mmdb1.asn

ncbi源码

--
-- ===========================================================================
-- PRODUCTION $Log: mmdb1.asn,v $
-- PRODUCTION Revision 1000.0  2003/10/29 21:21:26  gouriano
-- PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R6.0
-- PRODUCTION
-- ===========================================================================
--

--$Revision: 1000.0 $
--**********************************************************************
--
--  Biological Macromolecule 3-D Structure Data Types for MMDB,
--                A Molecular Modeling Database
--
--  Definitions for a biomolecular assembly and the MMDB database
--
--  By Hitomi Ohkawa, Jim Ostell, Chris Hogue, and Steve Bryant 
--
--  National Center for Biotechnology Information
--  National Institutes of Health
--  Bethesda, MD 20894 USA
--
--  July 1995
--
--**********************************************************************

-- Contents of the MMDB database are currently based on files distributed by
-- the Protein Data Bank, PDB.  These data are changed in form, as described
-- in this specification. To some extent they are also changed in content, in 
-- that many data items implicit in PDB are made explicit, and others are
-- corrected or omitted as a consequence of validation checks.  The semantics
-- of MMDB data items are indicated by comments within the specification below.
-- These comments explain in detail the manner in which data items from  PDB 
-- have been mapped into MMDB. 

MMDB DEFINITIONS ::=

BEGIN

EXPORTS Biostruc, Biostruc-id, Biostruc-set, Biostruc-annot-set,
	Biostruc-residue-graph-set;

IMPORTS Biostruc-graph, Biomol-descr, Residue-graph FROM MMDB-Chemical-graph 
	Biostruc-model FROM MMDB-Structural-model
	Biostruc-feature-set FROM MMDB-Features
	Pub FROM NCBI-Pub
	Date, Object-id, Dbtag FROM NCBI-General;

-- A structure report or "biostruc" describes the components of a biomolecular 
-- assembly in terms of their names and descriptions, and a chemical graph 
-- giving atomic formula, connectivity and chirality. It also gives one or more
-- three-dimensional model structures, literally a mapping of the atoms, 
-- residues and/or molecules of each component into a measured three-
-- dimensional space. Structure may also be described by named features, which 
-- associate nodes in the chemical graph, or regions in space, with text or 
-- numeric descriptors.

-- Note that a biostruc may also contain cross references to other databases,
-- including citations to relevant scientific literature. These cross 
-- references use object types from other NCBI data specifications, which are 
-- "imported" into MMDB, and not repeated in this specification. 

Biostruc ::= SEQUENCE {
	id			SEQUENCE OF Biostruc-id,
	descr			SEQUENCE OF Biostruc-descr OPTIONAL,
	chemical-graph		Biostruc-graph,
	features		SEQUENCE OF Biostruc-feature-set OPTIONAL,
	model			SEQUENCE OF Biostruc-model OPTIONAL }

-- A Biostruc-id is a collection identifiers for the molecular assembly.
-- Mmdb-id's are NCBI-assigned, and are intended to be unique and stable 
-- identifiers.  Other-id's are synonyms.

Biostruc-id ::= CHOICE {
	mmdb-id			Mmdb-id,
	other-database		Dbtag,
	local-id		Object-id }

Mmdb-id ::= INTEGER


-- The description of a biostruc refers to both the reported chemical and 
-- spatial structure of a biomolecular assembly.  PDB-derived descriptors
-- which refer specifically to the chemical components or spatial structure
-- are not provided here, but instead as descriptors of the biostruc-graph or 
-- biostruc-model. For PDB-derived structures the biostruc name is the PDB 
-- id-code.  PDB-derived citations appear as publications within the biostruc 
-- description, and include a data-submission citation derived from PDB AUTHOR 
-- records.  Citations are described using the NCBI Pub specification.

Biostruc-descr ::= CHOICE {
	name			VisibleString,
	pdb-comment		VisibleString,
	other-comment		VisibleString,
	history			Biostruc-history, 
	attribution		Pub }


-- The history of a biostruc indicates it's origin and it's update history
-- within MMDB, the NCBI-maintained molecular structure database.  

Biostruc-history ::= SEQUENCE {
	replaces		Biostruc-replace OPTIONAL,
	replaced-by		Biostruc-replace OPTIONAL,
	data-source		Biostruc-source OPTIONAL }

Biostruc-replace ::= SEQUENCE {
	id			Biostruc-id,
	date			Date }

-- The origin of a biostruc is a reference to another database.  PDB release 
-- date and PDB-assigned id codes are recorded here, as are the PDB-assigned 
-- entry date and replacement history.

