diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5cef38d6f9c31c589e0dd89fa3ba0abbb53f3c11..833e1ec5731d551bbf4af55bb18f6e7b4f7e689a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,18 +6,28 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+## [v3.25.0] - 2022-11-16
+
+- Fix handling of gzipped assets (reverts #615)
+
+## [v3.24.0] - 2022-11-13
+
- Make `PluginContext.initContainer` checkered canvas background optional
+- Store URL of downloaded assets to detect zip/gzip based on extension (#615)
+- Add optional `operator.key`; can be referenced in `IndexPairBonds`
+- Add overpaint/transparency/substance theme strength to representations
+- Fix viewport color for transparent background
## [v3.23.0] - 2022-10-19
- Add `PluginContext.initContainer/mount/unmount` methods; these should make it easier to reuse a plugin context with both custom and built-in UI
- Add `PluginContext.canvas3dInitialized`
- `createPluginUI` now resolves after the 3d canvas has been initialized
-- Change EM Volume Streaming default from `Whote Structure` to `Auto`
+- Change EM Volume Streaming default from `Whole Structure` to `Auto`
## [v3.22.0] - 2022-10-17
-- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
+- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
## [v3.21.0] - 2022-10-17
diff --git a/package-lock.json b/package-lock.json
index 1f882cb3578af5905d3e9d9c54e0c7fae325e90a..5783bdba84d314108e330689641b73e5e2771926 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 87946d0b46c5fd22acbd8e9c2a8690b840a22760..7af4063623318644926dc43c10d64fcd19244461 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
"name": "molstar",
- "version": "3.23.0",
+ "version": "3.25.0",
"description": "A comprehensive macromolecular library.",
"homepage": "https://github.com/molstar/molstar#readme",
"repository": {
@@ -97,44 +97,44 @@
"license": "MIT",
"devDependencies": {
"@graphql-codegen/add": "^3.2.1",
- "@graphql-codegen/cli": "^2.13.7",
+ "@graphql-codegen/cli": "^2.13.11",
"@graphql-codegen/time": "^3.2.1",
- "@graphql-codegen/typescript": "^2.7.4",
+ "@graphql-codegen/typescript": "^2.8.1",
"@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
- "@graphql-codegen/typescript-graphql-request": "^4.5.6",
- "@graphql-codegen/typescript-operations": "^2.5.4",
+ "@graphql-codegen/typescript-graphql-request": "^4.5.8",
+ "@graphql-codegen/typescript-operations": "^2.5.6",
"@types/cors": "^2.8.12",
- "@types/gl": "^4.1.1",
- "@types/jest": "^29.1.2",
- "@types/react": "^18.0.21",
- "@types/react-dom": "^18.0.6",
- "@typescript-eslint/eslint-plugin": "^5.40.0",
- "@typescript-eslint/parser": "^5.40.0",
+ "@types/gl": "^6.0.1",
+ "@types/jest": "^29.2.2",
+ "@types/react": "^18.0.25",
+ "@types/react-dom": "^18.0.8",
+ "@typescript-eslint/eslint-plugin": "^5.42.1",
+ "@typescript-eslint/parser": "^5.42.1",
"benchmark": "^2.1.4",
- "concurrently": "^7.4.0",
+ "concurrently": "^7.5.0",
"cpx2": "^4.2.0",
"crypto-browserify": "^3.12.0",
- "css-loader": "^6.7.1",
- "eslint": "^8.25.0",
+ "css-loader": "^6.7.2",
+ "eslint": "^8.27.0",
"extra-watch-webpack-plugin": "^1.0.3",
"file-loader": "^6.2.0",
"fs-extra": "^10.1.0",
"graphql": "^16.6.0",
"http-server": "^14.1.1",
- "jest": "^29.2.0",
+ "jest": "^29.3.1",
"mini-css-extract-plugin": "^2.6.1",
"path-browserify": "^1.0.1",
"raw-loader": "^4.0.2",
"react": "^18.2.0",
"react-dom": "^18.2.0",
- "sass": "^1.55.0",
- "sass-loader": "^13.1.0",
- "simple-git": "^3.14.1",
+ "sass": "^1.56.1",
+ "sass-loader": "^13.2.0",
+ "simple-git": "^3.15.0",
"stream-browserify": "^3.0.0",
"style-loader": "^3.3.1",
