Hi,
I have now reread all of the posts relating to the data model redesign and have updated the planning document. I have cut and paste the current version to the end of this email. If you notice any omissions or errors, please say.
Thanks,
Edward
P.S. Here is the entire text of the planning document:
###################################################### # The relax data model redesign -- planning document # ######################################################
# The proposal. ###############
The proposal was split into multiple posts to relax-devel. The posts are:
* The parent message 'Redesign of the relax data model: A HOWTO for breaking relax'. Located at https://mail.gna.org/public/relax-devel/2006-10/msg00053.html (Message-id: <1160550133.9523.54.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 1 'Redesign of the relax data model: 1. Why change?'. Located at https://mail.gna.org/public/relax-devel/2006-10/msg00054.html (Message-id: <1160551172.9523.60.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 2 'Subject: Redesign of the relax data model: 2. A new run concept'. Located at https://mail.gna.org/public/relax-devel/2006-10/msg00056.html (Message-id: <1160555137.9523.70.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 3 'Redesign of the relax data model: 3. Molecules, residues, and spins'. Located at https://mail.gna.org/public/relax-devel/2006-10/msg00057.html (Message-id: <1160557041.9523.74.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 4 'Redesign of the relax data model: 4. Conclusion'. Located at https://mail.gna.org/public/relax-devel/2006-10/msg00058.html (Message-id: <1160557876.9523.79.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
# Preparation. ##############
1 [Done]. Firstly release relax version 1.3.0 prior to any changes (to allow a functional version which handles RNA better, has the tensor PDB representation code, etc).
2. Redesign 'self.relax.data'.
3. Create the data pipe looping function for the 'pipes' argument (Chris MacRaild, https://mail.gna.org/public/relax-devel/2006-10/msg00060.html, Message-id: <1160562239.14487.98.camel@mrspell>). The user functions could be implemented as functors (Chris MacRaild, https://mail.gna.org/public/relax-devel/2007-01/msg00020.html, Message-ID: <1168432131.7569.338.camel@mrspell>). The design will need to take into account the user function docstrings, relax help system, and the relax manual docstring fetching code.
4. Create the spin_loop function (Edward d'Auvergne, https://mail.gna.org/public/relax-devel/2006-10/msg00057.html, Message-id: <1160557041.9523.74.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>). Use a generator function, using the yield statement, to return the spin data containers which are essentially pointers to the data (Gary Thompson, https://mail.gna.org/public/relax-devel/2007-01/msg00014.html, Message-id: <f001463a0701071417w6bd7927cp8fdd052e698575ec@xxxxxxxxxxxxxx>). The implementation was essentially given by Chris MacRaild at https://mail.gna.org/public/relax-devel/2007-01/msg00036.html (Message-ID: <1168883717.7569.511.camel@mrspell>).
5. Implement a parser for the following molecule/residue/spin selection syntax (Gary Thompson, https://mail.gna.org/public/relax-devel/2007-01/msg00014.html, Message-id: <f001463a0701071417w6bd7927cp8fdd052e698575ec@xxxxxxxxxxxxxx>): #<molecule number> | <molecule_name>:<residue_selection>[,<residue_selection>...]@<atom_selection> [,<atom_selection>] residue_selection=<residue_number> | <residue_range> | <residue_type> residue_selection=<residue_number>-<residue_number> atom_selection=<string_and_wildcards> This syntax will need to be properly referenced (in addition to being fully described) in the user function docstrings. I.e. the reference for Molmol syntax, the reference for UCSF syntax, etc. We need to find the source and name of the syntax.
6. Convert the methods of the class 'Selection' from the file 'generic_fns/selection.py' into methods and then add the following functions (Chris MacRaild at https://mail.gna.org/public/relax-devel/2007-01/msg00036.html Message-ID: <1168883717.7569.511.camel@mrspell>; Edward d'Auvergne, https://mail.gna.org/public/relax-devel/2007-01/msg00041.html, Message-ID: <7f080ed10701190408i8a5dee3y8ccbe1aba11bcba@xxxxxxxxxxxxxx>): parse_token() tokenise()
7. Create the spin_command function (Chris MacRaild, https://mail.gna.org/public/relax-devel/2007-01/msg00036.html, Message-ID: <1168883717.7569.511.camel@mrspell>).
8. Rename 'prompt/run.py' to 'prompt/pipe.py'. Rename 'generic_fns/runs.py' to 'generic_fns/pipes.py'.
9. Create the new pipe user functions (from the old run user functions): pipe.copy() # Create a new pipe with the current contents of another pipe. pipe.create() # Create a new pipe. Switch to this pipe by default. pipe.current() # Print the current pipe name. pipe.delete() # Delete the pipe. pipe.delete_all() # Delete all pipes. Essentially deleting 'self.relax.data'. pipe.hybridise() # Fuse two pipes into the current pipe. Overlapping data in the two pipes must be identical! pipe.list() # Print the details of all pipes. pipe.switch() # Switch to a different pipe.
10. Create the 'molecule' user function class: molecule.add()