Entity Example using Draft Macromolecular DDL (V 1.2.10)
John Westbrook (jwest@wormhole)
Sun, 16 Oct 94 16:52:12 -0400
#
#
# 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 *
****************************************************************************