"ts-jest": "^29.0.3",
"typescript": "^4.8.4",
- "webpack": "^5.74.0",
+ "webpack": "^5.75.0",
"webpack-cli": "^4.10.0"
},
"dependencies": {
@@ -142,7 +142,7 @@
"@types/benchmark": "^2.1.2",
"@types/compression": "1.7.2",
"@types/express": "^4.17.14",
- "@types/node": "^16.11.66",
+ "@types/node": "^16.18.3",
"@types/node-fetch": "^2.6.2",
"@types/swagger-ui-dist": "3.30.1",
"argparse": "^2.0.1",
@@ -151,12 +151,12 @@
"cors": "^2.8.5",
"express": "^4.18.2",
"h264-mp4-encoder": "^1.0.12",
- "immer": "^9.0.15",
+ "immer": "^9.0.16",
"immutable": "^4.1.0",
"node-fetch": "^2.6.7",
"rxjs": "^7.5.7",
- "swagger-ui-dist": "^4.14.3",
- "tslib": "^2.4.0",
+ "swagger-ui-dist": "^4.15.5",
+ "tslib": "^2.4.1",
"util.promisify": "^1.1.1",
"xhr2": "^0.2.1"
},
diff --git a/src/mol-geo/geometry/overpaint-data.ts b/src/mol-geo/geometry/overpaint-data.ts
index 3c90b2bf0d46319461118aa639b47d0fd03a71ad..680a5eafeea9f79e2cbbdc39448f8437896fb7a4 100644
--- a/src/mol-geo/geometry/overpaint-data.ts
+++ b/src/mol-geo/geometry/overpaint-data.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -21,6 +21,7 @@ export type OverpaintData = {
uOverpaintGridDim: ValueCell<Vec3>,
uOverpaintGridTransform: ValueCell<Vec4>,
dOverpaintType: ValueCell<string>,
+ uOverpaintStrength: ValueCell<number>,
}
export function applyOverpaintColor(array: Uint8Array, start: number, end: number, color: Color) {
@@ -54,6 +55,7 @@ export function createOverpaint(count: number, type: OverpaintType, overpaintDat
uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
dOverpaintType: ValueCell.create(type),
+ uOverpaintStrength: ValueCell.create(1),
};
}
}
@@ -74,6 +76,7 @@ export function createEmptyOverpaint(overpaintData?: OverpaintData): OverpaintDa
uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
dOverpaintType: ValueCell.create('groupInstance'),
+ uOverpaintStrength: ValueCell.create(1),
};
}
}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/substance-data.ts b/src/mol-geo/geometry/substance-data.ts
index 554d7e9f40fdcedc413249f5566decb70ad3e56c..d85a724556d636adff0f031e0acddd8fe4a4f4e2 100644
--- a/src/mol-geo/geometry/substance-data.ts
+++ b/src/mol-geo/geometry/substance-data.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
@@ -21,6 +21,7 @@ export type SubstanceData = {
uSubstanceGridDim: ValueCell<Vec3>,
uSubstanceGridTransform: ValueCell<Vec4>,
dSubstanceType: ValueCell<string>,
+ uSubstanceStrength: ValueCell<number>,
}
export function applySubstanceMaterial(array: Uint8Array, start: number, end: number, material: Material) {
@@ -54,6 +55,7 @@ export function createSubstance(count: number, type: SubstanceType, substanceDat
uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
dSubstanceType: ValueCell.create(type),
+ uSubstanceStrength: ValueCell.create(1),
};
}
}
@@ -74,6 +76,7 @@ export function createEmptySubstance(substanceData?: SubstanceData): SubstanceDa
uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
dSubstanceType: ValueCell.create('groupInstance'),
+ uSubstanceStrength: ValueCell.create(1),
};
}
}
\ No newline at end of file
diff --git a/src/mol-geo/geometry/transparency-data.ts b/src/mol-geo/geometry/transparency-data.ts
index a619443a7b99c42efc6db9e6e43f6e6abf6e4f36..942f95c278e6424b012b31fd715a92383d3cf137 100644
--- a/src/mol-geo/geometry/transparency-data.ts
+++ b/src/mol-geo/geometry/transparency-data.ts
@@ -21,6 +21,7 @@ export type TransparencyData = {
uTransparencyGridDim: ValueCell<Vec3>,
uTransparencyGridTransform: ValueCell<Vec4>,
dTransparencyType: ValueCell<string>,
+ uTransparencyStrength: ValueCell<number>,
}
