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mmcif_ddl_v2.4.1.dic
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mmcif_ddl_v2.4.1.dic
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data_mmcif_ddl.dic
_datablock.id mmcif_ddl.dic
_datablock.description
;
This data block holds the core DDL.
;
#
_dictionary.datablock_id mmcif_ddl.dic
_dictionary.title mmcif_ddl.dic
_dictionary.version 2.4.1
#
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.1 1994-07-25
;
DDL 1.1 from Syd Hall et. al.
;
1.2.1 1994-09-18
;
Changes:.........etc. etc. John Westbrook
;
1.2.9 1994-10-05
;
Reflect the results of the Treaty of Brussels. JW.
;
2.0.1 1994-10-15
;
Adapted for closer mapping to DDL1.3 and clearer presentation. SRH/NS.
;
2.0.2 1994-10-16
;
Even closer................... SRH/NS.
;
2.0.3 1994-10-17
;
Coming to grips with the links and dependencies..... SRH/NS.
;
2.0.4 1994-10-20
;
Backed in changes from mm-ddl 1.2.12
Many other changes ... (JW)
;
2.0.5 1994-10-20
;
Some small adjustments..........SRH.
;
2.0.6 1994-10-20
;
More small adjustments..........JW.
;
2.0.7 1994-11-03
;
Changes: (JW)
+ Place all item and item_linked category definitions with the parent
item.
+ Fixed a number of not so trivial typos.
+ Corrected errors in the data type conversion table.
+ Corrected key item inconsistencies.
+ Added the item_aliases category.
;
2.0.8 1994-11-10
;
Miscellaneous corrections: (JW)
+ defined sub_category_group
+ corrected typo in category_examples.id definition
+ added _item_type_conditions.name in item category
+ added _item_structure.name in item category
+ corrected typo in item_aliases category definition
+ corrected typo in sub_category.method_id definition
;
2.0.9 1994-11-14
;
Changes: (JW)
+ added ITEM_UNITS, ITEM_UNITS_LIST, and UNITS_CONVERSION
categories.
+ added an additional primitive type for character type items
for which comparisons must be case insensitive.
Since it is customary to permit item names and category
identifiers to be specified in mixed case, it is necessary
to declare that case should NOT be considered in any
comparisons of these items.
;
2.0.10 1994-11-23
;
Changes: (JW)
+ Several name category changes for the sake of consistency:
enumeration -> item_enumeration
enumeration_default -> item_enumeration_default
enumeration_limit -> item_enumeration_limit
units_conversion -> item_units_conversion
+ Added _item_related.function_code alternate_exclusive
to identify mutually exclusive alternative declarations
of the same item.
+ Added structure options for real symmetric matrices.
+ Changed from zero based indices to one based indices
for compatibility with existing matrix component
definitions.
+ Add _item_linked.parent_name to the key of the item_linked
category.
+ Reorder items in the DDL so be alphabetical within
category groups.
;
2.0.11 1994-11-28
;
Changes: (JW)
+ Corrected spelling error for the data type code in
the DICTIONARY_HISTORY category.
+ Add category BLOCK to hold the data block name and data
block description. The block identifier was also added
to the key of the item category. The block identifier
can be implicitly derived from the STAR "data_" delimiter.
This identifier is required to form the key for categories
which are conceptually related to the data block as a
whole.
;
2.0.12 1994-11-30
;
Changes: (JW)
+ Added a data item _block.scope to indicate the scope of
data item names defined within included data blocks.
;
2.0.13 1994-12-12
;
Changes: (JW)
+ Deleted data item _block.scope.
+ Changed DICTIONARY category key to _dictionary.block_id
to guarantee only one dictionary definition per block.
+ Deleted data item _item.block_id as this will be replaced
by an item address syntax that will include block, save
frame, and url.
;
2.0.14 1994-12-15
;
Changes: (JW)
+ Made some terminology changes suggested by PMDF
_item_enumeration.code -> _item_enumeration.value
ITEM_ENUMERATION_DEFAULT -> ITEM_DEFAULT
ITEM_ENUMERATION_LIMIT -> ITEM_RANGE
+ Added item _item_type_list.detail
+ Version 2.0.14 is being frozen and exported.
;
2.0.15 1995-02-13
;
Changes: (JW)
+ Added '_' prefix to all data item save frame names.
References to data item names now always include
a leading underscore independent of the usage context.
+ A few miscellaneous corrections.
;
2.0.16 1995-06-18
;
Changes: (JW)
+ Revised the block level categories in the following ways:
Changed category BLOCK to DATA_BLOCK.
