[Molecularmechanics] Recycling CML

[Pengyu Ren]

I understand the atom can be refered to using a path.It is certainly possible for the individual program to parse the structure (have to be done anyway) and assign global ids. What is the "id" for atom in your generic tree? is it within the group (residure or chain)? 

I think the generic tree is a good choice since I think flexibility is critical. So the next question is how to specify connectivity/topology?   


Pengyu


======= 2003-11-06 04:24:12 original messages===

>
>--- Konrad Hinsen <hinsen@cnrs-orleans.fr> wrote:
>> 
>> > About the atom ID, can we assign a _global_ label to each atom
>> (smallest
>> > unit), like 1,2,3,4... for easy acess?
>> 
>> Only if we have an explicit element for each atom. And even then, as
>> Peter 
>> explained, this can cause headaches when trying to merge two files.
>> 
>> On the other hand, I am not sure that this is needed. For what
>> purpose would 
>> you want to be able to refer to one particular atom from an arbitrary
>> place 
>> in the file?
>
>Perhaps one could have some kind of optional, global atom-id, where the
> standard specifies that they may be lost when merging files.  On the
>other hand, is it useful.  It could always be added to the standard
>later, if needed.
>
>/Jakob
>
>
>
>=====
>Jakob Schiotz, CAMP and Dept. of Physics, Tech. Univ. of
>Denmark, DK-2800 Lyngby, Denmark.  This email address is
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