Text abuse....

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• Previous message: Paula Fitzgerald: "Re: mmCIF: A few little things, and one big problem."

Hi all.

A small point first: lines 13231 and 13232 are identical:

   '_phasing_MIR.entry_id'           '_entry.id'

Now, a lot of items have _item_type.code defined as char, when in fact,
they should clearly be text (the difference being that text can cover
several lines, where char is limited to one). This is of crucial
importance in the kind of thing which I am doing, where I have to provide
a Fortran interface to my library. Also, I hope at some point to do
automatic data validation using a regular expression package and the
contents of _item_type_list.construct provided in the dictionary - so the
dictionary has to be right! It is worth pointing out that a number of
these definitions are inconsistent with the examples, both those on the
server, and those within the dictionary itself. 

I have been through all the items defined as char in the dictionary (which
gives me a special relationship with it now, and a new perspective on
Paula's work!), and I've appended a list of items which I think should (x)
or may (?) be better defined as text. I haven't been through the Journal
category, although there are some items (e.g._journal.coeditor_address
which clearly should be text). 

Also, I have noticed that the char construct doesn't include the single
quote character. In the STAR syntax, quotes (both single and double) are 
ordinary characters under some circumstances, e.g. within a quoted string 
when not followed by a space, tab or newline. For example:

  'Peter's example'

is a valid single quoted text string in STAR, because the string is closed
by the trailing <quote><whitespace> digraph, not the second quote. If this
is not allowed by mmCIF, and single quotes are treated differently from
double quotes, this is a CIF restriction on STAR, and should be documented
somwhere, sometime. [This is not a DDL issue - these constructs are
defined differently in the DDL, where they are more consistent with STAR.]
Otherwise, single quotes should be allowed in char's, and CIF applications
should rely on STAR lexical analysis to find incorrect usage. 

Regards,
Peter.

========================================================================
Peter Keller.            \ 
Dept. of Biology and      \ "Not even the greatest nonsense is beyond
    Biochemistry,          \  the reach of human invention."
University of Bath,         \ 
Bath, BA2 7AY, UK.           \          --- Ryszard Kapuscinski
------------------------------\-----------------------------------------
Tel. (+44/0)1225 826826 x 4302 | Email: P.A.Keller@bath.ac.uk (Internet)
Fax. (+44/0)1225 826449        |   P.A.Keller%bath.ac.uk@UKACRL (BITNET)
========================================================================

? save__atom_site.constraints
x save__atom_site.details
x save__atom_site.restraints
x save__atom_sites.cartn_transform_axes
x save__atom_sites_footnote.text
? save__atom_type.description
x save__atom_type.scat_versus_stol_list
? save__audit.creation_method
? save__audit.update_record
x save__audit_author.address
x save__audit_contact_author.address
x save__cell.details
? save__chem_comp.model_details
x save__chem_comp.model_source
? save__chem_comp.mon_nstd_class
x save__chem_comp.mon_nstd_details
x save__chem_link.details
? save__chemical.compound_source
x save__chemical.name_systematic    (You'd better believe this one!)
? save__chemical_formula.analytical
? save__chemical_formula.moiety
? save__chemical_formula.structural
x save__citation.abstract
x save__citation.book_title
x save__citation.details
? save__citation.journal_full
x save__citation.title
? save__computing.cell_refinement
? save__computing.data_collection
? save__computing.data_reduction
? save__computing.molecular_graphics
? save__computing.publication_material
? save__computing.structure_refinement
? save__computing.structure_solution
x save__database_PDB_rev_record.details
? save__diffrn.crystal_treatment
x save__diffrn.details
x save__diffrn_measurement.details
x save__diffrn_measurement.device_details
? save__diffrn_measurement.method
x save__diffrn_orient_matrix.type
x save__diffrn_radiation.detector_details
? save__diffrn_radiation.monochromator
x save__diffrn_radiation.source_details
x save__diffrn_reflns.reduction_process
? save__entity_keywords.text
x save__entity_name_sys.name
x save__entity_poly.type_details
x save__entity_poly_seq_dif.details
x save__entity_reference.details
x save__entity_src_gen.gene_src_details
x save__entity_src_gen.host_org_details
x save__entity_src_gen.plasmid_details
x save__entity_src_nat.details
? save__exptl.absorpt_process_details
x save__exptl.details
x save__exptl_crystal.description
x save__exptl_crystal.preparation
x save__exptl_crystal_grow.details
? save__exptl_crystal_grow.method
? save__exptl_crystal_grow.method_ref
x save__exptl_crystal_grow.seeding
? save__exptl_crystal_grow.seeding_ref
x save__exptl_crystal_grow_comp.details
x save__geom.details
x save__phasing_averaging.details
x save__phasing_averaging.method
x save__phasing_isomorphous.details
x save__phasing_isomorphous.method
? save__phasing_isomorphous.parent
x save__phasing_mad.details
x save__phasing_mad.method
x save__phasing_mir.details
x save__phasing_mir.method
x save__phasing_mir_der.details
? save__phasing_mir_der.reflns_criteria
x save__phasing_mir_der_site.details
x save__publ.contact_author
x save__publ.contact_letter
? save__publ.manuscript_creation
x save__publ.manuscript_processed
x save__publ.manuscript_text
x save__publ.section_abstract
x save__publ.section_acknowledgements
x save__publ.section_comment
x save__publ.section_discussion
x save__publ.section_experimental
x save__publ.section_exptl_prep
x save__publ.section_exptl_refinement
x save__publ.section_figure_captions
x save__publ.section_introduction
x save__publ.section_references
x save__publ.section_table_legends
x save__publ.section_title
x save__publ_author.address
x save__publ_manuscript_incl.extra_info
x save__refine_hist.details
x save__refine.details
x save__refine.ls_abs_structure_details
x save__refine.ls_extinction_expression
x save__refine.ls_extinction_method
x save__refine.ls_weighting_details
x save__refine_b_iso.details
? save__refine_ls_restr.type
x save__refine_occupancy.details
x save__reflns.data_reduction_details
x save__reflns.data_reduction_method
x save__reflns.details
? save__reflns.observed_criterion
x save__reflns.R_free_details
x save__struct.title
x save__struct_asym.details
x save__struct_biol.details
x save__struct_biol_gen.details
x save__struct_biol_view.details
x save__struct_conf.details
? save__struct_conf_type.criteria
? save__struct_conf_type.reference
x save__struct_conn.details
x save__struct_conn_type.criteria
? save__struct_conn_type.reference
x save__struct_mon_details.RSCC
x save__struct_mon_details.RSR
x save__struct_ncs_dom.details
x save__struct_ncs_ens.details
x save__struct_ncs_ens_oper.details
x save__struct_sheet.details
x save__struct_site.details
x save__struct_site_gen.details
x save__struct_site_view.details

• Previous message: Paula Fitzgerald: "Re: mmCIF: A few little things, and one big problem."