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