diff --git a/src/apps/render-test/components/detail.tsx b/src/apps/render-test/components/detail.tsx
index a53c64f826c6b77a33af5aeb258d90e00d53ab7c..9bbd84a6de3b6f208ece2c5d52f959f463a9b9d9 100644
--- a/src/apps/render-test/components/detail.tsx
+++ b/src/apps/render-test/components/detail.tsx
@@ -38,7 +38,7 @@ export default class Detail extends Observer<{ state: State } & WithStyles, Deta
render() {
const { classes } = this.props;
- const items = [0, 1, 2].map((value, idx) => {
+ const items = [0, 1, 2, 3].map((value, idx) => {
return <MenuItem key={idx} value={value}>{value.toString()}</MenuItem>
})
diff --git a/src/mol-geo/primitive/icosahedron.ts b/src/mol-geo/primitive/icosahedron.ts
index 7e73afb419daeef55278241fafe2cfef5f7dbeaf..07e544e07fcfdd7cddb36940173f2841c58da169 100644
--- a/src/mol-geo/primitive/icosahedron.ts
+++ b/src/mol-geo/primitive/icosahedron.ts
@@ -23,6 +23,10 @@ const indices = [
4, 9, 5, 2, 4, 11, 6, 2, 10, 8, 6, 7, 9, 8, 1
];
+export function icosahedronVertexCount(detail: number) {
+ return 10 * Math.pow(Math.pow(2, detail), 2) + 2
+}
+
export const DefaultIcosahedronProps = {
radius: 1,
detail: 0
diff --git a/src/mol-geo/representation/structure/point.ts b/src/mol-geo/representation/structure/point.ts
index b95347fb17e7035214d95963c38d896bf2002262..73884615d0dbaf21f78d746862c4d42b89cbc86e 100644
--- a/src/mol-geo/representation/structure/point.ts
+++ b/src/mol-geo/representation/structure/point.ts
@@ -7,7 +7,7 @@
import { ValueCell } from 'mol-util/value-cell'
import { createPointRenderObject, RenderObject, PointRenderObject } from 'mol-gl/scene'
import { OrderedSet } from 'mol-data/int'
-import { Unit, ElementGroup } from 'mol-model/structure';
+import { Unit, ElementGroup, Element } from 'mol-model/structure';
import { Task } from 'mol-task'
import { fillSerial } from 'mol-gl/renderable/util';
@@ -26,13 +26,17 @@ export type PointProps = Partial<typeof DefaultPointProps>
export function createPointVertices(unit: Unit, elementGroup: ElementGroup) {
const elementCount = OrderedSet.size(elementGroup.elements)
const vertices = new Float32Array(elementCount * 3)
- const { x, y, z } = unit.model.atomSiteConformation
+
+ const { x, y, z } = unit
+ const l = Element.Location()
+ l.unit = unit
+
for (let i = 0; i < elementCount; i++) {
- const e = OrderedSet.getAt(elementGroup.elements, i)
+ l.element = ElementGroup.getAt(elementGroup, i)
const i3 = i * 3
- vertices[i3] = x[e]
- vertices[i3 + 1] = y[e]
- vertices[i3 + 2] = z[e]
+ vertices[i3] = x(l.element)
+ vertices[i3 + 1] = y(l.element)
+ vertices[i3 + 2] = z(l.element)
}
return vertices
}
diff --git a/src/mol-geo/representation/structure/spacefill.ts b/src/mol-geo/representation/structure/spacefill.ts
index 4e2f9168361a547201b789eb28fdbddc9b66309b..47d238d2de34c249e29b7bdbe3f7afa217d2fc88 100644
--- a/src/mol-geo/representation/structure/spacefill.ts
+++ b/src/mol-geo/representation/structure/spacefill.ts
@@ -10,15 +10,15 @@ import { RenderObject, createMeshRenderObject, MeshRenderObject } from 'mol-gl/s
// import { createColorTexture } from 'mol-gl/util';
import { Vec3, Mat4 } from 'mol-math/linear-algebra'
import { OrderedSet } from 'mol-data/int'
-import { Unit, ElementGroup } from 'mol-model/structure';
+import { Unit, ElementGroup, Element, Queries } from 'mol-model/structure';
import { RepresentationProps, UnitsRepresentation } from './index';
import { Task } from 'mol-task'
import { MeshBuilder } from '../../shape/mesh-builder';
-import { VdwRadius } from 'mol-model/structure/model/properties/atomic';
import { createTransforms, createColors } from './utils';
import { ColorTheme } from '../../theme';
import VertexMap from '../../shape/vertex-map';
import CoarseGrained from 'mol-model/structure/model/properties/coarse-grained';
+import { icosahedronVertexCount } from '../../primitive/icosahedron';
export const DefaultSpacefillProps = {
detail: 0,
@@ -26,72 +26,43 @@ export const DefaultSpacefillProps = {
}
export type SpacefillProps = Partial<typeof DefaultSpacefillProps>
-function buildAtomSpheres(meshBuilder: MeshBuilder, unit: Unit, elementGroup: ElementGroup, detail: number) {
- return Task.create('Atom spheres', async ctx => {