Added connection from _data_block.id to _category.implicit_key
in order to provide a formal means of merging the contents
of categories between data blocks.
+ Moved enumerations for _method_list.code and
method_list.language to examples.
+ Removed symmetric matrix options from the enumerations
for _item_structure.organization.
+ Added _item_related.function codes for 'associated_value',
'associated_esd', 'replaces' and 'replacedby'
+ Added data items _item_aliases.dictionary and
_item_aliases.dictionary_version.
+ Reorganized method categories such that multiple methods can
be applied at each level of data structure. Introduced a
consistent set of categories to hold method associations:
ITEM_METHODS, CATEGORY_METHODS, SUB_CATEGORY_METHODS, and
DATA_BLOCK_METHODS. Removed data items _category.method_id
_sub_category.method_id.
;
2.0.17 1995-06-22
;
Changes: (JW)
+ Quoted data values containing the leading string 'data_'.
;
2.1.0 1995-07-20
;
Changes: (JW)
Final adjustments before the first release of the mmCIF dictionary:
+ changed data_block to datablock to avoid any problems with
the STAR data_ reserved token.
+ created new category to hold item subcategory associations
and deleted the subcategory attribute from ITEM category.
+ modified regular expressions to reflect limitations observed
on several platforms.
+ expanded the enumeration of _item_related.function_code.
+ removed default value from _item.mandatory_code.
+ removed type construct for date and changed date data type
to yyyy-mm-dd
+ added less restrictive data type for alias names.
;
2.1.1 1995-09-26
;
Changes: (JW)
+ Changed regular expressions for type code to permit
single quote.
+ Corrected regular expression syntax for type name and
type date.
+ Corrected lower bound description for item_range.minimum.
The incorrect <= condition is changed to <.
+ _item_mandatory.code has been now a mandatory item.
+ _item_aliases.dictionary and _item_aliases.dictionary_version
are added to the composite key for category ITEM_ALIASES.
+ _datablock.id data type changes to type code.
+ Shortened the name _item_aliases.dictionary_version to
_item_aliases.version
;
2.1.2 1997-01-24
;
Changes: (JW)
+ Added associated_error to the enumeration list of
_item_related.function_code.
;
2.1.3 2000-10-16
;
Changes: (JW)
+ Changed data type for regular expression in
_item_type_list.construct to type text.
;
2.1.5 2003-06-23
; Changes: (JW)
+ NDB extensions adopted into ddl_core
+ New partitioning scheme implemented
;
2.1.6 2004-04-15
; Changes: (JW)
+ Name changed to mmcif_ddl.dic
;
2.1.7 2007-05-30
; Changes: (JW)
_items_examples.case, _item_range.minimum/maximum made mandatory.
;
2.1.8 2008-10-31
; Changes: (JW)
+ Add categories pdbx_item_link_group and pdbx_item_link_group_list
;
2.1.9 2009-01-15
; Changes: (JW)
+ _ndb_item_examples.detail made optional
;
2.1.10 2009-01-19
; Changes: (JW)
+ Add _item.mandatory_code enumeration implicit-ordinal to provide
an automatically generated ordinal index data item. This feature
is added to address problems where the natural category key may
contain an undefined value (e.g. '.').
;
2.1.11 2009-11-02
; Changes: (JW)
+ Add categories pdbx_item_context and pdbx_category_context
;
2.1.12 2012-09-01
; Changes: (JW) -
+ Add categories ndb_item_range, ndb_item and ndb_item_type
+ Add alternate categories under PDBx prefix:
pdbx_item_range,pdbx_item_type,pdbx_item,pdbx_category_description,
pdbx_category_examples,pdbx_item_description,pdbx_item_enumeration,
and pdbx_item_examples.
;
2.1.13 2013-09-23
; Changes: (JW) -
+ Add _category.NX_mapping_details for Nexus correspondences.
;
2.1.14 2013-10-14
; Changes: (JW) -
+ Add category pdbx_item_enumeration_details describing additional controls
for enumerated data items at deposition.
;
2.1.15 2014-03-10
; Changes: (JW) -
+ Add enumerations for pdbx_item_enumeration_details.closed_flag
;
2.1.16 2017-08-17
; Changes: (JW) -
+ Add extension categories pdbx_include_dictionary, pdbx_include_category,
pdbx_include_item, pdbx_dictionary_component and pdbx_dictionary_component_history,
pdbx_item_linked, pdbx_item_value_condition, and pdbx_item_value_condition_list.
