I guess I should just read the code :)
Thanks!
On Fri, Aug 17, 2012 at 11:07 AM, Ben Webb <> wrote:
> On 8/15/12 11:57 AM, Dina Schneidman wrote:
>>
>> I want to add bonds, angles and dihedrals to my structure. It has some
>> missing atoms, but I don't want them there on purpose.
>> When I create the topology, those atoms are automatically added to the
>> structure.
>> Is there a way to tell it not to add any missing atoms?
>
>
> When in doubt, read the documentation. ;)
>
>> topology->setup_hierarchy(mhd_);
>
>
> This is for the common use case "tidy up the hierarchy so it matches the
> topology, by adding/removing atoms as necessary". If you don't want to do
> that, call the functions it calls yourself, leaving out add_missing_atoms().
>
> Ben
> --
> http://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> - Sir Arthur Conan Doyle
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