src/objects/mmdb3/mmdb3.asn
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--$Revision: 48795 $
--**********************************************************************
--
-- Biological Macromolecule 3-D Structure Data Types for MMDB,
-- A Molecular Modeling Database
--
-- Definitions for structural features and biostruc addressing
--
-- By Hitomi Ohkawa, Jim Ostell, Chris Hogue and Steve Bryant
--
-- National Center for Biotechnology Information
-- National Institutes of Health
-- Bethesda, MD 20894 USA
--
-- July, 1996
--
--**********************************************************************
MMDB-Features DEFINITIONS ::=
BEGIN
EXPORTS Biostruc-feature-set, Chem-graph-pntrs, Atom-pntrs,
Chem-graph-alignment, Chem-graph-interaction, Sphere,
Cone, Cylinder, Brick, Transform, Biostruc-feature-set-id,
Biostruc-feature-id;
IMPORTS Biostruc-id FROM MMDB
Molecule-id, Residue-id, Atom-id FROM MMDB-Chemical-graph
Model-id, Model-coordinate-set-id FROM MMDB-Structural-model
User-object FROM NCBI-General
Pub FROM NCBI-Pub;
-- Named model features refer to sets of residues or atoms, or a region in
-- the model space. A few specific feature types are allowed for compatibility
-- with PDB usage, but the purpose of a named model feature is simply to
-- associate various types of information with a set of atoms or
-- residues, or a spatially-defined region of the model structure. They also
-- support association of various properties with each residue or atom of a
-- set.
-- PDB-derived secondary structure defines a single feature, represented as a
-- sequence of residue motifs, as are the contents of PDB SITE and
-- FTNOTE records. NCBI-assigned core and secondary structure descriptions
-- are also represented as a sequence of residue motifs.
Biostruc-feature-set ::= SEQUENCE {
id Biostruc-feature-set-id,
descr SEQUENCE OF Biostruc-feature-set-descr OPTIONAL,
features SEQUENCE OF Biostruc-feature }
Biostruc-feature-set-id ::= INTEGER
Biostruc-feature-set-descr ::= CHOICE {
name VisibleString,
pdb-comment VisibleString,
other-comment VisibleString,
attribution Pub }
-- An explicitly specified type in Biostruc-feature allows for
-- efficient extraction and indexing of feature sets of a specific type.
-- Special types are provided for coloring and rendering, as
-- as needed by molecular graphics programs.
Biostruc-feature ::= SEQUENCE {
id Biostruc-feature-id OPTIONAL,
name VisibleString OPTIONAL,
type INTEGER { helix(1),
strand(2),
sheet(3),
turn(4),
site(5),
footnote(6),
comment(7), -- new
interaction(8), -- interaction Data
subgraph(100), -- NCBI domain reserved
region(101),
core(102), -- user core definition
supercore(103), -- NCBI reserved
color(150), -- new
render(151), -- new
label(152), -- new
transform(153), -- new
camera(154), -- new
script(155), -- for scripts
alignment(200), -- VAST reserved
similarity(201),
multalign(202), -- multiple alignment
indirect(203), -- new
cn3dstate(254), -- Cn3D reserved
other(255) } OPTIONAL,
property CHOICE {
color Color-prop,
render Render-prop,
transform Transform,
camera Camera,
script Biostruc-script,
user User-object } OPTIONAL,
location CHOICE {
subgraph Chem-graph-pntrs,
region Region-pntrs,
alignment Chem-graph-alignment,
interaction Chem-graph-interaction,
similarity Region-similarity,
indirect Other-feature } OPTIONAL } -- new
-- Other-feature allows for specifying location via reference to another
-- Biostruc-feature and its location.