;
2.1.17 2019-04-04
; Changes: (JW)
+ Add extension item _item_sub_category.pdbx_label
;
2.2.1 2019-06-05
; Changes (JW):
+ Add items _method_list.method_source and _method_list.implementation_source
+ Make item _method_list.inline optional
+ Update examples for items in category method_list
;
2.2.2 2020-06-05
; Changes (JW):
+ Add items _item_enumeration.rcsb_detail_brief and _item_enumeration.rcsb_type_units_code
;
2.3.0 2021-04-07
; Changes (JW):
+ Add generator for pdbx_dictionary_include/pdbx_category_include/pdbx_item_include
+ Miscellaneous updates in item/category descriptions
+ Add DATA or DEFINITION contexts to all DDL categories.
;
2.3.1 2021-05-29
; Changes (JW):
+ Updated mmcif_ddl-ext-pdbx.dic extension including new items _pdbx_item_enumeration.value_display
and _item_enumeration.pdbx_value_display
;
2.3.2 2021-06-02
; Changes (JW):
+ Updated mmcif_ddl-ext-pdbx.dic extension including new categories pdbx_item_set and pdbx_item_set_type_list
;
2.4.0 2021-08-02
; Merge the previous changes: (Masashi Yokochi, BMRBj) -
+ Rename _pdbx_item_enumeration_details.item_name to _pdbx_item_enumeration_details.name (V5).
+ Add _pdbx_item_external_ref category by mixing _item_alias and _item_linked propeties
for description of data item relationship across separated dictionaries, whereas parent
data item is located in external dictionary defined.
+ Add _pdbx_item_aliases category for description of data item relationship between item on
mmCIF dictionary and information items on associated XML Schema. For the purpose, data type,
aliasnode, is also defined that allows to specify information node on XML document using
expression of W3C XML Path Language (XPath) Version 1.0.
- Remove save__pdbx_item_enumeration_details.flag
+ Relax construct for aliasnode
;
2.4.1 2021-08-03
; Changes (MY):
- Remove pdbx_dictionary_component and pdbx_dictionary_component_history categories
;
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.detail
_item_type_list.construct
code char "A single word" '[^\t\n "]*'
char char "A single line of text" "[^\n]*"
text char "Text which may span lines" .*
int numb "Unsigned integer data" "[0-9]+"
name uchar "A data item name (restrictive type)" "_[_A-Za-z0-9]+[.][][_A-Za-z0-9\<\>%/-]+"
aliasname uchar "A DDL 1.4 data item name (less restrictive type)" '_[^\t\n "]+'
idname uchar "A data item name component or identifier" "[_A-Za-z0-9]+"
any char "Any data type" .*
yyyy-mm-dd char "A date format" "[0-9][0-9][0-9][0-9]-[0-9]?[0-9]-[0-9][0-9]"
url char "Universal resource locator (URL) pattern"
;(?i)\b((?:[a-z][\w-]+:(?:/{1,3}|[a-z0-9%])|www\d{0,3}[.]|[a-z0-9.\-]+[.][a-z]{2,4}/)(?:[^\s()<>]+|\(([^\s()<>]+|(\([^\s()<>]+\)))*\))+(?:\(([^\s()<>]+|(\([^\s()<>]+\)))*\)|[^\s`!()\[\]{};:'".,<>?«»“”‘’]))
;
aliasnode char 'XPath 1.0 expression for node selection ignoring namespace' '(\/[^\t\n]+)+'
#
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
ddl_group .
;
Component categories of the macromolecular DDL
;
datablock_group ddl_group
;
Categories that describe the characteristics of data blocks.
;
category_group ddl_group
;
Categories that describe the characteristics of categories.
;
sub_category_group ddl_group
;
Categories that describe the characteristics of subcategories.
;
item_group ddl_group
;
Categories that describe the characteristics of data items.
;
dictionary_group ddl_group
;
Categories that describe the dictionary.
;
compliance_group ddl_group
;
Categories that are retained specifically for compliance with
older versions of the DDL.
;
extension_group ddl_group
;
Categories that contain extensions used by the NDB and wwPDB.
;
#
save_datablock
_category.description
;
Attributes defining the characteristics of a data block.
;
_category.id datablock
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
_category_key.id datablock
_category_key.name "_datablock.id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group datablock
datablock_group datablock
#
_pdbx_category_context.category_id datablock
_pdbx_category_context.type DATA
#
save_
#
save__datablock.id
_item_description.name "_datablock.id"
_item_description.description
;
The identity of the data block.
