Jonathon, I know and use some of those programs and I am not proposing that Jmol should have a builder section. All I am talking about developing is dialogs that can save the currently viewed molecule (wherever that came from) as an input file for the codes I mentioned. I agree that it would be reinventing the wheel to have a full builder.
Babel provides a conversion utility but it does not have a graphical dialog for selecting calculation options. Marvin will save Gaussian input but does not allow you to customize the route line. Argus Lab has an interface to Gaussian but it is Windows only and not open source. I suppose I am proposing something similar to the Argus Lab interface. I probably did not make my intentions clear enough in the original e-mail. Andy Jonathan Gutow wrote: > Andy, > Molecule building is already available in Ghemical and wxMacMolPlt > (sometimes just MacMolPlt) which are open source and run on a > variety of platforms. Ghemical and wxMacMolPlt are not java based so > there might be some value to making a java molecule builder, but > there are two "commercial" things available: 1) the builder in WebMO > and ChemAxon's Marvin sketch. So, I wonder if it is a good place > for us to put our effort when there are other tool available. In > most cases we are all overburdened enough that we should not reinvent > the wheel if we can avoid it. > > If you do pursue this, I suggest that it should be an offshoot of > Jmol and not something to be folded into the main code. I find that > programs that do "everything" become hard to use. > > My two cents. > > Jonathan > On Mar 12, 2008, at 8:43 AM, Andrew Turner wrote: > >> Hi >> >> Bob, thanks for the pointers they are really useful. >> >> I work at the University of Edinburgh trying to get experimental >> research chemists to use computational chemistry tools. Not just as >> collaboration, but teaching them to use then so it becomes second >> nature >> in their research (like getting an NMR spectrum or running MS >> analysis). >> Part of this consists of finding tools that are easy for them to >> use (on >> whatever platform) for building input, submitting calculations and >> analysing output. >> >> My ideas for contributions reflect my user base and are mainly on the >> application side I guess. Things I would like to add: >> >> * A save molecule dialog that can write the system in a variety of >> formats. Some coordinate types but also input for common codes that we >> use (Gaussian, MOLPRO, Castep, CPMD). There may be a role for Babel >> here. It might also need different dialogs to deal with different >> codes. >> * A dialog for controlling the plotting of surfaces from cube files. >> Pretty simple initially but moving on to handling mapping and slices. >> * An interface to Globus Toolkit for submitting jobs using UK e- >> Science >> certificates. We are developing a Gaussian submission portlet and >> would >> like to use the Jmol applet within it for viewing input and output, it >> would be nice if we could integrate the submission into the Jmol >> application. >> >> I have had a quick look through the feature enhancements on the >> wiki and >> cannot see these things. But please correct me if people are already >> working on them. >> >> Regards >> >> Andy >> >> >> >> Bob Hanson wrote: >>> Andy, welcome aboard! Tell us about yourself. >>> >>> I'm probably the only one right now who really knows everything >>> that is >>> in the code and how it works. So ask me anything. One thing you >>> can look >>> at is the viewer.gif file in >>> http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/ >>> jmol/_documents/ >>> >>> It's a bit out of date, but it shows the basics of how the different >>> classes are related. Primarily, Viewer is the key player here, and >>> all >>> the "managers" work with it. >>> >>> In answer to your specific question, the script goes into a queue >>> and is >>> processed within the ScriptManager class. When its turn comes up, >>> it is >>> sent to Viewer.evalStringWaitStatus, where it is then sent to Eval >>> for >>> processing. Eval passes the script to Compiler for compiling and some >>> syntax error checking, after which it takes the form of a set of >>> commands, each of which consists of a Token[] array. There are some >>> replacements that go on late in the game, and the result is a Token >>> array called "statement". This is the currently processing command in >>> token form. The main loop in Eval is the method >>> instructionDispatchLoop. >>> >>> If you are interested in contributing, that's great. We can set up a >>> branch for you, and you can play all you want, letting us know if you >>> are having success or problems. If something looks good, we'll >>> merge it >>> into 11.5, which is the trunk for current development. I recommend >>> not >>> doing major code refactoring or modifications without first checking >>> with this list to see if it would make merging too difficult. >>> >>> What sort of ideas are you thinking of in terms of contributions? >>> >>> Bob >>> >>> >>> Andrew Turner wrote: >>> >>>> Hi, >>>> >>>> I am new to developing Jmol and have a few ideas as to what I could >>>> contribute. I have been to the Jmol wiki and checked out the Jmol >>>> source >>>> into eclipse. >>>> >>>> My question is this, is there anywhere that provides a overview >>>> of how >>>> the Jmol package fits together. I have had a look through the >>>> source for >>>> a few hours and feel I am no closer to understanding which bits >>>> do what. >>>> >>>> For example, if I type 'write COORD "file.xyz"' in the scripting >>>> dialog >>>> of the application, where does the final file writing actually >>>> get done. >>>> I can trace the command to Viewer.evalStringQuiet but start to >>>> get lost >>>> pretty soon after that. >>>> >>>> If anyone has anything useful I would be glad to see it. >>>> >>>> Regards >>>> >>>> Andy >>>> >>>> >>> >> -- >> ================================== >> Dr Andrew R. Turner >> Research Computing Officer >> e: [EMAIL PROTECTED] >> t: +44 (0)131 650 7748 >> w: http://www.eastchem.ac.uk/rcf >> icq: 370-899-715 >> p: School of Chemistry >> University of Edinburgh >> EH9 3JJ >> ================================== >> >> >> ---------------------------------------------------------------------- >> --- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Jmol-developers mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-developers > > Dr. Jonathan H. Gutow > Chemistry Department [EMAIL PROTECTED] > UW-Oshkosh Office:920-424-1326 > 800 Algoma Boulevard FAX:920-424-2042 > Oshkosh, WI 54901 > http://www.uwosh.edu/faculty_staff/gutow/ > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Jmol-developers mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- ================================== Dr Andrew R. Turner Research Computing Officer e: [EMAIL PROTECTED] t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