Other-feature ::= SEQUENCE {
biostruc-id Biostruc-id,
set Biostruc-feature-set-id,
feature Biostruc-feature-id }
Biostruc-feature-id ::= INTEGER
-- Atom, residue or molecule motifs describe a substructure defined by a set
-- of nodes from the chemical graph. PDB secondary structure features are
-- described as a residue motif, since they are not associated with any one of
-- the multiple models that may be provided in a PDB file. NCBI-assigned
-- secondary structure is represented in the same way, even though it is
-- model specific, since this allows for simple mapping of the structural
-- feature onto a sequence-only representation. This addressing mode may also
-- be used to describe features to be associated with particular atoms,
-- as, for example, the chemical shift observed in an NMR experiment.
Biostruc-molecule-pntr ::= SEQUENCE {
biostruc-id Biostruc-id,
molecule-id Molecule-id }
Chem-graph-pntrs ::= CHOICE {
atoms Atom-pntrs,
residues Residue-pntrs,
molecules Molecule-pntrs }
Atom-pntrs ::= SEQUENCE {
number-of-ptrs INTEGER,
molecule-ids SEQUENCE OF Molecule-id,
residue-ids SEQUENCE OF Residue-id,
atom-ids SEQUENCE OF Atom-id }
Residue-pntrs ::= CHOICE {
explicit Residue-explicit-pntrs,
interval SEQUENCE OF Residue-interval-pntr }
Residue-explicit-pntrs ::= SEQUENCE {
number-of-ptrs INTEGER,
molecule-ids SEQUENCE OF Molecule-id,
residue-ids SEQUENCE OF Residue-id }
Residue-interval-pntr ::= SEQUENCE {
molecule-id Molecule-id,
from Residue-id,
to Residue-id }
Molecule-pntrs ::= SEQUENCE {
number-of-ptrs INTEGER,
molecule-ids SEQUENCE OF Molecule-id }
-- Region motifs describe features defined by spatial location, such as the
-- site specified by a coordinate value, or a rgeion within a bounding volume.
Region-pntrs ::= SEQUENCE {
model-id Model-id,
region CHOICE {
site SEQUENCE OF Region-coordinates,
boundary SEQUENCE OF Region-boundary } }
-- Coordinate sites describe a region in space by reference to individual
-- coordinates, in a particular model. These coordinates may be either the
-- x, y and z values of atomic coordinates, the triangles of a surface mesh,
-- or the grid points of a density model. All are addressed in the same manner,
-- as coordinate indices which give offsets from the beginning of the
-- coordinate data arrays. A coordinate-index of 5, for example, refers to
-- the 5th x, y and z values of an atomic coordinate set, the 5th v1, v2, and v3
-- values of a triangle mesh, or the 5th value in a density grid.
-- PDB SITE and FTNOTE records refer to particular atomic coordinates, and they
-- are represented as a region motif with addresses of type Region-coordinates.
-- Any names or descriptions provided by PDB are thus associated with the
-- indicated sites, in the indicated model.
Region-coordinates ::= SEQUENCE {
model-coord-set-id Model-coordinate-set-id,
number-of-coords INTEGER OPTIONAL,
coordinate-indices SEQUENCE OF INTEGER OPTIONAL }
-- Region boundaries are defined by regular solids located in the model space.
Region-boundary ::= CHOICE { sphere Sphere,
cone Cone,
cylinder Cylinder,
brick Brick }
-- A biostruc alignment establishes an equivalence of nodes in the chemical
-- graphs of two or more biostrucs. This may be mapped to a sequence
-- alignment in the case of biopolymers.
-- The 'dimension' component indicates the number of participants
-- in the alignment. For pairwise alignments, such as VAST
-- structure-structure alignments, the dimension will be always 2, with
-- biostruc-ids, alignment, and domain each containing two entries for an
-- aligned pair. The 'alignment' component contains a pair of Chem-graph-pntrs
-- specifying a like number of corresponding residues in each structure.
-- The 'domain' component specifies a region of each structure considered
-- in the alignment. Only one transform (for the second structure) and
-- one aligndata (for the pair) are provided for each VAST alignment.
--
-- For multiple alignments, a set of components are treated as
-- parallel arrays of length 'dimension'.
