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Ghemical: Molecular modelling - Message forums
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Expanded view | Monitor forum | Save place
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Message
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I think this actually works, in a way... :)
You see, you have to use in "erase" exactly same logic as in "draw" when you add a bond. So, erasing is an "un-adding" operation: to remove a bond, press MB down at 1st atom, move mouse to 2nd atom, and release MB.
The reason why it works this way is, that the OpenGL selection code can detect only atoms, and no bonds. So we just select the atoms, and later figure out what bond the user meant.
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This is just a thread for potential feature requests. Post ideas, suggestions, etc. here.
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Need a preferences dialog box and the ability to save settings to project files as well.
(Easy way of setting rendering detail, etc.)
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We need a way of allowing plugins written in scripting languages like Perl or Python. These could interface with other programs, perform various changes on the molecules, etc.
Suggestions for an "All Atoms" API:
GetCurrentCRD()
SetCurrentCRD()
AddAtom()
AddBond()
DeleteAtom()
DeleteBond()
...
This probably also needs some sort of "global hook" for putting in a menu item and then calling main() for the plugin.
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The "Save As" menu item should also have a "Save" for just saving the file to the current filename/path (if it exists.) If no path exists, this should work like the Save As.
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A revert menu item would be nice--silently close the current buffer and open it again from disk.
This should probably include a question to be sure the user wants to discard the changes!
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Ideally, the engine should allow exporting the graphics--e.g. create an offscreen buffer that's potentially larger than the screen and then save it to a file.
This would allow high-res JPEG or PNG files for presentations.
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Yep. At least the MESA opengl variant supports off-screen rendering directly.
Then we have had that idea of coverting the current view to commands for a ray-tracing program; a nice idea but I guess I don't have time for that very soon.... :(
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This is a bit complicated, but it would be fantastic to have an undo/redo feature to undo the last action. (This is especially a big deal if the geometry optimization screws up.)
I don't know a good way of dealing with this--though an easy (but memory intensive) solution would be to keep a copy of the current coordinate set and camera as the "undo" buffer.
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It would be great if the current selection could be copied/pasted. (Cut is probably not quite as useful.)
This should work across files, so this needs to be some sort of global buffer.
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Ideally you should be able to drag the select tool around and select a region of space. This would be a bit like the "lasso" or "rectangle" tool in GIMP, etc.
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Here's an idea for the "library" feature.
Have a user-definable folder for the library--default to the same path as the parameters, etc. The user could set this in the prefs.
The library/ directory could have one level of directories, then a bunch of Ghemical files. So a menu could contain items for each of the directories and these would list the files. Choosing a file would Open/Insert it into the current project.
This allows the user to easily file and modify items in the library. (And it's not too hard to code.)
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This is done, though we'll need to make up some example molecules and change the installation portion of the Makefile.in.
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Not much to say. These need to work--maybe through an "all atoms" interface class.
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Yep.
We haven't really specified a file format for QM files, but it looks like the MM file format would be just fine.
There we have those !Sections, and for QM models we might have some different !Sections present,
but we can always ignore those !Sections that we don't need...
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New sections for the file format (previous versions would just ignore them)
!Unit Cell
a= b= c= alpha= beta= gamma=
!Charge
!Hamiltonian or !Basis
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It would be nice to animate vibrational modes based on QM output from other programs.
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I think we could even compute the vibrations ourselves... For all models, we can calculate the 1st derivatives, and using those I think we could calculate 2nd derivatives numerically. Then from 2nd derivatives it is possible to solve the vibrations somehow... I guess :)
Anyways, when we have the displacement vectors, it would be very easy to animate them!
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Ideally, the QM mode should be able to read output from other popular programs (e.g. Gaussian, Q-Chem, Jaguar, HyperChem...) -- maybe this could work by translating the eigenvectors to MPQC format?
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Trajectory format should allow importing trajectories from other programs (VMD pops to mind).
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Like in Spartan, which has a dialog with:
formula
molecular weight
surface area
volume
total energy
HOMO energyLUMO energy
Dipole
...
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For measuring, it's sometimes useful to define a temporary dummy atom as a centroid. (Either cartesian or mass-weighted)
This would obviously not necessarily be updated by other actions, but at the least it would make some measurements easier.
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Some tools to set bond lengths, angles, torsions, etc. to particular values would be helpful.
Along the same line, it might be helpful sometimes to have "alignment" tools to set the position to a particular X, Y, Z, etc. (Yes, you can edit the file, but it's sometimes nice to do this in the editor.)
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Maybe a "Draw Vector" object that illustrates the dipole vector including scaling to the appropriate magnitude.
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I think the MOPAC code can calculate both partial charges for atoms, and the dipole moment.
This could be done, if we could take the dipole componenets from MOPAC...
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I think it can be done for MM-calculated charges as well--it just won't be as accurate as MOPAC or MPQC-dervied dipoles.
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It would be nice to "erase" bonds as possible. One way would be to have a "No Bond" bond order as a choice in the Bondtype dialog--this would just delete the bond when it's redrawn.
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humm... I think the "erase" mouse tool can do this pretty well?
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No, it always seems to "grab" the nearest atom too. So it doesn't just erase the bond, it erases an atom and usually more than one bond.
Try it--make a nice giant bond and click right in the middle!
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I think this actually works, in a way... :)
You see, you have to use in "erase" exactly same logic as in "draw" when you add a bond. So, erasing is an "un-adding" operation: to remove a bond, press MB down at 1st atom, move mouse to 2nd atom, and release MB.
The reason why it works this way is, that the OpenGL selection code can detect only atoms, and no bonds. So we just select the atoms, and later figure out what bond the user meant.
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This sounds like something that should be added to the OpenGL selection code, at least for the erase tool. Granted, you're correct that this works, but it seems more intuitive to click on the middle of a bond to see it disappear.
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Currently the file import doesn't attempt to determine double bonds, etc. This would be useful.
Beyond that, the same code might be useful for "retyping" after a QM calculation or in a trajectory--recognizing aromatics, etc.
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I'm currently working for some improvements for molecular mechanics force field and it's parameters. So, I expect that some improvements could appear there during 2002.
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I actually have code to do this--calculate the symmetry of any given set of coords. Need to import and "tie in."
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This might be an addition to oelib/openbabel as well...
Michael
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Yes, it's certainly a nice idea to add it to the base OpenBabel library. However, the code is not strictly under the GPL--but the author gave me an OK to include it in Ghemical.
I'm not sure how he would feel about including it in a library where the source is more exposed. But I'll contact him about it. Obviously it would be nice to put in symmetry elements for filetypes that support it.
-Geoff
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Spartan calculates the volume and surface area of a model--this would be very useful for comparing solvent properties, crystal packing, etc.
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The file format currently supports having multiple coordinate sets in the same project. Ideally, the interface should support this as well--it might make copy/paste and other features easier.
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