas arise.
For me, the audience is education. JME is perfect EXCEPT that it is not open
source and never will be. MarvinSketch is beautiful, but it comes at a price
of 2MB of download. Same for JChemPaint. We know that JME is only 39K, so
the task CAN be accomplished in roughly that amount of space.

2. I like the idea of extending the capabilities of JME to inorganic
chemists. Nothing really that fancy in that, other than being able to
indicate the full range of stereochemistry

3. Graphically, just a basic interface -- as simple as possible.
Programmatically, as rich as possible.

Bob

On Thu, May 13, 2010 at 6:27 AM, Philip Bays  wrote:

> Boy, you are an eager beaver.   And on a sleep cycle much different from
> mine:-)
>
> I would ask several questions about the goals of such a project:
> 1. What would be the audience?  Primarily teaching situations or a more
> general, even commercial setting?
> 2. How much of the periodic table do you want to use? Is this for
> organikers, or all brands of chemists?
> 3. How flexible an interface?
>
> I have previously made a couple of comments about MarvinSketch on the list.
>  There are things I like about that interface better than JME and others
> that I like better in JME.  For example:
>The ability to arrange the icons in the interface differently,
> omitting some if necessary (Marvin)
>You can choose a ChemDraw, Isis, or Marvin style interface.
> and rearrange the icons to your hearts delight.
>The ability to use the standard select, copy, paste, erase, keyboard
> shortcuts (Marvin)
>The option to separate the single bond, wedge up, wedge down, double
> and triple bond in the interface, or use them all in a single popup, or use
> the click method that JME uses.   I have not fully decided which I like
> better here.  For a beginning student, seeing them all as separate entities
> might be easiest. On the other hand, simply clicking on a wedge to make it
> up or down is convenient for the more experienced user as in JME.
>The applet layout size (JME).  MarvinSketch seems designed to be the
> central focus of the page.  For my use, I want to be able to have a
> sketching applet, a visualization applet (Jmol), and a teacher/student
> interaction space all on the same page.  MarvinSketch is more difficult to
> work around for that purpose in my experience.  Of course that may be the
> product of interface flexibility.
>
> Just a few early morning thoughts.
>
> Phil
>
> On May 12, 2010, at 11:12 PM, Robert Hanson wrote:
>
> > Probably what we should do is write a simple open-source version of JME
> to provide a frame to JmolSmilesApplet. It's too bad that Peter's work is
> not extensible in that regard. Peter, you sure you don't want to do this?
> But it would be a nice project - either to use a streamlined version of
> JChemPaint or just start from scratch. I mostly like Peter's interface, but
> there are some very good ideas in JChemPaint as well. Suggestions? What we
> are looking for is a very small, simple interface. Nothing fancy. If it
> comes from CDK it will need to be VERY highly streamlined. Interestingly, my
> first version was 120K, then I refactored Jmol and got it down to 43K, then
> I did a clean build and discovered it was only 39K. Interesting process.
>
> J. Philip Bays
> Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> (574) 284-4663
> pb...@saintmarys.edu
>
>
>
>
>
> --
>
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] JmolSmilesApplet.jar

[Philip Bays]

Boy, you are an eager beaver.   And on a sleep cycle much different from mine:-)

I would ask several questions about the goals of such a project:
1. What would be the audience?  Primarily teaching situations or a more 
general, even commercial setting?
2. How much of the periodic table do you want to use? Is this for organikers, 
or all brands of chemists?
3. How flexible an interface?

I have previously made a couple of comments about MarvinSketch on the list.  
There are things I like about that interface better than JME and others that I 
like better in JME.  For example:
The ability to arrange the icons in the interface differently, omitting 
some if necessary (Marvin)
You can choose a ChemDraw, Isis, or Marvin style interface. and 
rearrange the icons to your hearts delight.
The ability to use the standard select, copy, paste, erase, keyboard 
shortcuts (Marvin)
The option to separate the single bond, wedge up, wedge down, double 
and triple bond in the interface, or use them all in a single popup, or use the 
click method that JME uses.   I have not fully decided which I like better 
here.  For a beginning student, seeing them all as separate entities might be 
easiest. On the other hand, simply clicking on a wedge to make it up or down is 
convenient for the more experienced user as in JME.
The applet layout size (JME).  MarvinSketch seems designed to be the 
central focus of the page.  For my use, I want to be able to have a sketching 
applet, a visualization applet (Jmol), and a teacher/student interaction space 
all on the same page.  MarvinSketch is more difficult to work around for that 
purpose in my experience.  Of course that may be the product of interface 
flexibility.

Just a few early morning thoughts.

Phil

On May 12, 2010, at 11:12 PM, Robert Hanson wrote:

> Probably what we should do is write a simple open-source version of JME to 
> provide a frame to JmolSmilesApplet. It's too bad that Peter's work is not 
> extensible in that regard. Peter, you sure you don't want to do this? But it 
> would be a nice project - either to use a streamlined version of JChemPaint 
> or just start from scratch. I mostly like Peter's interface, but there are 
> some very good ideas in JChemPaint as well. Suggestions? What we are looking 
> for is a very small, simple interface. Nothing fancy. If it comes from CDK it 
> will need to be VERY highly streamlined. Interestingly, my first version was 
> 120K, then I refactored Jmol and got it down to 43K, then I did a clean build 
> and discovered it was only 39K. Interesting process.

J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
pb...@saintmarys.edu




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Re: [Jmol-users] [BlueObelisk-SMILES] JmolSmilesApplet.jar

[Egon Willighagen]

Hi Bob,

On Thu, May 13, 2010 at 5:12 AM, Robert Hanson  wrote:
> Probably what we should do is write a simple open-source version of JME to
> provide a frame to JmolSmilesApplet. It's too bad that Peter's work is not
> extensible in that regard. Peter, you sure you don't want to do this? But it
> would be a nice project - either to use a streamlined version of JChemPaint
> or just start from scratch. I mostly like Peter's interface, but there are
> some very good ideas in JChemPaint as well. Suggestions? What we are looking
> for is a very small, simple interface. Nothing fancy. If it comes from CDK
> it will need to be VERY highly streamlined.

I'll try to find some time for the further refactoring of the
CDK-JChemPaint architecture, and work on a minimal applet.

> Interestingly, my first version
> was 120K, then I refactored Jmol and got it down to 43K, then I did a clean
> build and discovered it was only 39K. Interesting process.

Impressive!

This only strengthens my opinion with the right effort we can get a
small JChemPaint applet too.

Egon

-- 
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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