-- The 'transform' component moves each structure to align it with
-- the structure specified as the first element in the "parallel" array,
-- so necessarily the first transform is a NULL transform.
-- Align-stats are placeholders for scores.
Chem-graph-alignment ::= SEQUENCE {
dimension INTEGER DEFAULT 2,
biostruc-ids SEQUENCE OF Biostruc-id,
alignment SEQUENCE OF Chem-graph-pntrs,
domain SEQUENCE OF Chem-graph-pntrs OPTIONAL,
transform SEQUENCE OF Transform OPTIONAL,
aligndata SEQUENCE OF Align-stats OPTIONAL }
Chem-graph-interaction ::= SEQUENCE {
type INTEGER { protein-protein(1),
protein-dna(2),
protein-rna(3),
protein-chemical(4),
dna-dna(5),
dna-rna(6),
dna-chemical(7),
rna-rna(8),
rna-chemical(9),
other(255) } OPTIONAL,
distance-threshold RealValue OPTIONAL,
interactors SEQUENCE OF Biostruc-molecule-pntr,
residue-contacts SEQUENCE OF Chem-graph-pntrs OPTIONAL,
atom-contacts SEQUENCE OF Chem-graph-pntrs OPTIONAL,
atom-distance SEQUENCE OF RealValue OPTIONAL}
Align-stats ::= SEQUENCE {
descr VisibleString OPTIONAL,
scale-factor INTEGER OPTIONAL,
vast-score INTEGER OPTIONAL,
vast-mlogp INTEGER OPTIONAL,
align-res INTEGER OPTIONAL,
rmsd INTEGER OPTIONAL,
blast-score INTEGER OPTIONAL,
blast-mlogp INTEGER OPTIONAL,
other-score INTEGER OPTIONAL }
-- A biostruc similarity describes spatial features which are similar between
-- two or more biostrucs. Similarities are model dependent, and the model and
-- coordinate set ids of the biostrucs must be specified. They do not
-- necessarily map to a sequence alignment, as the regions referenced may
-- be pieces of a surface or grid, and thus not uniquely mapable to particular
-- chemical components.
Region-similarity ::= SEQUENCE {
dimension INTEGER DEFAULT 2,
biostruc-ids SEQUENCE OF Biostruc-id,
similarity SEQUENCE OF Region-pntrs,
transform SEQUENCE OF Transform }
-- Geometrical primitives are used in the definition of region motifs, and
-- also non-atomic coordinates. Spheres, cones, cylinders and bricks are
-- defined by a few points in the model space.
Sphere ::= SEQUENCE {
center Model-space-point,
radius RealValue }
Cone ::= SEQUENCE {
axis-top Model-space-point,
axis-bottom Model-space-point,
radius-bottom RealValue }
Cylinder ::= SEQUENCE {
axis-top Model-space-point,
axis-bottom Model-space-point,
radius RealValue }
-- A brick is defined by the coordinates of eight corners. These are assumed
-- to appear in the order 000, 001, 010, 011, 100, 101, 110, 111, where the
-- digits 0 and 1 refer to respectively to the x, y and z axes of a unit cube.
-- Opposite edges are assumed to be parallel.
Brick ::= SEQUENCE {
corner-000 Model-space-point,
corner-001 Model-space-point,
corner-010 Model-space-point,
corner-011 Model-space-point,
corner-100 Model-space-point,
corner-101 Model-space-point,
corner-110 Model-space-point,
corner-111 Model-space-point }
Model-space-point ::= SEQUENCE {
scale-factor INTEGER,
x INTEGER,
y INTEGER,
z INTEGER }
RealValue ::= SEQUENCE {
scale-factor INTEGER,
scaled-integer-value INTEGER }
Transform ::= SEQUENCE {
id INTEGER,
moves SEQUENCE OF Move }
Move ::= CHOICE {
rotate Rot-matrix,
translate Trans-matrix }
-- A rotation matrix is defined by 9 numbers, given by row, i.e.,
-- with column indices varying fastest.
