From 7f0fae3916a94f17d8d11badc9166488f8edab52 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 1 Feb 2019 16:20:30 -0800
Subject: [PATCH] added StructureUnitTransforms, added unitTransforms to
StructureRepresentationState
---
src/mol-geo/geometry/transform-data.ts | 4 +-
.../structure/util/unit-transforms.ts | 46 +++++++++++++++++++
src/mol-repr/shape/representation.ts | 4 +-
.../structure/complex-representation.ts | 16 +++++--
src/mol-repr/structure/complex-visual.ts | 2 +-
.../structure/units-representation.ts | 18 ++++++--
src/mol-repr/structure/units-visual.ts | 2 +-
src/mol-repr/visual.ts | 9 ++--
8 files changed, 82 insertions(+), 19 deletions(-)
create mode 100644 src/mol-model/structure/structure/util/unit-transforms.ts
diff --git a/src/mol-geo/geometry/transform-data.ts b/src/mol-geo/geometry/transform-data.ts
index 87f0b7ac9..de4b2b797 100644
--- a/src/mol-geo/geometry/transform-data.ts
+++ b/src/mol-geo/geometry/transform-data.ts
@@ -85,8 +85,8 @@ export function updateTransformData(transformData: TransformData) {
const extraTransform = transformData.extraTransform.ref.value
for (let i = 0; i < instanceCount; i++) {
const i16 = i * 16
- Mat4.mulOffset(aTransform, transform, extraTransform, i16, i16, i16)
- Mat4.mulOffset(aTransform, aTransform, matrix, i16, i16, 0)
+ Mat4.mulOffset(aTransform, extraTransform, transform, i16, i16, i16)
+ Mat4.mulOffset(aTransform, matrix, aTransform, i16, 0, i16)
}
ValueCell.update(transformData.aTransform, aTransform)
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/util/unit-transforms.ts b/src/mol-model/structure/structure/util/unit-transforms.ts
new file mode 100644
index 000000000..84f2c5d6b
--- /dev/null
+++ b/src/mol-model/structure/structure/util/unit-transforms.ts
@@ -0,0 +1,46 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Structure, Unit } from 'mol-model/structure';
+import { Mat4 } from 'mol-math/linear-algebra';
+import { IntMap } from 'mol-data/int';
+import { fillIdentityTransform } from 'mol-geo/geometry/transform-data';
+
+export class StructureUnitTransforms {
+ private unitTransforms: Float32Array
+ private groupUnitTransforms: Float32Array[] = []
+ /** maps unit.id to offset of transform in unitTransforms */
+ private unitOffsetMap = IntMap.Mutable<number>();
+ private groupIndexMap = IntMap.Mutable<number>();
+
+ constructor(readonly structure: Structure) {
+ this.unitTransforms = new Float32Array(structure.units.length * 16)
+ fillIdentityTransform(this.unitTransforms, structure.units.length)
+ let groupOffset = 0
+ for (let i = 0, il = structure.unitSymmetryGroups.length; i <il; ++i) {
+ const g = structure.unitSymmetryGroups[i]
+ this.groupIndexMap.set(g.hashCode, i)
+ const groupTransforms = this.unitTransforms.subarray(groupOffset, groupOffset + g.units.length * 16)
+ this.groupUnitTransforms.push(groupTransforms)
+ for (let j = 0, jl = g.units.length; j < jl; ++j) {
+ this.unitOffsetMap.set(g.units[j].id, groupOffset + j * 16)
+ }
+ groupOffset += g.units.length * 16
+ }
+ }
+
+ setTransform(matrix: Mat4, unit: Unit) {
+ Mat4.toArray(matrix, this.unitTransforms, this.unitOffsetMap.get(unit.id))
+ }
+
+ getTransform(out: Mat4, unit: Unit) {
+ return Mat4.fromArray(out, this.unitTransforms, this.unitOffsetMap.get(unit.id))
+ }
+
+ getSymmetryGroupTransforms(group: Unit.SymmetryGroup): Float32Array {
+ return this.groupUnitTransforms[this.groupIndexMap.get(group.hashCode)]
+ }
+}
\ No newline at end of file
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index 96faec9f8..d0cec8c69 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/src/mol-repr/shape/representation.ts
@@ -196,9 +196,7 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
if (_renderObject) {
if (state.visible !== undefined) Visual.setVisibility(_renderObject, state.visible)
if (state.pickable !== undefined) Visual.setPickable(_renderObject, state.pickable)
- if (state.transform !== undefined || state.instanceTransforms !== undefined) {
- Visual.setTransform(_renderObject, state.transform, state.instanceTransforms)
- }
+ if (state.transform !== undefined) Visual.setTransform(_renderObject, state.transform)
}
Representation.updateState(_state, state)
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index ba7be4eec..b3ca4d235 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -52,12 +52,20 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
return visual ? visual.mark(loci, action) : false
}
- function setState(state: Partial<Representation.State>) {
- if (state.visible !== undefined && visual) visual.setVisibility(state.visible)
+ function setState(state: Partial<StructureRepresentationState>) {
+ StructureRepresentationStateBuilder.update(_state, state)
+
+ if (state.visible !== undefined && visual) {
+ // hide visual when _unitTransforms is set
+ visual.setVisibility(state.visible && _state.unitTransforms === null)
+ }
if (state.pickable !== undefined && visual) visual.setPickable(state.pickable)
if (state.transform !== undefined && visual) visual.setTransform(state.transform)
-
- Representation.updateState(_state, state)
+ if (state.unitTransforms !== undefined && visual) {
+ // Since ComplexVisuals always renders geometries between units the application of `unitTransforms`
+ // does not make sense. When given it is ignored here and sets the visual's visibility to `false`.
