cn3d.asn

ncbi源码

--
-- ===========================================================================
-- PRODUCTION $Log: cn3d.asn,v $
-- PRODUCTION Revision 1000.0  2003/10/29 21:09:42  gouriano
-- PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R1.14
-- PRODUCTION
-- ===========================================================================
--

--$Revision: 1000.0 $
--**********************************************************************
--
--  Definitions for Cn3D-specific data (rendering settings,
--    user annotations, etc.)
--
--  by Paul Thiessen
--
--  National Center for Biotechnology Information
--  National Institutes of Health
--  Bethesda, MD 20894 USA
--
-- asntool -m cn3d.asn -w 100 -o cn3d.h
-- asntool -B objcn3d -m cn3d.asn -G -w 100 -K cn3d.h -I mapcn3d.h \
--   -M ../mmdb1.asn,../mmdb2.asn,../mmdb3.asn
--**********************************************************************

NCBI-Cn3d DEFINITIONS ::=
-- Cn3D-specific information

BEGIN

EXPORTS  Cn3d-style-dictionary, Cn3d-user-annotations;

IMPORTS  Biostruc-id FROM MMDB
         Molecule-id, Residue-id FROM MMDB-Chemical-graph;


-- values of enumerations must match those in cn3d/style_manager.hpp!

Cn3d-backbone-type ::= ENUMERATED {     -- for different types of backbones
    off (1),
    trace (2),
    partial (3),
    complete (4)
}

Cn3d-drawing-style ::= ENUMERATED {     -- atom/bond/object rendering styles
    -- for atoms and bonds
    wire (1),
    tubes (2),
    ball-and-stick (3),
    space-fill (4),
    wire-worm (5),
    tube-worm (6),
    -- for 3d-objects
    with-arrows (7),
    without-arrows (8)
}

Cn3d-color-scheme ::= ENUMERATED {  -- available color schemes (not all
                                    -- necessarily applicable to all objects)
    element (1),
    object (2),
    molecule (3),
    domain (4),
    secondary-structure (5),
    user-select (6),
    -- different alignment conservation coloring (currently only for proteins)
    aligned (7),
    identity (8),
    variety (9),
    weighted-variety (10),
    information-content (11),
    fit (12),
    block-fit (17),
    block-z-fit (18),
    block-row-fit (19),
    -- other schemes
    temperature (13),
    hydrophobicity (14),
    charge (15),
    rainbow (16)
}

-- RGB triplet, interpreted (after division by the scale-factor) as floating
-- point values which should range from [0..1]. The default scale-factor is
-- 255, so that one can conveniently set integer byte values [0..255] for
-- colors with the scale-factor already set appropriately to map to [0..1].
--    An alpha value is allowed, but is currently ignored by Cn3D.
Cn3d-color ::= SEQUENCE {
    scale-factor INTEGER DEFAULT 255,
    red INTEGER,
    green INTEGER,
    blue INTEGER,
    alpha INTEGER DEFAULT 255
}

Cn3d-backbone-style ::= SEQUENCE {  -- style blob for backbones only
    type Cn3d-backbone-type,
    style Cn3d-drawing-style,
    color-scheme Cn3d-color-scheme,
    user-color Cn3d-color
}

Cn3d-general-style ::= SEQUENCE {   -- style blob for other objects
    is-on BOOLEAN,
    style Cn3d-drawing-style,
    color-scheme Cn3d-color-scheme,
    user-color Cn3d-color
}

Cn3d-backbone-label-style ::= SEQUENCE { -- style blob for backbone labels
    spacing INTEGER,        -- zero means none
    type ENUMERATED {
        one-letter (1),
        three-letter (2)
    },
    number ENUMERATED {
        none (0),
        sequential (1),     -- from 1, by residues present, to match sequence
        pdb (2)             -- use number assigned by PDB
    },
    termini BOOLEAN,
    white BOOLEAN           -- all white, or (if false) color of alpha carbon
}