export function applyTransparencyValue(array: Uint8Array, start: number, end: number, value: number) {
@@ -63,6 +64,7 @@ export function createTransparency(count: number, type: TransparencyType, transp
uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
dTransparencyType: ValueCell.create(type),
+ uTransparencyStrength: ValueCell.create(1),
};
}
}
@@ -84,6 +86,7 @@ export function createEmptyTransparency(transparencyData?: TransparencyData): Tr
uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
dTransparencyType: ValueCell.create('groupInstance'),
+ uTransparencyStrength: ValueCell.create(1),
};
}
}
\ No newline at end of file
diff --git a/src/mol-gl/renderable/schema.ts b/src/mol-gl/renderable/schema.ts
index 89b0752120f434019d180a3fab7f4773ab31dd77..23e7cbdb3df7b605f35226b73398fbcc279797c2 100644
--- a/src/mol-gl/renderable/schema.ts
+++ b/src/mol-gl/renderable/schema.ts
@@ -229,6 +229,7 @@ export const OverpaintSchema = {
uOverpaintGridTransform: UniformSpec('v4'),
tOverpaintGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
dOverpaintType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
+ uOverpaintStrength: UniformSpec('f', 'material'),
} as const;
export type OverpaintSchema = typeof OverpaintSchema
export type OverpaintValues = Values<OverpaintSchema>
@@ -242,7 +243,8 @@ export const TransparencySchema = {
uTransparencyGridDim: UniformSpec('v3'),
uTransparencyGridTransform: UniformSpec('v4'),
tTransparencyGrid: TextureSpec('texture', 'alpha', 'ubyte', 'linear'),
- dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance'])
+ dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
+ uTransparencyStrength: UniformSpec('f', 'material'),
} as const;
export type TransparencySchema = typeof TransparencySchema
export type TransparencyValues = Values<TransparencySchema>
@@ -256,6 +258,7 @@ export const SubstanceSchema = {
uSubstanceGridTransform: UniformSpec('v4'),
tSubstanceGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
dSubstanceType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
+ uSubstanceStrength: UniformSpec('f', 'material'),
} as const;
export type SubstanceSchema = typeof SubstanceSchema
export type SubstanceValues = Values<SubstanceSchema>
diff --git a/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts b/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
index 7be1d4ff06dad0026c22c578131295e7ea8f37b7..1d7d510a0fdda00f327b7c40e7ea5a0f6a94001e 100644
--- a/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
+++ b/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
@@ -42,6 +42,7 @@ export const assign_color_varying = `
#else
vOverpaint.rgb = mix(vColor.rgb, vOverpaint.rgb, vOverpaint.a);
#endif
+ vOverpaint *= uOverpaintStrength;
#endif
#ifdef dSubstance
@@ -58,6 +59,7 @@ export const assign_color_varying = `
// pre-mix to avoid artifacts due to empty substance
vSubstance.rgb = mix(vec3(uMetalness, uRoughness, uBumpiness), vSubstance.rgb, vSubstance.a);
+ vSubstance *= uSubstanceStrength;
#endif
#elif defined(dRenderVariant_pick)
#ifdef requiredDrawBuffers
@@ -86,5 +88,6 @@ export const assign_color_varying = `
vec3 tgridPos = (uTransparencyGridTransform.w * (vModelPosition - uTransparencyGridTransform.xyz)) / uTransparencyGridDim;
vTransparency = texture3dFrom2dLinear(tTransparencyGrid, tgridPos, uTransparencyGridDim, uTransparencyTexDim).a;
#endif
+ vTransparency *= uTransparencyStrength;
#endif
`;
\ No newline at end of file
diff --git a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts b/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