;
#
_item.name "_datablock.id"
_item.category_id datablock
_item.mandatory_code implicit
#
_item_type.name "_datablock.id"
_item_type.code code
#
loop_
_item_linked.parent_name
_item_linked.child_name
"_datablock.id" "_datablock_methods.datablock_id"
"_datablock.id" "_dictionary.datablock_id"
"_datablock.id" "_category.implicit_key"
#
save_
#
save__datablock.description
_item_description.name "_datablock.description"
_item_description.description
;
Text description of the data block.
;
#
_item.name "_datablock.description"
_item.category_id datablock
_item.mandatory_code yes
#
_item_type.name "_datablock.description"
_item_type.code text
#
save_
#
save_datablock_methods
_category.description
;
Attributes specifying the association between data blocks and methods.
;
_category.id datablock_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
loop_
_category_key.id
_category_key.name
datablock_methods "_datablock_methods.method_id"
datablock_methods "_datablock_methods.datablock_id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group datablock_methods
datablock_group datablock_methods
#
_pdbx_category_context.category_id datablock_methods
_pdbx_category_context.type DATA
#
save_
#
save__datablock_methods.datablock_id
_item_description.name "_datablock_methods.datablock_id"
_item_description.description
;
Identifier of data block.
;
#
_item.name "_datablock_methods.datablock_id"
_item.category_id datablock_methods
_item.mandatory_code implicit
#
_item_type.name "_datablock_methods.datablock_id"
_item_type.code code
#
save_
#
save__datablock_methods.method_id
_item_description.name "_datablock_methods.method_id"
_item_description.description
;
Unique method identifier associated with a data block.
;
#
_item.name "_datablock_methods.method_id"
_item.category_id datablock_methods
_item.mandatory_code yes
#
_item_type.name "_datablock_methods.method_id"
_item_type.code idname
#
save_
#
save_category
_category.description
;
Attributes defining the functionality for the entire category.
;
_category.id category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
_category_key.id category
_category_key.name "_category.id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group category
category_group category
#
_pdbx_category_context.category_id category
_pdbx_category_context.type DEFINITION
#
save_
#
save__category.id
_item_description.name "_category.id"
_item_description.description
;
The identity of the data category. Data items may only be looped
with items of the same category.
;
#
_item.name "_category.id"
_item.category_id category
_item.mandatory_code yes
#
_item_type.name "_category.id"
_item_type.code idname
#
loop_
_item_linked.child_name
_item_linked.parent_name
"_category_examples.id" "_category.id"
"_category_group.category_id" "_category.id"
"_category_key.id" "_category.id"
"_category_methods.category_id" "_category.id"
"_item.category_id" "_category.id"
#
save_
#
save__category.description
_item_description.name "_category.description"
_item_description.description
;
Text description of a category.
;
#
_item.name "_category.description"
_item.category_id category
_item.mandatory_code yes
#
_item_type.name "_category.description"
_item_type.code text
#
save_
#
save__category.implicit_key
_item_description.name "_category.implicit_key"
_item_description.description
;
An identifier that may be used to distinguish the contents of
like categories between data blocks.
;
#
_item.name "_category.implicit_key"
_item.category_id category
_item.mandatory_code implicit
#
_item_type.name "_category.implicit_key"
_item_type.code code
#
save_
#
save__category.mandatory_code
_item_description.name "_category.mandatory_code"
_item_description.description
;
Whether the category must be specified in a dictionary.
;
#
_item.name "_category.mandatory_code"
_item.category_id category
_item.mandatory_code yes
#
_item_type.name "_category.mandatory_code"
_item_type.code code
#
save_
#
save_category_examples
_category.description
;
Example applications and descriptions of data items in this category.
;
_category.id category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
loop_
_category_key.id
_category_key.name
category_examples "_category_examples.id"
category_examples "_category_examples.case"
#
_pdbx_category_context.category_id category_examples
_pdbx_category_context.type DEFINITION
#
save_
#
save__category_examples.id
_item_description.name "_category_examples.id"
_item_description.description
;
The name of category.
;
#
_item.name "_category_examples.id"
_item.category_id category_examples
_item.mandatory_code implicit
#
_item_type.name "_category_examples.id"
_item_type.code idname
#
save_
#
save__category_examples.case
_item_description.name "_category_examples.case"
_item_description.description
;
A case of examples involving items in this category.
;
#
_item.name "_category_examples.case"
_item.category_id category_examples
_item.mandatory_code yes
#
_item_type.name "_category_examples.case"
_item_type.code text
#
save_
#
save__category_examples.detail
_item_description.name "_category_examples.detail"
_item_description.description
;
A description of an example _category_examples.case
;
#
_item.name "_category_examples.detail"
_item.category_id category_examples
_item.mandatory_code no
#
_item_type.name "_category_examples.detail"
_item_type.code text
#
save_
#
save_category_key
_category.description
;
This category holds a list of the item names that uniquely
identify the elements of the category.
