On Tue, Apr 7, 2009 at 3:57 PM, Aidar Mahmutov <[email protected]> wrote: > Is it real to take Jmol as a basis for editor? Add, delete, create atoms. > Construct multiatomic structures, manipulate them. Fill some space > with same atoms... I'm interested mainly in crystallography. May be someone > can manage or help in this way. What is needed, time for > realising it?
Is a 3D editor realistic? Well, for example look at Avogadro (or pymol), which allow the user to add/remove atoms to a 3D structure. In general this is quite hard - but clearly it is possible. By analogy with the 2D molecular editor that we have been recently making for the CDK, a 3D editor would need to do some of the same things. Take adding an atom to a structure by clicking on an existing atom; the 3D editor would need to layout the new atom - place the the atom the right distance and at a default angle to the atom it is added to. A simpler way to do this with the CDK might be to run the whole structure through a 3D model builder for every change to the atoms and bonds. One tricky example would be deletion of a bond that connects two parts of a molecule, and the need to lay out the disconnected parts (ie: the new molecules). In fact, an approach that I would favour would be to use a 2D editor (such as the CDK's) and connecting this to a 3D viewer (such as Jmol). This would work for many cases, and may only really be problematic for truly three dimensional structures like complex fused ring systems. The idea of running the molecule through the 3D model builder for each change would work well with this MVC-like setup, I think. Of course, this all depends on what kind of crystallography you are talking about - if you mean small molecules, then fine; if you mean macromolecules, then I'm not so sure! Using a 2D editor on a protein would not work at all well... gilleain ------------------------------------------------------------------------------ This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
