Bob wrote:
> > http://www.bmrb.wisc.edu/referenc/aa_chem.html
>
> Second reference on this page:
> http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl
> It seems to me that this is the sort of thing you are looking for?
> Holy cow! That's quite a list.
It certainly is! But it is too much data for me ... I don't understand it.
> Would you like, basically, to add a CIF or mmCIF column?
Well, that would help.
> Or isn't this the right list?
> (From which perhaps you could design an algorithm?)
Truth is, I don't want to design the algorithm ... I assume that someone
else has already done it.
The people at the PDB have converted everythign to CIF ... what algorithm
did they use?
>> see the files in the pdb ftp area under directory
>> data/monomers/
>> components.cif (PDB names)
>> components_iupac.cif (mmcif iupac names)
Boy, these files look awfully big and ugly to me.
> The above two look like a good bet. What exactly are you after, Miguel?
> What are the desired inputs and outputs?
Assuming that CIF follows the IUPAC standard, I want someone to give me
the implementation of:
String convertPdbNameToIupacName(String pdbAtomName) { ... }
The problem I am trying to solve is this: The RasMol/Chime expression
language is very specific to .pdb files. Jmol now does a pretty good job
of supporting .cif files. But the expression language does not work
because of the */' confusion. Therefore (in the best of all possible
worlds) I would like to have the Jmol internal representation be the IUPAC
standard. Then, I would convert the expression language into IUPAC and we
could do queries regardless of the source of the file.
Miguel
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