+ visual.setVisibility(_state.visible && state.unitTransforms === null)
+ }
}
function setTheme(theme: Theme) {
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index e32467d1a..833e2126c 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -200,7 +200,7 @@ export function ComplexVisual<G extends Geometry, P extends ComplexParams & Geom
setPickable(pickable: boolean) {
Visual.setPickable(renderObject, pickable)
},
- setTransform(matrix?: Mat4, instanceMatrices?: Float32Array) {
+ setTransform(matrix?: Mat4, instanceMatrices?: Float32Array | null) {
Visual.setTransform(renderObject, matrix, instanceMatrices)
},
destroy() {
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index 5f3484040..ccf0e37f3 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -162,15 +162,23 @@ export function UnitsRepresentation<P extends UnitsParams>(label: string, ctx: R
return changed
}
- function setState(state: Partial<Representation.State>) {
- const { visible, pickable, transform, instanceTransforms } = state
+ function setState(state: Partial<StructureRepresentationState>) {
+ const { visible, pickable, transform, unitTransforms } = state
if (visible !== undefined) visuals.forEach(({ visual }) => visual.setVisibility(visible))
if (pickable !== undefined) visuals.forEach(({ visual }) => visual.setPickable(pickable))
- if (transform !== undefined || instanceTransforms !== undefined) {
- visuals.forEach(({ visual }) => visual.setTransform(transform, instanceTransforms))
+ if (transform !== undefined) visuals.forEach(({ visual }) => visual.setTransform(transform))
+ if (unitTransforms !== undefined) {
+ visuals.forEach(({ visual, group }) => {
+ if (unitTransforms) {
+ // console.log(group.hashCode, unitTransforms.getSymmetryGroupTransforms(group))
+ visual.setTransform(undefined, unitTransforms.getSymmetryGroupTransforms(group))
+ } else {
+ visual.setTransform(undefined, null)
+ }
+ })
}
- Representation.updateState(_state, state)
+ StructureRepresentationStateBuilder.update(_state, state)
}
function setTheme(theme: Theme) {
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 0d16a1029..f7ed2da1b 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -246,7 +246,7 @@ export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry
setPickable(pickable: boolean) {
Visual.setPickable(renderObject, pickable)
},
- setTransform(matrix?: Mat4, instanceMatrices?: Float32Array) {
+ setTransform(matrix?: Mat4, instanceMatrices?: Float32Array | null) {
Visual.setTransform(renderObject, matrix, instanceMatrices)
},
destroy() {
diff --git a/src/mol-repr/visual.ts b/src/mol-repr/visual.ts
index e72cf38f2..7c24baaa9 100644
--- a/src/mol-repr/visual.ts
+++ b/src/mol-repr/visual.ts
@@ -13,7 +13,7 @@ import { ParamDefinition as PD } from 'mol-util/param-definition';
import { WebGLContext } from 'mol-gl/webgl/context';
import { Theme } from 'mol-theme/theme';
import { Mat4 } from 'mol-math/linear-algebra';
-import { updateTransformData } from 'mol-geo/geometry/transform-data';
+import { updateTransformData, fillIdentityTransform } from 'mol-geo/geometry/transform-data';
import { calculateTransformBoundingSphere } from 'mol-gl/renderable/util';
import { ValueCell } from 'mol-util';
@@ -33,7 +33,7 @@ interface Visual<D, P extends PD.Params> {
mark: (loci: Loci, action: MarkerAction) => boolean
setVisibility: (visible: boolean) => void
setPickable: (pickable: boolean) => void
- setTransform: (matrix?: Mat4, instanceMatrices?: Float32Array) => void
+ setTransform: (matrix?: Mat4, instanceMatrices?: Float32Array | null) => void
destroy: () => void
}
namespace Visual {
@@ -45,7 +45,7 @@ namespace Visual {
if (renderObject) renderObject.state.pickable = pickable
}
- export function setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array) {
+ export function setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array | null) {
if (renderObject && (transform || instanceTransforms)) {
const { values } = renderObject
if (transform) {
@@ -55,6 +55,9 @@ namespace Visual {
if (instanceTransforms) {
values.extraTransform.ref.value.set(instanceTransforms)
ValueCell.update(values.extraTransform, values.extraTransform.ref.value)
+ } else if (instanceTransforms === null) {
+ fillIdentityTransform(values.extraTransform.ref.value, values.instanceCount.ref.value)
+ ValueCell.update(values.extraTransform, values.extraTransform.ref.value)
}
updateTransformData(values)
const boundingSphere = calculateTransformBoundingSphere(values.invariantBoundingSphere.ref.value, values.aTransform.ref.value, values.instanceCount.ref.value)
--
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