This post is proposal for the redesign the relax data model. This will
affect how data is input into the program, how data is selected, how
molecular structures are handled, how spin systems are handled, and how
many other parts of relax function. Importantly the internal structure
of 'self.relax.data' will completely change. These modifications will
essentially break every part of relax (the isolated code in the
directories 'minimise', 'maths_fns', and 'docs' will be safe from the
carnage, as will a few files in the base directory). If you have any
ideas for extending or improving the proposed data model, can see any
short-comings, deficiencies, or flaws, are familiar with the PDB
conventions, etc., your input is very much sought after. The changes
should occur in the 1.3 line of the repository. 1.2 versions will be
unaffected - scripts will remain compatible and the 1.2 line will
continue to be supported with bug fixes, etc.
I have to apologise in advance for the size of this proposal, to
simplify it I have divided the text into numbered sections. Once this
initial parent message has been sent I will respond to it with the text
of the 4 major sections. This will allow 4 major threads to branch off
from this message on the mailing list archive
(https://mail.gna.org/public/relax-devel). If you have an opinion,
idea, etc. about a specific section, could you please post a separate
message in response to the relevant major section post? Also if you
have unrelated ideas for one of these sections, could you post these as
separate messages as well? For example if you have separate points
about sections 3.1 and 3.5.1, two different posts responding to the
parent Section 3 post would be appreciated. Thanks. This will help to
focus each discussion point into specific threads.
Edward
Redesign of the relax data model
Index:
1. Why change?
1.1 The runs
1.2 The molecules
1.3 The residues
1.4 The spins
2. A new run concept
2.1 Parcelling up an abstract space
2.2 The run data model
2.3 The pipe concept
3. Molecules, residues, and spins
3.1 The spin data model
3.2 The data selection concept - identifying spin systems
3.2.1 Function arguments
3.2.2 NH data of a single protein macromolecule
3.2.3 A single organic molecule (non-polymeric)
3.2.4 A single RNA or DNA macromolecule
3.2.5 Complexes
3.3 Regular expression
3.4 The spin loop
3.5 Molecule, sequence, and spin user function classes
3.5.1 The 'molecule' user function class
3.5.2 The 'sequence' user function class
3.5.3 The 'spin' user function class
3.6 The input and output files
4. Conclusion
Redesign of the relax data model: A HOWTO for breaking relax.