[Cdk-devel] explicit valencies of atoms

[Egon W. <eg...@sc...>]

Hi all,

last week (upon request) I've added a Fragment class... where a fragment
constitutes a substructure with open valencies... i.e. it is part of something 
to which it is not yet bonded...

At this moment the class only defines the number of bonds it can still make,
but it does not say which Atoms provide the valencies...

There is this:

1. the atom has bonds with which it connects to other atoms
2. the Atom class has a field hydrogencount for implicitely? bonded hydrogen
3. there is a tools.SaturationChecker which can calculate the open valencies
    for a particular Atom given an AtomContainer

But it seems to me that this disregards the actual number of open valencies
of an atom... i.e. the hydrogencount field might not be set; the absence of 
hydrogen might not definately mean that there are open valencies...

Therefore, I would like to propose to add a field openValencies (with get/set
methods) that explicitely holds the number of open valencies for the atom...
SaturationChecker would then calculate the number of open valencies only
when this field is not set... (is a null value possible for int's?)

Egon