index 30a830ad73651982363871cbb3fe8b1fcc20d431..aa9e5dff0b6d14581f917e18d676938398f6ed6d 100644
--- a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
+++ b/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
@@ -39,6 +39,7 @@ uniform float uBumpiness;
uniform vec4 uOverpaintGridTransform;
uniform sampler2D tOverpaintGrid;
#endif
+ uniform float uOverpaintStrength;
#endif
#ifdef dSubstance
@@ -53,6 +54,7 @@ uniform float uBumpiness;
uniform vec4 uSubstanceGridTransform;
uniform sampler2D tSubstanceGrid;
#endif
+ uniform float uSubstanceStrength;
#endif
#elif defined(dRenderVariant_pick)
#if __VERSION__ == 100 || !defined(dVaryingGroup)
@@ -86,5 +88,6 @@ uniform float uBumpiness;
uniform vec4 uTransparencyGridTransform;
uniform sampler2D tTransparencyGrid;
#endif
+ uniform float uTransparencyStrength;
#endif
`;
\ No newline at end of file
diff --git a/src/mol-gl/webgl/compat.ts b/src/mol-gl/webgl/compat.ts
index 8fa3aab180bfd5d0ffdded37f45290bb553c964f..48f6b2b67e73dee7c6e4959d8a1eb827cf352df6 100644
--- a/src/mol-gl/webgl/compat.ts
+++ b/src/mol-gl/webgl/compat.ts
@@ -19,6 +19,9 @@ export function isWebGL2(gl: any): gl is WebGL2RenderingContext {
return typeof WebGL2RenderingContext !== 'undefined' && gl instanceof WebGL2RenderingContext;
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/ANGLE_instanced_arrays/
+ */
export interface COMPAT_instanced_arrays {
drawArraysInstanced(mode: number, first: number, count: number, primcount: number): void;
drawElementsInstanced(mode: number, count: number, type: number, offset: number, primcount: number): void;
@@ -46,6 +49,9 @@ export function getInstancedArrays(gl: GLRenderingContext): COMPAT_instanced_arr
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/OES_standard_derivatives/
+ */
export interface COMPAT_standard_derivatives {
readonly FRAGMENT_SHADER_DERIVATIVE_HINT: number;
}
@@ -60,6 +66,9 @@ export function getStandardDerivatives(gl: GLRenderingContext): COMPAT_standard_
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/OES_element_index_uint/
+ */
export interface COMPAT_element_index_uint {
}
@@ -67,6 +76,9 @@ export function getElementIndexUint(gl: GLRenderingContext): COMPAT_element_inde
return isWebGL2(gl) ? {} : gl.getExtension('OES_element_index_uint');
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/OES_vertex_array_object/
+ */
export interface COMPAT_vertex_array_object {
readonly VERTEX_ARRAY_BINDING: number;
bindVertexArray(arrayObject: WebGLVertexArrayObject | null): void;
@@ -132,6 +144,9 @@ export function getTextureHalfFloatLinear(gl: GLRenderingContext): COMPAT_textur
return gl.getExtension('OES_texture_half_float_linear');
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/EXT_blend_minmax/
+ */
export interface COMPAT_blend_minmax {
readonly MIN: number
readonly MAX: number
@@ -147,6 +162,9 @@ export function getBlendMinMax(gl: GLRenderingContext): COMPAT_blend_minmax | nu
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/EXT_frag_depth/
+ */
export interface COMPAT_frag_depth {
}
@@ -196,6 +214,9 @@ export function getColorBufferHalfFloat(gl: GLRenderingContext): COMPAT_color_bu
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/WEBGL_draw_buffers/
+ */
export interface COMPAT_draw_buffers {
drawBuffers(buffers: number[]): void;
readonly COLOR_ATTACHMENT0: number;
@@ -268,6 +289,73 @@ export function getDrawBuffers(gl: GLRenderingContext): COMPAT_draw_buffers | nu
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/OES_draw_buffers_indexed/
+ */
+export interface COMPAT_draw_buffers_indexed {
+ /**
+ * Enables blending for an individual draw buffer.
