[Jmol-developers] atoms / models

[Miguel <mi...@jm...>]

Rene wrote:

> I had expected the implementation of a method in the Viewer that would
> allow one to get the array of atoms for a particular ModelIndex, as
> opposed to having to loop through all the atoms and determining whether=

> they are in the desired model to see whether or not they need to be
> ignored.

I am thinking of making a change to the implementation.

Atom Indexes are currently sequential within a model.

Therefore, the set of atoms in a model could be defined by a starting
index and an atom count.

(One of the main problems with this is that it would preclude/complicate
things if we wanted to add atoms to a model after it was created)

> If one were to write a multi-step xyz file for a subset of
> models in the input, one would have to loop through all atoms for every=

> model to be output in a step...

I agree that it is not pretty. But in reality the cost of this iteration
is insignificant.

> Then again, if one returns an array of references to the the low level
> atom class,

*please* do not do that.

I consolidated several packages into org.jmol.viewer so that the methods
would not be public. I did this to try to prevent people from looking
inside the data structures.

> one probably could modify them, which would cause problems
> since the viewer may not know about the modifications (i.e., one would
> really want a 'read-only' version of the AtomSet that is associated
> with a modelIndex...).

I know that the JmolViewer API needs more functionality in some areas. It=

also needs to have many entry points removed.

Even the Jmol application should be accessing everything through the api.=

That is how we will ensure that the API has adequate functionality.


Miguel