Biostruc-source ::= SEQUENCE {
	name-of-database	VisibleString,
	version-of-database	CHOICE {
		release-date		Date,
		release-code		VisibleString } OPTIONAL,
	database-entry-id	Biostruc-id,
	database-entry-date	Date,
	database-entry-history	SEQUENCE OF VisibleString OPTIONAL}


-- A biostruc set is a means to collect ASN.1 data for many biostrucs in 
-- one file, as convenient for application programs.  The object type is not
-- inteded to imply similarity of the biostrucs grouped together.

Biostruc-set ::= SEQUENCE {
	id		SEQUENCE OF Biostruc-id OPTIONAL,
	descr		SEQUENCE OF Biostruc-descr OPTIONAL,
	biostrucs	SEQUENCE OF Biostruc }


-- A biostruc annotation set is a means to collect ASN.1 data for biostruc
-- features into one file. The object type is intended as a means to store 
-- feature annotation of similar type, such as "core" definitions for a 
-- threading program, or structure-structure alignments for a structure-
-- similarity browser.

Biostruc-annot-set ::= SEQUENCE {
	id		SEQUENCE OF Biostruc-id OPTIONAL,
	descr		SEQUENCE OF Biostruc-descr OPTIONAL,
	features	SEQUENCE OF Biostruc-feature-set }


-- A biostruc residue graph set is a collection of residue graphs.  The object
-- type is intended as a means to record dictionaries containing the chemical
-- subgraphs of "standard" residue types, which are used as a means to 
-- simplify discription of the covalent structure of a biomolecular assembly.
-- The standard residue graph dictionary supplied with the MMDB database 
-- contains 20 standard L amino acids and 8 standard ribonucleotide groups. 
-- These graphs are complete, including explicit hydrogen atoms and separate 
-- instances for the terminal polypeptide and polynucleotide residues. 

Biostruc-residue-graph-set ::= SEQUENCE {
	id			SEQUENCE OF Biostruc-id OPTIONAL,
	descr			SEQUENCE OF Biomol-descr OPTIONAL,
	residue-graphs		SEQUENCE OF Residue-graph }

END



--**********************************************************************
--
--  Biological Macromolecule 3-D Structure Data Types for MMDB,
--                A Molecular Modeling Database
--
--  Definitions for a chemical graph
--
--  By Hitomi Ohkawa, Jim Ostell, Chris Hogue and Steve Bryant 
--
--  National Center for Biotechnology Information
--  National Institutes of Health
--  Bethesda, MD 20894 USA
--
--  July, 1995
--
--**********************************************************************

MMDB-Chemical-graph DEFINITIONS ::=

BEGIN

EXPORTS Biostruc-graph, Biomol-descr, Residue-graph,
	Molecule-id, Residue-id, Atom-id;

IMPORTS Pub FROM NCBI-Pub
	BioSource FROM NCBI-BioSource
	Seq-id FROM NCBI-Seqloc
	Biostruc-id FROM MMDB;

-- A biostruc graph contains the complete chemical graph of the biomolecular 
-- assembly.  The assembly graph is defined hierarchically, in terms of 
-- subgraphs graphs of component molecules.  For PDB-derived biostrucs,
-- the molecules forming the assembly are the individual biopolymer chains and 
-- any non-polymer or "heterogen" groups which are present. 

-- The PDB-derived  "compound name" field appears as the name within the
-- biostruc-graph description.  PDB "class" and "source" fields appear as 
-- explicit attributes.  PDB-derived structures are assigned an assembly type 
-- of "other" unless they have been further classified as the "physiological
-- form" or "crystallographic cell" contents.  If they have, the source of the 
-- type classification appears as a citation within the  assembly description. 

-- Note that the biostruc-graph also includes as literals the subgraphs of 
-- any nonstandard residues present within it. For PDB-derived biostrucs these 
-- subgraphs are constructed automatically, with validation as described below.

Biostruc-graph ::= SEQUENCE {
	descr			SEQUENCE OF Biomol-descr OPTIONAL,
	molecule-graphs		SEQUENCE OF Molecule-graph,
	inter-molecule-bonds	SEQUENCE OF Inter-residue-bond OPTIONAL,
	residue-graphs		SEQUENCE OF Residue-graph OPTIONAL }

-- A biomolecule description refers to the chemical structure of a molecule or 
-- component substructures.  This descriptor type is used at the level of
-- assemblies, molecules and residues, and also for residue-graph dictionaries.
-- The BioSource object type is drawn from NCBI taxonomy data specifications,
-- and is not repeated here.

Biomol-descr ::= CHOICE {
	name			VisibleString,
	pdb-class		VisibleString,
	pdb-source		VisibleString,
	pdb-comment		VisibleString,
	other-comment		VisibleString,
	organism		BioSource,
	attribution		Pub,
	assembly-type		INTEGER {	physiological-form(1),