+ *
+ * @param target must be BLEND.
+ * @param index is an integer i specifying the draw buffer associated with the symbolic constant DRAW_BUFFERi.
+ */
+ enablei: (target: number, index: number) => void;
+ /**
+ * Disables blending for an individual draw buffer.
+ *
+ * @param target must be BLEND.
+ * @param index is an integer i specifying the draw buffer associated with the symbolic constant DRAW_BUFFERi.
+ */
+ disablei: (buf: number, mode: number) => void;
+ /**
+ * The buf argument is an integer i that indicates that the blend equations should be modified for DRAW_BUFFERi.
+ *
+ * mode accepts the same tokens as mode in blendEquation.
+ */
+ blendEquationi: (target: number, index: number) => void;
+ /**
+ * The buf argument is an integer i that indicates that the blend equations should be modified for DRAW_BUFFERi.
+ *
+ * modeRGB and modeAlpha accept the same tokens as modeRGB and modeAlpha in blendEquationSeparate.
+ */
+ blendEquationSeparatei: (buf: number, modeRGB: number, modeAlpha: number) => void;
+ /**
+ * The buf argument is an integer i that indicates that the blend functions should be modified for DRAW_BUFFERi.
+ *
+ * src and dst accept the same tokens as src and dst in blendFunc.
+ */
+ blendFunci: (buf: number, src: number, dst: number) => void;
+ /**
+ * The buf argument is an integer i that indicates that the blend functions should be modified for DRAW_BUFFERi.
+ *
+ * srcRGB, dstRGB, srcAlpha, and dstAlpha accept the same tokens as srcRGB, dstRGB, srcAlpha, and dstAlpha parameters in blendEquationSeparate.
+ */
+ blendFuncSeparatei: (buf: number, srcRGB: number, dstRGB: number, srcAlpha: number, dstAlpha: number) => void;
+ /**
+ * The buf argument is an integer i that indicates that the write mask should be modified for DRAW_BUFFERi.
+ *
+ * r, g, b, and a indicate whether R, G, B, or A values, respectively, are written or not (a value of TRUE means that the corresponding value is written).
