I vote for 1 too, since we basically have it, except for optional dictionary.
On Fri, Aug 7, 2009 at 12:02 PM, Daniel Russel<> wrote:
> So where do we stand? The key question is what do we want AtomType to mean?
>
> A couple of options:
> 1)
> - we use PDB atom types for AtomType
> - AtomType is only guaranteed to be unique when paired with the ResidueType
> or XXXType of its parent (we need LigandType or something)
> - code that creates atoms must fill in element for all atoms it creates (so
> add another argument to the setup_particle function)
> - we could later add a function that generates a unique atom type by
> combining the parent type and the atomtype
> - we don't have to parse the whole dictionary unless we want to get other
> information about the ligands or to fix broken names
>
> 2)
> - we generate unique atom types by prefixing the pdb atom types with, for
> example, the residue name
> - AtomType is then globally unique
>
> I would vote for 1 but don't feel too strongly either way. We should
> probably get input from Hao too.
>
>
> On Aug 7, 2009, at 11:49 AM, Dina Schneidman wrote:
>
>> yes, that's of course the ultimate solution.
>> I wanted to do that, however changed my mind when I saw the size of
>> this dictionary.
>> It seems not reasonable to load it for each PDB parsing.
>> However I do think it will be nice to have it as optional.
>>
>> On Fri, Aug 7, 2009 at 11:47 AM, Ben Webb<> wrote:
>>>
>>> On 08/07/2009 11:42 AM, Dina Schneidman wrote:
>>>>
>>>> Do you mean to his dictionary of chemical components?
>>>> www.wwpdb.org/ccd.html
>>>
>>> Yes, that looks about right. Their Ligand Expo tool will even give you
>>> pretty pictures of a given residue.
>>>
>>> Ben
>>> --
>>> http://salilab.org/~ben/
>>> "It is a capital mistake to theorize before one has data."
>>> - Sir Arthur Conan Doyle
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