PDBx/mmCIF
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Supporting Data mmcif_ddl.dic

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Dictionary Revision History

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Version Revision Date Revision Description
2.3.3 2021-08-31 Changes (EP):
+ Updated mmcif_ddl-ext-pdbx.dic extension including new categories
pdbx_category_conditional_context, pdbx_item_conditional_context
and pdbx_conditional_context_list		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.2.2 2020-06-05 Changes (JW):
+ Add items _item_enumeration.rcsb_detail_brief and _item_enumeration.rcsb_type_units_code		 mmcif_ddl.dic
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		 mmcif_ddl.dic
2.1.17 2019-04-04 Changes: (JW)
+ Add extension item _item_sub_category.pdbx_label		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.1.15 2014-03-10 Changes: (JW) -
+ Add enumerations for pdbx_item_enumeration_details.closed_flag		 mmcif_ddl.dic
2.1.14 2013-10-14 Changes: (JW) -
+ Add category pdbx_item_enumeration_details describing additional controls
for enumerated data items at deposition.		 mmcif_ddl.dic
2.1.13 2013-09-23 Changes: (JW) -
+ Add _category.NX_mapping_details for Nexus correspondences.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.1.11 2009-11-02 Changes: (JW)
+ Add categories pdbx_item_context and pdbx_category_context		 mmcif_ddl.dic
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. '.').		 mmcif_ddl.dic
2.1.9 2009-01-15 Changes: (JW)
+ _ndb_item_examples.detail made optional		 mmcif_ddl.dic
2.1.8 2008-10-31 Changes: (JW)
+ Add categories pdbx_item_link_group and pdbx_item_link_group_list		 mmcif_ddl.dic
2.1.7 2007-05-30 Changes: (JW)
_items_examples.case, _item_range.minimum/maximum made mandatory.		 mmcif_ddl.dic
2.1.6 2004-04-15 Changes: (JW)
+ Name changed to mmcif_ddl.dic		 mmcif_ddl.dic
2.1.5 2003-06-23 Changes: (JW)
+ NDB extensions adopted into ddl_core
+ New partitioning scheme implemented		 mmcif_ddl.dic
2.1.3 2000-10-16
Changes: (JW)
+ Changed data type for regular expression in
_item_type_list.construct to type text.		 mmcif_ddl.dic
2.1.2 1997-01-24
Changes: (JW)
+ Added associated_error to the enumeration list of
_item_related.function_code.		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.0.17 1995-06-22
Changes: (JW)
+ Quoted data values containing the leading string 'data_'.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.0.6 1994-10-20
More small adjustments..........JW.		 mmcif_ddl.dic
2.0.5 1994-10-20
Some small adjustments..........SRH.		 mmcif_ddl.dic
2.0.4 1994-10-20
Backed in changes from mm-ddl 1.2.12
Many other changes ... (JW)		 mmcif_ddl.dic
2.0.3 1994-10-17
Coming to grips with the links and dependencies..... SRH/NS.		 mmcif_ddl.dic
2.0.2 1994-10-16
Even closer................... SRH/NS.		 mmcif_ddl.dic
2.0.1 1994-10-15
Adapted for closer mapping to DDL1.3 and clearer presentation. SRH/NS.		 mmcif_ddl.dic
1.2.9 1994-10-05
Reflect the results of the Treaty of Brussels. JW.		 mmcif_ddl.dic
1.2.1 1994-09-18
Changes:.........etc. etc. John Westbrook		 mmcif_ddl.dic
1.1 1994-07-25
DDL 1.1 from Syd Hall et. al.		 mmcif_ddl.dic
2.3.3 2021-08-31 Changes (EP):
+ Updated mmcif_ddl-ext-pdbx.dic extension including new categories
pdbx_category_conditional_context, pdbx_item_conditional_context
and pdbx_conditional_context_list		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.2.2 2020-06-05 Changes (JW):
+ Add items _item_enumeration.rcsb_detail_brief and _item_enumeration.rcsb_type_units_code		 mmcif_ddl.dic
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		 mmcif_ddl.dic
2.1.17 2019-04-04 Changes: (JW)