+ */
+ colorMaski: (buf: number, r: boolean, g: boolean, b: boolean, a: boolean) => void;
+}
+
+export function getDrawBuffersIndexed(gl: GLRenderingContext): COMPAT_draw_buffers_indexed | null {
+ const ext = gl.getExtension('OES_draw_buffers_indexed');
+ if (ext === null) return null;
+ return {
+ enablei: ext.enableiOES.bind(ext),
+ disablei: ext.disableiOES.bind(ext),
+ blendEquationi: ext.blendEquationiOES.bind(ext),
+ blendEquationSeparatei: ext.blendEquationSeparateiOES.bind(ext),
+ blendFunci: ext.blendFunciOES.bind(ext),
+ blendFuncSeparatei: ext.blendFuncSeparateiOES.bind(ext),
+ colorMaski: ext.colorMaskiOES.bind(ext),
+ };
+}
+
+/**
+ * See https://registry.khronos.org/webgl/extensions/EXT_shader_texture_lod/
+ */
export interface COMPAT_shader_texture_lod {
}
@@ -275,6 +363,9 @@ export function getShaderTextureLod(gl: GLRenderingContext): COMPAT_shader_textu
return isWebGL2(gl) ? {} : gl.getExtension('EXT_shader_texture_lod');
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/WEBGL_depth_texture/
+ */
export interface COMPAT_depth_texture {
readonly UNSIGNED_INT_24_8: number;
}
@@ -293,6 +384,9 @@ export function getDepthTexture(gl: GLRenderingContext): COMPAT_depth_texture |
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/EXT_sRGB/
+ */
export interface COMPAT_sRGB {
readonly FRAMEBUFFER_ATTACHMENT_COLOR_ENCODING: number;
readonly SRGB8_ALPHA8: number;
@@ -320,6 +414,9 @@ export function getSRGB(gl: GLRenderingContext): COMPAT_sRGB | null {
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/EXT_disjoint_timer_query/ and https://registry.khronos.org/webgl/extensions/EXT_disjoint_timer_query_webgl2/
+ */
export interface COMPAT_disjoint_timer_query {
/** A GLint indicating the number of bits used to hold the query result for the given target. */
QUERY_COUNTER_BITS: number
@@ -401,6 +498,31 @@ export function getDisjointTimerQuery(gl: GLRenderingContext): COMPAT_disjoint_t
}
}
+/**
+ * See https://registry.khronos.org/webgl/extensions/KHR_parallel_shader_compile/
+ */
+export interface COMPAT_parallel_shader_compile {
+ readonly COMPLETION_STATUS: number;
+}
+
+export function getParallelShaderCompile(gl: GLRenderingContext): COMPAT_parallel_shader_compile | null {
+ const ext = gl.getExtension('KHR_parallel_shader_compile');
+ if (ext === null) return null;
+ return {
+ COMPLETION_STATUS: ext.COMPLETION_STATUS_KHR,
+ };
+}
+
+/**
+ * See https://registry.khronos.org/webgl/extensions/OES_fbo_render_mipmap/
+ */
+export interface COMPAT_fboRenderMipmap {
+}
+
+export function getFboRenderMipmap(gl: GLRenderingContext): COMPAT_fboRenderMipmap | null {
+ return isWebGL2(gl) ? {} : gl.getExtension('OES_fbo_render_mipmap');
+}
+
export function getNoNonInstancedActiveAttribs(gl: GLRenderingContext): boolean {
if (!isWebGL2(gl)) return false;
diff --git a/src/mol-gl/webgl/extensions.ts b/src/mol-gl/webgl/extensions.ts
index 0d360170b9a09676ff594f1737ed9d949e806fec..e4a4eaf97ac181d14452ac55e7c72d0f1f268dcf 100644
--- a/src/mol-gl/webgl/extensions.ts
+++ b/src/mol-gl/webgl/extensions.ts
@@ -4,14 +4,14 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import { GLRenderingContext, COMPAT_instanced_arrays, COMPAT_standard_derivatives, COMPAT_vertex_array_object, getInstancedArrays, getStandardDerivatives, COMPAT_element_index_uint, getElementIndexUint, COMPAT_texture_float, getTextureFloat, COMPAT_texture_float_linear, getTextureFloatLinear, COMPAT_blend_minmax, getBlendMinMax, getFragDepth, COMPAT_frag_depth, COMPAT_color_buffer_float, getColorBufferFloat, COMPAT_draw_buffers, getDrawBuffers, getShaderTextureLod, COMPAT_shader_texture_lod, getDepthTexture, COMPAT_depth_texture, COMPAT_sRGB, getSRGB, getTextureHalfFloat, getTextureHalfFloatLinear, COMPAT_texture_half_float, COMPAT_texture_half_float_linear, COMPAT_color_buffer_half_float, getColorBufferHalfFloat, getVertexArrayObject, getDisjointTimerQuery, COMPAT_disjoint_timer_query, getNoNonInstancedActiveAttribs } from './compat';