-- rendering settings for Cn3D (mirrors StyleSettings class)
Cn3d-style-settings ::= SEQUENCE {
    name VisibleString OPTIONAL,                -- a name (for favorites)
    protein-backbone Cn3d-backbone-style,       -- backbone styles
    nucleotide-backbone Cn3d-backbone-style,
    protein-sidechains Cn3d-general-style,      -- styles for other stuff
    nucleotide-sidechains Cn3d-general-style,
    heterogens Cn3d-general-style,
    solvents Cn3d-general-style,
    connections Cn3d-general-style,
    helix-objects Cn3d-general-style,
    strand-objects Cn3d-general-style,
    virtual-disulfides-on BOOLEAN,              -- virtual disulfides
    virtual-disulfide-color Cn3d-color,
    hydrogens-on BOOLEAN,                       -- hydrogens
    background-color Cn3d-color,                -- background
    -- floating point parameters - scale-factor applies to all the following:
    scale-factor INTEGER,
    space-fill-proportion INTEGER,
    ball-radius INTEGER,
    stick-radius INTEGER,
    tube-radius INTEGER,
    tube-worm-radius INTEGER,
    helix-radius INTEGER,
    strand-width INTEGER,
    strand-thickness INTEGER,
    -- backbone labels (no labels if not present)
    protein-labels Cn3d-backbone-label-style OPTIONAL,
    nucleotide-labels Cn3d-backbone-label-style OPTIONAL,
    -- ion labels
    ion-labels BOOLEAN OPTIONAL
}

Cn3d-style-settings-set ::= SET OF Cn3d-style-settings

Cn3d-style-table-id ::= INTEGER

Cn3d-style-table-item ::= SEQUENCE {
    id Cn3d-style-table-id,
    style Cn3d-style-settings
}

-- the global settings, and a lookup table of styles for user annotations.
Cn3d-style-dictionary ::= SEQUENCE {
    global-style Cn3d-style-settings,
    style-table SEQUENCE OF Cn3d-style-table-item OPTIONAL
}

-- a range of residues in a chain, identified by MMDB residue-id
-- (e.g., numbered from 1)
Cn3d-residue-range ::= SEQUENCE {
    from Residue-id,
    to Residue-id
}

-- set of locations on a particular chain
Cn3d-molecule-location ::= SEQUENCE {
    molecule-id Molecule-id,    -- MMDB molecule id
    -- which residues; whole molecule implied if absent
    residues SEQUENCE OF Cn3d-residue-range OPTIONAL
}

-- set of locations on a particular structure object (e.g., a PDB/MMDB
-- structure), which may include multiple ranges of residues each on
-- multiple chains.
Cn3d-object-location ::= SEQUENCE {
    structure-id Biostruc-id,
    residues SEQUENCE OF Cn3d-molecule-location
}

-- information for an individual user annotation
Cn3d-user-annotation ::= SEQUENCE {
    name VisibleString,                 -- a (short) name for this annotation
    description VisibleString OPTIONAL, -- an optional longer description
    style-id Cn3d-style-table-id,       -- how to draw this annotation
    residues SEQUENCE OF Cn3d-object-location,  -- which residues to cover
    is-on BOOLEAN   -- whether this annotation is to be turned on in Cn3D
}

-- a GL-ordered transformation matrix
Cn3d-GL-matrix ::= SEQUENCE {
    m0  REAL, m1  REAL, m2  REAL, m3  REAL,
    m4  REAL, m5  REAL, m6  REAL, m7  REAL,
    m8  REAL, m9  REAL, m10 REAL, m11 REAL,
    m12 REAL, m13 REAL, m14 REAL, m15 REAL
}

-- a floating point 3d vector
Cn3d-vector ::= SEQUENCE {
    x REAL,
    y REAL,
    z REAL
}

-- parameters used to set up the camera in Cn3D
Cn3d-view-settings ::= SEQUENCE {
    camera-distance REAL,       -- camera on +Z axis this distance from origin
    camera-angle-rad REAL,      -- camera angle
    camera-look-at-X REAL,      -- X,Y of point in Z=0 plane camera points at
    camera-look-at-Y REAL,
    camera-clip-near REAL,      -- distance of clipping planes from camera
    camera-clip-far REAL,
    matrix Cn3d-GL-matrix,      -- transformation of objects in the scene
    rotation-center Cn3d-vector -- center of rotation of whole scene
}

-- The list of annotations for a given CDD/mime. If residue regions overlap
-- between annotations that are turned on, the last annotation in this list
-- that contains these residues will be used as the display style for these
-- residues.
--   Also contains the current viewpoint, so that user's camera angle
-- can be stored and reproduced, for illustrations, on-line figures, etc.
Cn3d-user-annotations ::= SEQUENCE {
    annotations SEQUENCE OF Cn3d-user-annotation OPTIONAL,
    view Cn3d-view-settings OPTIONAL
}

END