;
_category.id category_key
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
loop_
_category_key.id
_category_key.name
category_key "_category_key.name"
category_key "_category_key.id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group category_key
category_group category_key
#
_pdbx_category_context.category_id category_key
_pdbx_category_context.type DEFINITION
#
save_
#
save__category_key.name
_item_description.name "_category_key.name"
_item_description.description
;
The name of a data item that serves as a key identifier for the
category (eg. a component of the primary key).
;
#
_item.name "_category_key.name"
_item.category_id category_key
_item.mandatory_code yes
#
_item_type.name "_category_key.name"
_item_type.code name
#
save_
#
save__category_key.id
_item_description.name "_category_key.id"
_item_description.description
;
The identifier of the category (eg. a component of the primary key).
;
#
_item.name "_category_key.id"
_item.category_id category_key
_item.mandatory_code implicit
#
_item_type.name "_category_key.id"
_item_type.code idname
#
save_
#
save_category_group
_category.description
;
Provides a list of category groups to which the base category
belongs.
;
_category.id category_group
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
loop_
_category_key.id
_category_key.name
category_group "_category_group.id"
category_group "_category_group.category_id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group category_group
category_group category_group
#
_pdbx_category_context.category_id category_group
_pdbx_category_context.type DEFINITION
#
save_
#
save__category_group.id
_item_description.name "_category_group.id"
_item_description.description
;
The name of a category group ...
;
#
_item.name "_category_group.id"
_item.category_id category_group
_item.mandatory_code yes
#
_item_type.name "_category_group.id"
_item_type.code idname
#
save_
#
save__category_group.category_id
_item_description.name "_category_group.category_id"
_item_description.description
;
The name of a category ...
;
#
_item.name "_category_group.category_id"
_item.category_id category_group
_item.mandatory_code implicit
#
_item_type.name "_category_group.category_id"
_item_type.code idname
#
save_
#
save_category_group_list
_category.description
;
This category provides the definition of each category group.
A category group is a collection of related categories.
;
_category.id category_group_list
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
_category_key.id category_group_list
_category_key.name "_category_group_list.id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group category_group_list
category_group category_group_list
#
_pdbx_category_context.category_id category_group_list
_pdbx_category_context.type DATA
#
save_
#
save__category_group_list.id
_item_description.name "_category_group_list.id"
_item_description.description
;
The name of a category group ...
;
#
_item.name "_category_group_list.id"
_item.category_id category_group_list
_item.mandatory_code yes
#
_item_type.name "_category_group_list.id"
_item_type.code idname
#
loop_
_item_linked.child_name
_item_linked.parent_name
"_category_group.id" "_category_group_list.id"
"_category_group_list.parent_id" "_category_group_list.id"
#
save_
#
save__category_group_list.description
_item_description.name "_category_group_list.description"
_item_description.description
;
Text description of a category group...
;
#
_item.name "_category_group_list.description"
_item.category_id category_group_list
_item.mandatory_code yes
#
_item_type.name "_category_group_list.description"
_item_type.code text
#
save_
#
save__category_group_list.parent_id
_item_description.name "_category_group_list.parent_id"
_item_description.description
;
The name of the optional parent category group.
;
#
_item.name "_category_group_list.parent_id"
_item.category_id category_group_list
_item.mandatory_code no
#
_item_type.name "_category_group_list.parent_id"
_item_type.code idname
#
save_
#
save_category_methods
_category.description
;
Attributes specifying the association between categories and methods.
;
_category.id category_methods
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
#
loop_
_category_key.id
_category_key.name
category_methods "_category_methods.method_id"
category_methods "_category_methods.category_id"
#
loop_
_category_group.id
_category_group.category_id
ddl_group category_methods
category_group category_methods
#
_pdbx_category_context.category_id category_methods
_pdbx_category_context.type DEFINITION
#
save_
#
save__category_methods.category_id
_item_description.name "_category_methods.category_id"
_item_description.description
;
The name of the category
;
#
_item.name "_category_methods.category_id"
_item.category_id category_methods
_item.mandatory_code implicit
#
_item_type.name "_category_methods.category_id"
_item_type.code idname
#
save_
#
save__category_methods.method_id
_item_description.name "_category_methods.method_id"
_item_description.description
;
The name of the method
;