cn3d.asn
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上传日期:2007-06-13
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- --
- -- ===========================================================================
- -- 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