- if (!Unit.isAtomic(unit)) return
-
- const v = Vec3.zero()
- const m = Mat4.identity()
-
- const { x, y, z } = unit.model.atomSiteConformation
- const { type_symbol } = unit.model.hierarchy.atoms
+function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: number) {
+ return Task.create('Sphere mesh', async ctx => {
const elementCount = OrderedSet.size(elementGroup.elements)
- for (let i = 0; i < elementCount; i++) {
- const e = OrderedSet.getAt(elementGroup.elements, i)
- v[0] = x[e]
- v[1] = y[e]
- v[2] = z[e]
- Mat4.setTranslation(m, v)
+ const vertexCount = elementCount * icosahedronVertexCount(detail)
+ const meshBuilder = MeshBuilder.create(vertexCount)
- meshBuilder.setId(i)
- meshBuilder.addIcosahedron(m, { radius: VdwRadius(type_symbol.value(e)), detail })
-
- if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Atom spheres', current: i, max: elementCount });
- }
+ let radius: Element.Property<number>
+ if (Unit.isAtomic(unit)) {
+ radius = Queries.props.atom.vdw_radius
+ } else if (Unit.isCoarse(unit) && unit.elementType === CoarseGrained.ElementType.Sphere) {
+ radius = Queries.props.coarse_grained.sphere_radius
+ } else {
+ console.warn('Unsupported unit type')
+ return meshBuilder.getMesh()
}
- })
-}
-
-function buildCoarseSpheres(meshBuilder: MeshBuilder, unit: Unit, elementGroup: ElementGroup, detail: number) {
- return Task.create('Coarse spheres', async ctx => {
- if (!Unit.isCoarse(unit) || unit.elementType !== CoarseGrained.ElementType.Sphere) return
const v = Vec3.zero()
const m = Mat4.identity()
- const { x, y, z, radius } = unit.model.coarseGrained.spheres
- const elementCount = OrderedSet.size(elementGroup.elements)
- console.log('building coarse spheres', elementCount)
+ const { x, y, z } = unit
+ const l = Element.Location()
+ l.unit = unit
+
for (let i = 0; i < elementCount; i++) {
- const e = OrderedSet.getAt(elementGroup.elements, i)
- v[0] = x[e]
- v[1] = y[e]
- v[2] = z[e]
+ l.element = ElementGroup.getAt(elementGroup, i)
+ v[0] = x(l.element)
+ v[1] = y(l.element)
+ v[2] = z(l.element)
Mat4.setTranslation(m, v)
meshBuilder.setId(i)
- meshBuilder.addIcosahedron(m, { radius: radius.value(e), detail })
+ meshBuilder.addIcosahedron(m, { radius: radius(l), detail })
if (i % 10000 === 0 && ctx.shouldUpdate) {
- await ctx.update({ message: 'Coarse spheres', current: i, max: elementCount });
+ await ctx.update({ message: 'Sphere mesh', current: i, max: elementCount });
}
}
- })
-}
-
-function createSpacefillMesh(unit: Unit, elementGroup: ElementGroup, detail: number) {
- return Task.create('Spacefill', async ctx => {
- const meshBuilder = MeshBuilder.create()
-
- if (Unit.isAtomic(unit)) {
- await ctx.runChild(buildAtomSpheres(meshBuilder, unit, elementGroup, detail))
- }
-
- if (Unit.isCoarse(unit) && unit.elementType === CoarseGrained.ElementType.Sphere) {
- console.log('building coarse spheres')
- await ctx.runChild(buildCoarseSpheres(meshBuilder, unit, elementGroup, detail))
- }
return meshBuilder.getMesh()
})
diff --git a/src/mol-geo/representation/structure/utils.ts b/src/mol-geo/representation/structure/utils.ts
index 65f7b35962d4b6eb769b8d34de2d4ff3ece77f59..fba67c536e46e9447fd19b170299d25771b19996 100644
--- a/src/mol-geo/representation/structure/utils.ts
+++ b/src/mol-geo/representation/structure/utils.ts
@@ -9,7 +9,7 @@ import { Mat4 } from 'mol-math/linear-algebra'
import { createUniformColor } from '../../util/color-data';
import { createUniformSize } from '../../util/size-data';
-import { vdwSizeData } from '../../theme/structure/size/vdw';
+import { elementSizeData } from '../../theme/structure/size/element';
import VertexMap from '../../shape/vertex-map';
import { ColorTheme, SizeTheme } from '../../theme';
import { elementIndexColorData, elementSymbolColorData, instanceIndexColorData, chainIdColorData } from '../../theme/structure/color';
@@ -43,6 +43,6 @@ export function createSizes(units: ReadonlyArray<Unit>, elementGroup: ElementGro
case 'uniform':
return createUniformSize(props)
case 'vdw':
- return vdwSizeData({ units, elementGroup, vertexMap })
+ return elementSizeData({ units, elementGroup, vertexMap })
}
