On 08/07/2013 03:54 PM, James Stroud wrote:
On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote:
On 08/07/2013 01:51 PM, James Stroud wrote:
In the long term, the MM structure community should perhaps get its inspiration
from SQL
For this to work, a particular interface must monopolize access to structural
data.
Not necessarily, although the alternative pathway might be more idealistic and
hence unrealistic.
All that needs to happen is that the community agree on
1. What is the finite set of essential/useful attributes of macromolecular
structural data.
2. What is the syntax of (a) accessing and (b) modifying those attributes.
3. What is the syntax of selecting subsets of structural data based on those
attributes.
The resulting syntax (i.e. language) itself should be terse, easy to learn,
easy to use, and preferably easy to implement.
If such a standard is created, then I believe awk-ing/grep-ing/sed-ing/etc PDBs
and mmCIFs would quickly become historical.
James
James,
frankly, I am not sure which part of your description is not equivalent
to "monopolistic interface".
If I understand your proposal and reference to SQL correctly, you want
some scripting language that sounds like simple English. Is the
advantage over existing APIs here that one does not need to learn
Python, C++, (or, heaven forbid, FORTRAN)? I.e. programs would look
like this
---
GRAB protein FROM FILE "best_model_ever.cif";
SELECT CHAIN A FROM protein AS chA;
SET chA BFACTORS TO 30.0;
GRAB data FROM FILE "best_data_ever.cif";
BIND protein TO data;
REFINE protein USING BUSTER WITH TLS+ANISO;
DROP protein INTO FILE "better_model_yet.cif";
---
Not necessarily a bad idea but now through the fog of time I remember
something oddly reminiscent... ah, CNS! (for those googling for it it's
not the "central nervous system" :).
Cheers,
Ed.
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