+ Add extension item _item_sub_category.pdbx_label		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.1.15 2014-03-10 Changes: (JW) -
+ Add enumerations for pdbx_item_enumeration_details.closed_flag		 mmcif_ddl.dic
2.1.14 2013-10-14 Changes: (JW) -
+ Add category pdbx_item_enumeration_details describing additional controls
for enumerated data items at deposition.		 mmcif_ddl.dic
2.1.13 2013-09-23 Changes: (JW) -
+ Add _category.NX_mapping_details for Nexus correspondences.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.1.11 2009-11-02 Changes: (JW)
+ Add categories pdbx_item_context and pdbx_category_context		 mmcif_ddl.dic
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. '.').		 mmcif_ddl.dic
2.1.9 2009-01-15 Changes: (JW)
+ _ndb_item_examples.detail made optional		 mmcif_ddl.dic
2.1.8 2008-10-31 Changes: (JW)
+ Add categories pdbx_item_link_group and pdbx_item_link_group_list		 mmcif_ddl.dic
2.1.7 2007-05-30 Changes: (JW)
_items_examples.case, _item_range.minimum/maximum made mandatory.		 mmcif_ddl.dic
2.1.6 2004-04-15 Changes: (JW)
+ Name changed to mmcif_ddl.dic		 mmcif_ddl.dic
2.1.5 2003-06-23 Changes: (JW)
+ NDB extensions adopted into ddl_core
+ New partitioning scheme implemented		 mmcif_ddl.dic
2.1.3 2000-10-16
Changes: (JW)
+ Changed data type for regular expression in
_item_type_list.construct to type text.		 mmcif_ddl.dic
2.1.2 1997-01-24
Changes: (JW)
+ Added associated_error to the enumeration list of
_item_related.function_code.		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.0.17 1995-06-22
Changes: (JW)
+ Quoted data values containing the leading string 'data_'.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
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		 mmcif_ddl.dic
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.		 mmcif_ddl.dic
2.0.6 1994-10-20
More small adjustments..........JW.		 mmcif_ddl.dic
2.0.5 1994-10-20
Some small adjustments..........SRH.		 mmcif_ddl.dic
2.0.4 1994-10-20
Backed in changes from mm-ddl 1.2.12
Many other changes ... (JW)		 mmcif_ddl.dic
2.0.3 1994-10-17
Coming to grips with the links and dependencies..... SRH/NS.		 mmcif_ddl.dic
2.0.2 1994-10-16
Even closer................... SRH/NS.		 mmcif_ddl.dic
2.0.1 1994-10-15
Adapted for closer mapping to DDL1.3 and clearer presentation. SRH/NS.		 mmcif_ddl.dic
1.2.9 1994-10-05
Reflect the results of the Treaty of Brussels. JW.		 mmcif_ddl.dic
1.2.1 1994-09-18
Changes:.........etc. etc. John Westbrook		 mmcif_ddl.dic
1.1 1994-07-25
DDL 1.1 from Syd Hall et. al.		 mmcif_ddl.dic

Data Type List

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Data Type Code Primitive Type Code Regular Expression Description
aliasname uchar _[^\t\n "]+ A DDL 1.4 data item name (less restrictive type)
any char .* Any data type
char char [^\n]* A single line of text
code char [^\t\n "]* A single word
idname uchar [_A-Za-z0-9]+ A data item name component or identifier
int numb [0 -9]+ Unsigned integer data
name uchar _[_A-Za-z0-9]+[.][][_A-Za-z0-9\<\>%/-]+ A data item name (restrictive type)
text char .* Text which may span lines
url char (?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`!()\[\]{};:'".,<>?&#171;&#187;&#8220;&#8221;&#8216;&#8217;])) Universal resource locator (URL) pattern
yyyy-mm-dd char [0-9][0-9][0-9][0-9]-[0-9]?[0-9]-[0-9][0-9] A date format

SubCategory List

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SubCategory Identifier Description

Units List

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Units Identifier Description

Units Conversion List

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From Units&Identifier To Units&Identifier Operator Conversion Factor