+import { GLRenderingContext, COMPAT_instanced_arrays, COMPAT_standard_derivatives, COMPAT_vertex_array_object, getInstancedArrays, getStandardDerivatives, COMPAT_element_index_uint, getElementIndexUint, COMPAT_texture_float, getTextureFloat, COMPAT_texture_float_linear, getTextureFloatLinear, COMPAT_blend_minmax, getBlendMinMax, getFragDepth, COMPAT_frag_depth, COMPAT_color_buffer_float, getColorBufferFloat, COMPAT_draw_buffers, getDrawBuffers, getShaderTextureLod, COMPAT_shader_texture_lod, getDepthTexture, COMPAT_depth_texture, COMPAT_sRGB, getSRGB, getTextureHalfFloat, getTextureHalfFloatLinear, COMPAT_texture_half_float, COMPAT_texture_half_float_linear, COMPAT_color_buffer_half_float, getColorBufferHalfFloat, getVertexArrayObject, getDisjointTimerQuery, COMPAT_disjoint_timer_query, getNoNonInstancedActiveAttribs, getDrawBuffersIndexed, COMPAT_draw_buffers_indexed, getParallelShaderCompile, COMPAT_parallel_shader_compile, getFboRenderMipmap, COMPAT_fboRenderMipmap } from './compat';
import { isDebugMode } from '../../mol-util/debug';
export type WebGLExtensions = {
instancedArrays: COMPAT_instanced_arrays
elementIndexUint: COMPAT_element_index_uint
+ standardDerivatives: COMPAT_standard_derivatives
- standardDerivatives: COMPAT_standard_derivatives | null
textureFloat: COMPAT_texture_float | null
textureFloatLinear: COMPAT_texture_float_linear | null
textureHalfFloat: COMPAT_texture_half_float | null
@@ -23,9 +23,12 @@ export type WebGLExtensions = {
colorBufferFloat: COMPAT_color_buffer_float | null
colorBufferHalfFloat: COMPAT_color_buffer_half_float | null
drawBuffers: COMPAT_draw_buffers | null
+ drawBuffersIndexed: COMPAT_draw_buffers_indexed | null
shaderTextureLod: COMPAT_shader_texture_lod | null
sRGB: COMPAT_sRGB | null
disjointTimerQuery: COMPAT_disjoint_timer_query | null
+ parallelShaderCompile: COMPAT_parallel_shader_compile | null
+ fboRenderMipmap: COMPAT_fboRenderMipmap | null
noNonInstancedActiveAttribs: boolean
}
@@ -94,6 +97,10 @@ export function createExtensions(gl: GLRenderingContext): WebGLExtensions {
if (isDebugMode && drawBuffers === null) {
console.log('Could not find support for "draw_buffers"');
}
+ const drawBuffersIndexed = getDrawBuffersIndexed(gl);
+ if (isDebugMode && drawBuffersIndexed === null) {
+ console.log('Could not find support for "draw_buffers_indexed"');
+ }
const shaderTextureLod = getShaderTextureLod(gl);
if (isDebugMode && shaderTextureLod === null) {
console.log('Could not find support for "shader_texture_lod"');
@@ -106,28 +113,39 @@ export function createExtensions(gl: GLRenderingContext): WebGLExtensions {
if (isDebugMode && disjointTimerQuery === null) {
console.log('Could not find support for "disjoint_timer_query"');
}
+ const parallelShaderCompile = getParallelShaderCompile(gl);
+ if (isDebugMode && parallelShaderCompile === null) {
+ console.log('Could not find support for "parallel_shader_compile"');
+ }
+ const fboRenderMipmap = getFboRenderMipmap(gl);
+ if (isDebugMode && fboRenderMipmap === null) {
+ console.log('Could not find support for "fbo_render_mipmap"');
