Entity Example using Draft Macromolecular DDL (V 1.2.10)

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#
#  
# This example uses version 1.2.10 of the proposed mmDDL.  This version 
# reflects changes that were made during the CIF Workshop in Brussels.    
#
#  This example is being placed on the DDL mailing list for the purposes of 
#                      review and discussion only.  
#

data_example

loop_
    _VirtualCategoryName
    _VirtualCategoryDescription
    _VirtualCategoryParent
     'Structure'   
     'Top level virtual category for molecular structure' 
     'Structure'


#
# ---------------------------------------------------------------------
#        Dictionary specification example for relation = "Entity"
#
save_Entity
   _CategoryKey.keyName                      'id'
   _Category.mandatory                       'yes'
   _VirtualCategoryList.virtualCategoryName  'Structure'
   _Category.description    
;
     Data items in the Entity category record details (such as
     chemical composition, name, and source) about the molecular 
     entities that are present in the crystallographic structure.
                           ....
;
#               ----------------------------------------------
   loop_
       _CategoryExamples.example
       _CategoryExamples.detail
;
    loop_
    _Entity.id
    _Entity.type
    _Entity.nameCommon
    _Entity.nameSystematic
    _Entity.source
    _Entity.details
      1  polymer      'HIV-1 protease' ECx.x.x.x
    ;                  Clone obtained from HIV strain NY-5.
                       Expressed in E. coli.
    ;
    ;                  The enzymatically competent form of HIV protease is a
                       dimer.  This entity corresponds to one monomer of an
                       active dimer.
    ;
      2  non-polymer  'acetyl-pepstatin'
                      'acetyl-Ile-Val-Asp-Sta-Ala-Ile-Sta'
                      'Natural product isolated from actinomycetes'
    ;                  Statine: ((4S,3S)-4-amino-3-hydroxy-6-methylheptanoic
                       acid. Acetyl-pepstatin was isolated by Dr. K. Oda, Osaka
                       Prefecture University, and provided to us by Dr. Ben
                       Dunn, University of Florida, and Dr. J. Kay, University
                       of Wales.
    ;
      3  water         'water'  .  .  .
;
;
    Example 1 - based on PDB entry 5HVP and/or laboratory records for the
                structure corresponding to PDB entry 5HVP
;
#
#
       
save_Entity.details
   _DataType.type                      'text'
   _Schema.mandatory                   'no'
   _Definition.definition   
;         
    A description of special aspects of the entity.     
;

save_Entity.id
   loop_
       _Schema.categoryName     
       _Schema.itemName         
       _Schema.mandatory        
       _Schema.parentCategory
       _Schema.parentItem
                 'Entity'  'id'       'yes'  'Entity' 'id'     
               'AtomSite'  'entityId' 'yes'  'Entity' 'id'     
         'EntityKeywords'  'entityId' 'yes'  'Entity' 'id'     
             'EntityNpol'  'entityId' 'yes'  'Entity' 'id'     
             'EntityPoly'  'entityId' 'yes'  'Entity' 'id'     
        'EntityReference'  'entityId' 'yes'  'Entity' 'id'     
             'StructAsym'  'entityId' 'yes'  'Entity' 'id'     
         'EntityNpolAtom'  'EntityId' 'yes'  'EntityNpol'      'entityId'
        'EntityNpolAngle'  'EntityId' 'yes'  'EntityNpolAtom'  'entityId'
         'EntityNpolBond'  'EntityId' 'yes'  'EntityNpolAtom'  'entityId'
         'EntityNpolChir'  'EntityId' 'yes'  'Entity'  'id'
        'EntityNpolPlane'  'EntityId' 'yes'  'Entity'  'id'
          'EntityNpolTor'  'EntityId' 'yes'  'Entity'  'id'
          'EntityPolySeq'  'EntityId' 'yes'  'EntityPoly' 'EntityId'
#
   _DataType.type                              'char'     
   _Definition.definition   
;
    The value of _Entity.id must uniquely identify a record in the
    Entity list.  Note that this item need not be a number;  it can 
    be any unique identifier.
;   

save_Entity.nameCommon
   _Schema.mandatory                   'no'
   _DataType.type                           'char'
   _Definition.definition   
;
    The common name for the entity.
;
   loop_
       _Examples.example
        'glucose'
        'hexokinase'
        '2-fluoro-1,4-dichloro benzene'

#
#

save_Entity.nameSystematic
   _Schema.mandatory                   'no'
   _DataType.type                           'char'
   _Definition.definition   
;
       The systematic name for the entity. .....

;
   loop_
       _Examples.example
        'x,x,pyranoside'
        'EC 2.1.1.1'
        '2-fluoro-1,4-dichloro benzene'

save_Entity.nameSystematicSystem
   _Schema.mandatory                    'no'
   _DataType.type                            'char'
   _Definition.definition   
;              
    The system used to generate the systematic name of the entity.
;
   loop_
       _Examples.example
        'chemical abstracts conventions'
        'enzyme convention'
        'Sigma catalog'

save_Entity.source
   _Schema.mandatory                   'no'
   _DataType.type                           'text'
   _Definition.definition   
;              The source from which the entity was obtained.
;
   loop_
       _Examples.example
        'beef liver'
        'dogfish muscle'
        'expressed in e. coli'
        'expressed in CHO cells'
        'c. atrox salivary gland'

save_Entity.type
   _Schema.mandatory                   'no'
   _DataType.type                           'char'
   _Definition.definition   
;
    Defines the type of the entity.

    Polymer entities will be expected to have corresponding
    EntityPoly and associated entries.

    Non-polymer entities will be expected to have corresponding
    EntityNpol and associated entries.

    Water entities are not expected to have corresponding
    entries in the Entity category.
;
    loop_
	_Enumeration.enumeration
        _Enumeration.detail      
         'polymer'       'entity is a polymer'
         'non-polymer'   'entity is not a polymer'
         'water'         'water in the solvent model'


#  ------------------  End of Example   -----------------------------




****************************************************************************
*  John Westbrook                       Ph:  (908) 445-5156                *
*  Department of Chemistry              Fax: (908) 445-5958                *
*  Rutgers University                                                      *
*  PO Box 939                        e-mail: jwest@rutchem.rutgers.edu     *
*  Piscataway, NJ 08855-0939                                               *
****************************************************************************

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