-- Coordinates, as a matrix with columns x, y, an z, are rotated
-- via multiplication with the rotation matrix.
-- A translation matrix is defined by 3 numbers, which is added to
-- the rotated coordinates for specified amount of translation.
Rot-matrix ::= SEQUENCE {
scale-factor INTEGER,
rot-11 INTEGER,
rot-12 INTEGER,
rot-13 INTEGER,
rot-21 INTEGER,
rot-22 INTEGER,
rot-23 INTEGER,
rot-31 INTEGER,
rot-32 INTEGER,
rot-33 INTEGER }
Trans-matrix ::= SEQUENCE {
scale-factor INTEGER,
tran-1 INTEGER,
tran-2 INTEGER,
tran-3 INTEGER }
-- The camera is a position relative to the world coordinates
-- of the structure referred to by a location.
-- this is used to set the initial position of the
-- camera using OpenGL. scale is the value used to scale the
-- other values from floating point to integer
Camera ::= SEQUENCE {
x INTEGER,
y INTEGER,
distance INTEGER,
angle INTEGER,
scale INTEGER,
modelview GL-matrix }
GL-matrix ::= SEQUENCE {
scale INTEGER,
m11 INTEGER,
m12 INTEGER,
m13 INTEGER,
m14 INTEGER,
m21 INTEGER,
m22 INTEGER,
m23 INTEGER,
m24 INTEGER,
m31 INTEGER,
m32 INTEGER,
m33 INTEGER,
m34 INTEGER,
m41 INTEGER,
m42 INTEGER,
m43 INTEGER,
m44 INTEGER }
Color-prop ::= SEQUENCE {
r INTEGER OPTIONAL,
g INTEGER OPTIONAL,
b INTEGER OPTIONAL,
name VisibleString OPTIONAL }
-- Note that Render-prop is compatible with the Annmm specification,
-- i.e., its numbering schemes do not clash with those in Render-prop.
Render-prop ::= INTEGER {
default (0), -- Default view
wire (1), -- use wireframe
space (2), -- use spacefill
stick (3), -- use stick model (thin cylinders)
ballNStick (4), -- use ball & stick model
thickWire (5), -- thicker wireframe
hide (9), -- don't show this
name (10), -- display its name next to it
number (11), -- display its number next to it
pdbNumber (12), -- display its PDB number next to it
objWireFrame (150), -- display MMDB surface object as wireframe
objPolygons (151), -- display MMDB surface object as polygons
colorsetCPK (225), -- color atoms like CPK models
colorsetbyChain (226), -- color each chain different
colorsetbyTemp (227), -- color using isotropic Temp factors
colorsetbyRes (228), -- color using residue properties
colorsetbyLen (229), -- color changes along chain length
colorsetbySStru (230), -- color by secondary structure
colorsetbyHydro (231), -- color by hydrophobicity
colorsetbyObject(246), -- color each object differently
colorsetbyDomain(247), -- color each domain differently
other (255)
}
-- When a Biostruc-Feature with a Biostruc-script is initiated,
-- it should play the specified steps one at a time, setting the feature-do
-- list as the active display.
-- The camera can be set using a feature-do,
-- but it may be moved independently with
-- camera-move, which specifies how to move
-- the camera dynamically during the step along the path defined (e.g.,
-- a zoom, a rotate).
-- Any value of pause (in 1:10th's of a second) will force a pause
-- after an image is shown.
-- If waitevent is TRUE, it will await a mouse or keypress and ignore
-- the pause value.
Biostruc-script ::= SEQUENCE OF Biostruc-script-step
Biostruc-script-step ::= SEQUENCE {
step-id Step-id,
step-name VisibleString OPTIONAL,
feature-do SEQUENCE OF Other-feature OPTIONAL,
camera-move Transform OPTIONAL,
pause INTEGER DEFAULT 10,
waitevent BOOLEAN,
extra INTEGER,
jump Step-id OPTIONAL }
Step-id ::= INTEGER
END