Search found 57 matches

by jcbollinger
Mon Feb 04, 2013 11:34 pm
Forum: CIF Application Programming Interface
Topic: Draft API specification
Replies: 7
Views: 7220

Re: Draft API specification

Though it may seem that I have been ignoring this area, I have in fact been working on a similar API definition as my time has permitted. To validate and flush out problems with the API, I have been working as well on an SQLite implementation. In retrospect, it would have been wiser to keep this gro...
by jcbollinger
Mon Feb 04, 2013 9:20 pm
Forum: CIF Application Programming Interface
Topic: CIF Data Model
Replies: 2
Views: 5268

Re: CIF Data Model

Inasmuch as the CIF specifications do not restrict values in the same column to be drawn from a common domain, and given that there seems no viable, general method for type coercion between table values and values any other CIF2 data type, I think we cannot justify incorporating domain restrictions ...
by jcbollinger
Tue Jan 29, 2013 4:26 pm
Forum: CIF dictionary namespace conventions
Topic: COMCIFS namespace and dictionary policy
Replies: 3
Views: 7016

Re: COMCIFS namespace and dictionary policy

To allow the above possibility, but reduce the amount of checking of the audit.domain tags in save frames, I suggest that the scope of the _audit.domain dataname (and indeed of any dataname) includes child frames *unless* it is overridden by that tag appearing in the child frame. The answer to your...
by jcbollinger
Tue Jan 15, 2013 6:35 pm
Forum: CIF dictionary namespace conventions
Topic: COMCIFS namespace and dictionary policy
Replies: 3
Views: 7016

Re: COMCIFS namespace and dictionary policy

Draft COMCIFS dataname and dictionary policy for bodies within the IUCr domain I think it would be better and clearer to delete "bodies within" from the policy title. COMCIFS must ensure the uniqueness of all extant datanames. The following policy is designed to maximise the chances that ...
by jcbollinger
Fri Jan 11, 2013 9:03 pm
Forum: CIF dictionary namespace conventions
Topic: The namespace problem and a possible solution
Replies: 8
Views: 8616

Re: The namespace problem and a possible solution

⋅ For the _audit.domain item to be of much use, its values need to be drawn from a list of standard alternatives. Domains could self-select, but if CIF were some day to spread to a large number of domains then the risk of domain collisions would be non-negligible. Thus, a complete solutio...
by jcbollinger
Thu Jan 03, 2013 3:55 pm
Forum: CIF dictionary namespace conventions
Topic: The namespace problem and a possible solution
Replies: 8
Views: 8616

Re: The namespace problem and a possible solution

Thanks, James, for the clarifications. If there are show-stoppers that I've missed, or there is a better alternative, please bring them forward. I will walk through some scenarios in a separate post. I don't see any show-stoppers, but I do see some issues that should be considered: ⋅ For t...
by jcbollinger
Wed Dec 12, 2012 2:08 pm
Forum: CIF Application Programming Interface
Topic: Survey of existing software
Replies: 12
Views: 13953

Re: Survey of existing software

The PDB have been interpreting CIF files as relational databases for well over 10 years so I can't take credit for the idea. If this is worth pursuing then we should start another thread, I think. Yes and no. As I understand it, PDB have been interpreting mmCIF files as relational databases, an act...
by jcbollinger
Tue Dec 11, 2012 6:10 pm
Forum: CIF Application Programming Interface
Topic: Level 1 CIF API compliance
Replies: 5
Views: 11965

Re: Level 1 CIF API compliance

After some thought and discussion with Nick Spadaccini, I think it might be better to pursue developing/adopting an official CIF library, and worry about compliance specifications later. I think it might be easier to develop enthusiasm for such a project, but without compliance specifications, what...
by jcbollinger
Tue Dec 11, 2012 5:42 pm
Forum: CIF Application Programming Interface
Topic: Survey of existing software
Replies: 12
Views: 13953

Re: Survey of existing software

I have finally returned to thinking about the CIFAPI, and would like to discuss the possibility that Richard Gildea's iotbx.cif work could form the basis of an API that we can go forward with. To summarise: cctbx contains an iotbx module which reads in CIF files. The parsing is done using C++ code ...
by jcbollinger
Tue Dec 11, 2012 3:55 pm
Forum: CIF dictionary namespace conventions
Topic: The namespace problem and a possible solution
Replies: 8
Views: 8616

Re: The namespace problem and a possible solution

What do you mean by "same simple name"? Option (1) results in datanames that are never identical, so even different namespaces will have different names. Option (2) provides a standard resolution mechanism for identical datanames and explicitly allows for mixing of datanames from various ...