-
Notifications
You must be signed in to change notification settings - Fork 3
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
add structure.id #6
add structure.id #6
Conversation
An example. I need to make up others with separate cell measurement conditions, and magnetic and modulated structures. Please note that (AFAIK) you don't need to explicitly give This links in with my idea (which I can't find the comment for) where single
As per PR (AFAIK)
|
That example does demonstrate exactly how I imagine this working. |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
As mentioned in a comment to #3, _cell.diffrn_id
and _cell_measurement.diffrn_id
should stay but are no longer key data names.
I suggest that we include the example given in (#6 (comment)) as distinct CIF files in the PR. This will definitely be useful, since people are already asking for usage examples. Furthermore, I have a comment on the following statement given in the example :
I think that having the same setting if not sufficient. For space groups to have the same identifier, their symmetry operations in the Consider the following example:
Semantically, the two space groups are identical (same name, same number, same setting, same symmetry operations), but due to the different ids assigned to the symops, they have to retain distinct ids. Furthermore, I do not think that we can achieve a more elegant solution in the constraints of the relational model since items like |
That sounds doable. A space group is the same iff it has the same name, number, setting, and symops in the same order. I can add this to the category description. I am also put together some example structures and multi block cifs. I agree that This also brings up the point as to the correct key for |
They already exist in core. The multiblock just alters the key dataname. I take this to mean that they remain in the dictionary, so no need to redefine them? |
Add detail on what gives you the ability to give two space groups that same ID value.
I'm not very good at naming. They can be easily changed.
I think that they should be moved to the multiblock dictionary, after which they will be removed from the core dictionary. This is because these data names have no use in the single-data-block paradigm (you can't refer to a |
Note that this is (mostly) just a particular case of the general rule that "if you repeat key data name values in different blocks, the rest of the values in the row must be identical". I don't think it warrants special mention in the category definition, but is worth pointing out to programmers as it is a useful consistency check. And I'd say that a space group is the same if the items in the |
I haven't put it in the category description; it's in the
I agree that changing the order of the symops doesn't change the symmetry, but it does change how the symmetry is represented. As @vaitkus pointed out, having different |
An analysis of implications of the new
A number of additional categories are defined that provide more modulation information. None of these have been made formal children of the above categories (yet) and so can be ignored - it is up to the ms_dic people to decide if they want to do more. The Conclusion: 'Structure' as we have defined it (
Here we come to an important point: we can imagine a The magnetism dictionary also has the idea of a parent space group, which is a non-magnetic structure that the magnetic structure is related to. This is a good use for a pointer to Conclusion : the structure category is a slight misnomer in the case of magnetism, but does not create practical problems. If we want to be more universal in our naming, we could change the name to something like |
I think this PR is ready for incorporation into the multi block dictionary following the above suggested changes and perhaps a change of the category from |
Specifically, _cell.structure_id and _cell_measurement.structure_id. Removed _cell.diffrn_id
Add missing terminal semicolon.
Co-authored-by: Antanas Vaitkus <antanas.vaitkus90@gmail.com>
Co-authored-by: Antanas Vaitkus <antanas.vaitkus90@gmail.com>
Finally merged. The examples may need improvement. |
Will close #3
I redid the PR, as I wanted to work through things in my head.
There are now:
STRUCTURE
id
space_group_id
diffrn_id
ATOM_SITE
,ATOM_SITE_ANISO
,CELL
,CELL_MEASUREMENT
, andCELL_MEASUREMENT_REFLN
structure_id
SPACE_GROUP
id
SPACE_GROUP_GENERATOR
,SPACE_GROUP_SYMOP
, andSPACE_GROUP_WYCKOFF
space_group_id
cell.diffrn_id
andcell_measurement.diffrn_id
have been removed.Modulated and magnetic structures need to be looked at.