src/objects/cn3d/cn3d.asn
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--$Revision: 32084 $
--**********************************************************************
--
-- 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),
residue (20),
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