}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/element.ts b/src/mol-geo/theme/structure/size/element.ts
new file mode 100644
index 0000000000000000000000000000000000000000..699bc071a499ab303d3e40d48c3befb465248afe
--- /dev/null
+++ b/src/mol-geo/theme/structure/size/element.ts
@@ -0,0 +1,31 @@
+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ElementGroup, Element, Unit, Queries } from 'mol-model/structure';
+import CoarseGrained from 'mol-model/structure/model/properties/coarse-grained';
+import { StructureSizeDataProps } from '.';
+import { createAttributeSize } from '../../../util/size-data';
+
+/** Create attribute data with the size of an element, i.e. vdw for atoms and radius for coarse spheres */
+export function elementSizeData(props: StructureSizeDataProps) {
+ const { units, elementGroup, vertexMap } = props
+ const unit = units[0]
+ let radius: Element.Property<number>
+ if (Unit.isAtomic(unit)) {
+ radius = Queries.props.atom.vdw_radius
+ } else if (Unit.isCoarse(unit) && unit.elementType === CoarseGrained.ElementType.Sphere) {
+ radius = Queries.props.coarse_grained.sphere_radius
+ }
+ const l = Element.Location()
+ l.unit = unit
+ return createAttributeSize({
+ sizeFn: (elementIdx: number) => {
+ l.element = ElementGroup.getAt(elementGroup, elementIdx)
+ return radius(l)
+ },
+ vertexMap
+ })
+}
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/index.ts b/src/mol-geo/theme/structure/size/index.ts
index b178ad42b9f9877bf819b0f2da71aa95e661219c..22caed502febf7ab0dd05a25201fe1c960335f07 100644
--- a/src/mol-geo/theme/structure/size/index.ts
+++ b/src/mol-geo/theme/structure/size/index.ts
@@ -13,4 +13,4 @@ export interface StructureSizeDataProps {
vertexMap: VertexMap
}
-export { vdwSizeData } from './vdw'
\ No newline at end of file
+export { elementSizeData } from './element'
\ No newline at end of file
diff --git a/src/mol-geo/theme/structure/size/vdw.ts b/src/mol-geo/theme/structure/size/vdw.ts
deleted file mode 100644
index 3010380904ab0810d3d79ff5f0a5b0a0d1f7a921..0000000000000000000000000000000000000000
--- a/src/mol-geo/theme/structure/size/vdw.ts
+++ /dev/null
@@ -1,23 +0,0 @@
-/**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { OrderedSet } from 'mol-data/int';
-import { VdwRadius } from 'mol-model/structure/model/properties/atomic';
-import { StructureSizeDataProps } from '.';
-import { createAttributeSize } from '../../../util/size-data';
-
-
-export function vdwSizeData(props: StructureSizeDataProps) {
- const { units, elementGroup, vertexMap } = props
- const { type_symbol } = units[0].model.hierarchy.atoms
- return createAttributeSize({
- sizeFn: (elementIdx: number) => {
- const e = OrderedSet.getAt(elementGroup.elements, elementIdx)
- return VdwRadius(type_symbol.value(e))
- },
- vertexMap
- })
-}
\ No newline at end of file
diff --git a/src/mol-model/structure/query/properties.ts b/src/mol-model/structure/query/properties.ts
index 8a766f9b5c6040a4fd7f7ebd8d23820f404bc7b7..98d22ce51ca05136bc70f0bf52c82399d8fbd400 100644
--- a/src/mol-model/structure/query/properties.ts
+++ b/src/mol-model/structure/query/properties.ts
@@ -1,11 +1,12 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
*/
import { Element, Unit } from '../structure'
import CoarseGrained from '../model/properties/coarse-grained';
+import { VdwRadius } from '../model/properties/atomic';
const constant = {
true: Element.property(l => true),
@@ -38,7 +39,10 @@ const atom = {
label_atom_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.hierarchy.atoms.label_atom_id.value(l.element)),
auth_atom_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.hierarchy.atoms.auth_atom_id.value(l.element)),
label_alt_id: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.hierarchy.atoms.label_alt_id.value(l.element)),
- pdbx_formal_charge: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.hierarchy.atoms.pdbx_formal_charge.value(l.element))
+ pdbx_formal_charge: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.hierarchy.atoms.pdbx_formal_charge.value(l.element)),
+
+ // Derived
+ vdw_radius: Element.property(l => !Unit.isAtomic(l.unit) ? notAtomic() : VdwRadius(l.unit.hierarchy.atoms.type_symbol.value(l.element))),
}
const residue = {