Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { ParamDefinition as PD } from 'mol-util/param-definition';
import { RepresentationParamsGetter, RepresentationContext, VisualContext } from 'mol-repr/representation';
import { ThemeRegistryContext, Theme } from 'mol-theme/theme';
import { Structure } from 'mol-model/structure';
import { StructureRepresentationProvider, StructureRepresentation, ComplexRepresentation, ComplexVisual } from 'mol-repr/structure/representation';
import { AssemblySymmetry } from '../assembly-symmetry';
import { Table } from 'mol-data/db';
import { MeshBuilder } from 'mol-geo/geometry/mesh/mesh-builder';
import { Tensor } from 'mol-math/linear-algebra';
import { addSphere } from 'mol-geo/geometry/mesh/builder/sphere';
import { addCylinder } from 'mol-geo/geometry/mesh/builder/cylinder';
import { VisualUpdateState } from 'mol-repr/util';
import { ComplexMeshVisual, ComplexMeshParams } from 'mol-repr/structure/complex-visual';
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
import { EmptyLoci } from 'mol-model/loci';
import { LocationIterator } from 'mol-geo/util/location-iterator';
import { NullLocation } from 'mol-model/location';
export const AssemblySymmetryAxesParams = {
...ComplexMeshParams,
sizeFactor: PD.Numeric(0.4, { min: 0, max: 3, step: 0.01 }),
radialSegments: PD.Numeric(16, { min: 3, max: 56, step: 1 }),
detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }),
symmetryId: PD.Select<number>(-1, []),
}
export type AssemblySymmetryAxesParams = typeof AssemblySymmetryAxesParams
export function getAssemblySymmetryAxesParams(ctx: ThemeRegistryContext, structure: Structure) {
const params = PD.clone(AssemblySymmetryAxesParams)
if (structure.models[0].customProperties.has(AssemblySymmetry.Descriptor)) {
const assemblySymmetry = AssemblySymmetry.get(structure.models[0])!
const assemblyName = structure.assemblyName
const s = assemblySymmetry.db.rcsb_assembly_symmetry
if (s._rowCount) {
params.symmetryId.options = []
for (let i = 0, il = s._rowCount; i < il; ++i) {
if (s.assembly_id.value(i) === assemblyName) {
params.symmetryId.options.push([
s.id.value(i), `${s.symbol.value(i)} ${s.kind.value(i)}`
])
}
}
params.symmetryId.defaultValue = params.symmetryId.options[0][0]
}
}
return params
}
export type AssemblySymmetryAxesRepresentation = StructureRepresentation<AssemblySymmetryAxesParams>
export function AssemblySymmetryAxesRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, AssemblySymmetryAxesParams>): AssemblySymmetryAxesRepresentation {
return ComplexRepresentation('RCSB Assembly Symmetry Axes', ctx, getParams, AssemblySymmetryAxesVisual)
}
export const AssemblySymmetryAxesRepresentationProvider: StructureRepresentationProvider<AssemblySymmetryAxesParams> = {
label: 'RCSB Assembly Symmetry Axes',
description: 'Displays assembly symmetry axes.',
factory: AssemblySymmetryAxesRepresentation,
getParams: getAssemblySymmetryAxesParams,
defaultValues: PD.getDefaultValues(AssemblySymmetryAxesParams),
defaultColorTheme: 'uniform',
defaultSizeTheme: 'uniform'
}
//
export function AssemblySymmetryAxesVisual(): ComplexVisual<AssemblySymmetryAxesParams> {
return ComplexMeshVisual<AssemblySymmetryAxesParams>({
defaultProps: PD.getDefaultValues(AssemblySymmetryAxesParams),
createGeometry: createAssemblySymmetryAxesMesh,
createLocationIterator,
getLoci: () => EmptyLoci,
mark: () => false,
setUpdateState: (state: VisualUpdateState, newProps: PD.Values<AssemblySymmetryAxesParams>, currentProps: PD.Values<AssemblySymmetryAxesParams>) => {
state.createGeometry = (
newProps.sizeFactor !== currentProps.sizeFactor ||
newProps.detail !== currentProps.detail ||
newProps.symmetryId !== currentProps.symmetryId
)
}
})
}
function createLocationIterator(structure: Structure) {
let groupCount = 0
const assemblySymmetry = AssemblySymmetry.get(structure.models[0])
if (assemblySymmetry) {
const axis = assemblySymmetry.db.rcsb_assembly_symmetry_axis
groupCount = axis._rowCount
}
return LocationIterator(groupCount, 1, () => NullLocation)
}
export function createAssemblySymmetryAxesMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<AssemblySymmetryAxesParams>, mesh?: Mesh) {
const { symmetryId, sizeFactor } = props
const assemblySymmetry = AssemblySymmetry.get(structure.models[0])
if (!assemblySymmetry) return Mesh.createEmpty(mesh)
const s = assemblySymmetry.db.rcsb_assembly_symmetry
const symmetry = Table.pickRow(s, i => s.id.value(i) === symmetryId)
if (!symmetry) return Mesh.createEmpty(mesh)
// symmetry.assembly_id not available for structure.assemblyName
if (symmetry.assembly_id !== structure.assemblyName) return Mesh.createEmpty(mesh)
const axes = assemblySymmetry.getAxes(symmetryId)
if (!axes._rowCount) return Mesh.createEmpty(mesh)
const vectorSpace = AssemblySymmetry.Schema.rcsb_assembly_symmetry_axis.start.space;
// const colors: Color[] = []
// const labels: string[] = []
const radius = 1 * sizeFactor
const cylinderProps = { radiusTop: radius, radiusBottom: radius }
const builderState = MeshBuilder.createState(256, 128, mesh)
for (let i = 0, il = axes._rowCount; i < il; ++i) {
const start = Tensor.toVec3(vectorSpace, axes.start.value(i))
const end = Tensor.toVec3(vectorSpace, axes.end.value(i))
builderState.currentGroup = i
addSphere(builderState, start, radius, 2)
addSphere(builderState, end, radius, 2)
addCylinder(builderState, start, end, 1, cylinderProps)
// colors.push(Color(0xCCEE11))
// labels.push(`Axis ${i + 1} for ${symmetry.kind} ${symmetry.type.toLowerCase()} symmetry`)
}
return MeshBuilder.getMesh(builderState)
}