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ddl2_with_methods.dic
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ddl2_with_methods.dic
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###########################################################################
#
# File: mmcif_ddl.dic
# Date: Mon Aug 9 02:48:08 EDT 2004
#
# Created from files in CVS module dict-mmcif_ddl.dic unless noted:
# mmcif_ddl-header.dic
# mmcif_ddl-data.dic
# mmcif_ddl-def-1.dic
# mmcif_ddl-def-2.dic
#
# Further hand-edited by JRH to include dREL methods for converting DDLm
# attributes and categories to DDL2 attributes
#
###########################################################################
###########################################################################
#
# File: mmcif_ddl-header.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Header Section
#
#
###########################################################################
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 2.1.6
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 ennumerations for _method_list.code and
method_list.language to examples.
+ Removed symmetric matrix options from the ennumerations
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 vaules 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 ennumeration of _item_related.function_code.
+ removed default value from _item.manadatory_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
;
### EOF mmcif_ddl-header.dic ####
###########################################################################
#
# File: mmcif_ddl-data.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Data Section
#
#
###########################################################################
# DATA TYPE CONVERSION TABLE
# --------------------------
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]'
#
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.
;
### EOF mmcif_ddl-data.dic
###########################################################################
#
# File: mmcif_ddl-def-1.dic
#
# mmCIF DDL Core Dictionary with NDB extensions
#
# This DDL dictionary is a mirror of ddl_core.dic-org with all implicit
# data items fully expanded and with NDB extensions added.
#
# Definition Section 1.
# (Core Definitions)
#
#
###########################################################################
# ----------------------------------------------------------------------------
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
_category_methods.method_id datablock
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
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
_category_methods.method_id category
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
_item_methods.method_id category.description
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_methods.method_id category.mandatory_code
_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'
_category_methods.method_id category_examples
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
_item_methods.method_id category_examples.detail
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
_category_methods.method_id category_key
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
_category_methods.method_id category_group
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
_category_methods.method_id category_group_list
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
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
;
_item.name '_category_methods.method_id'
_item.category_id category_methods
_item.mandatory_code yes
_item_type.name '_category_methods.method_id'
_item_type.code idname
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY
_category.description
;
The purpose of a sub-category is to define an association between
data items within a category and optionally provide a method to
validate the collection of items. The sub-category named
'cartesian' might be applied to the data items for the coordinates
x, y, and z.
;
_category.id sub_category
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
_category_key.id sub_category
_category_key.name '_sub_category.id'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category
'sub_category_group' sub_category
_category_methods.method_id sub_category
save_
save__sub_category.id
_item_description.name '_sub_category.id'
_item_description.description
;
The identity of the sub-category.
;
_item.name '_sub_category.id'
_item.category_id sub_category
_item.mandatory_code yes
_item_type.name '_sub_category.id'
_item_type.code idname
loop_
_item_linked.child_name
_item_linked.parent_name
'_sub_category_examples.id' '_sub_category.id'
'_sub_category_methods.sub_category_id' '_sub_category.id'
'_item_sub_category.id' '_sub_category.id'
save_
save__sub_category.description
_item_description.name '_sub_category.description'
_item_description.description
;
Description of the sub-category.
;
_item.name '_sub_category.description'
_item.category_id sub_category
_item.mandatory_code yes
_item_type.name '_sub_category.description'
_item_type.code text
save_
# ----------------------------------------------------------------------------
save_SUB_CATEGORY_EXAMPLES
_category.description
;
Example applications and descriptions of data items in this subcategory.
;
_category.id sub_category_examples
_category.mandatory_code no
_category.implicit_key mmcif_ddl.dic
loop_
_category_key.id
_category_key.name
sub_category_examples '_sub_category_examples.id'
sub_category_examples '_sub_category_examples.case'
loop_
_category_group.id
_category_group.category_id
'ddl_group' sub_category_examples
'sub_category_group' sub_category_examples
save_
save__sub_category_examples.id
_item_description.name '_sub_category_examples.id'
_item_description.description
;
The name for the subcategory.
;
_item.name '_sub_category_examples.id'
_item.category_id sub_category_examples
_item.mandatory_code yes
_item_type.name '_sub_category_examples.id'
_item_type.code idname