+ }
const noNonInstancedActiveAttribs = getNoNonInstancedActiveAttribs(gl);
return {
instancedArrays,
standardDerivatives,
+ elementIndexUint,
+
textureFloat,
textureFloatLinear,
textureHalfFloat,
textureHalfFloatLinear,
- elementIndexUint,
depthTexture,
-
blendMinMax,
vertexArrayObject,
fragDepth,
colorBufferFloat,
colorBufferHalfFloat,
drawBuffers,
+ drawBuffersIndexed,
shaderTextureLod,
sRGB,
disjointTimerQuery,
+ parallelShaderCompile,
+ fboRenderMipmap,
noNonInstancedActiveAttribs,
};
diff --git a/src/mol-math/geometry/symmetry-operator.ts b/src/mol-math/geometry/symmetry-operator.ts
index 3f848728976d022c1199434f64f17237d9d77db4..cbc2a5eda01f3d26d0f059e3e496d6743f8a4de9 100644
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -1,11 +1,11 @@
/**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { lerp as scalar_lerp } from '../../mol-math/interpolate';
-import { defaults } from '../../mol-util';
import { Mat3 } from '../linear-algebra/3d/mat3';
import { Mat4 } from '../linear-algebra/3d/mat4';
import { Quat } from '../linear-algebra/3d/quat';
@@ -29,11 +29,13 @@ interface SymmetryOperator {
readonly hkl: Vec3,
/** spacegroup symmetry operator index, -1 if not applicable */
readonly spgrOp: number,
+ /** unique (external) key, -1 if not available */
+ readonly key: number,
readonly matrix: Mat4,
- // cache the inverse of the transform
+ /** cache the inverse of the transform */
readonly inverse: Mat4,
- // optimize the identity case
+ /** optimize the identity case */
readonly isIdentity: boolean,
/**
@@ -51,19 +53,20 @@ namespace SymmetryOperator {
export const RotationTranslationEpsilon = 0.005;
- export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number }
+ export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number, key?: number }
export function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator {
- let { assembly, ncsId, hkl, spgrOp } = info || { };
+ let { assembly, ncsId, hkl, spgrOp, key } = info || { };
const _hkl = hkl ? Vec3.clone(hkl) : Vec3();
- spgrOp = defaults(spgrOp, -1);
+ spgrOp = spgrOp ?? -1;
+ key = key ?? -1;
ncsId = ncsId || -1;
const isIdentity = Mat4.isIdentity(matrix);
const suffix = getSuffix(info, isIdentity);
- if (isIdentity) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
+ if (isIdentity) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix, key };
if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) {
console.warn(`Symmetry operator (${name}) should be a composition of rotation and translation.`);
}
- return { name, assembly, matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId, suffix };
+ return { name, assembly, matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp, key, ncsId, suffix };
}
function isSymmetryOperator(x: any): x is SymmetryOperator {
diff --git a/src/mol-model-formats/structure/property/bonds/index-pair.ts b/src/mol-model-formats/structure/property/bonds/index-pair.ts
index c6021eb47183f67a6fee53a8bda06a2183f2e60a..81b3b3759121b290f7d8e706e381784b85764803 100644
--- a/src/mol-model-formats/structure/property/bonds/index-pair.ts
+++ b/src/mol-model-formats/structure/property/bonds/index-pair.ts
@@ -14,6 +14,8 @@ import { ElementIndex } from '../../../../mol-model/structure';
export type IndexPairsProps = {
readonly key: ArrayLike<number>
+ readonly operatorA: ArrayLike<number>
+ readonly operatorB: ArrayLike<number>
readonly order: ArrayLike<number>
readonly distance: ArrayLike<number>
readonly flag: ArrayLike<BondType.Flag>
@@ -24,18 +26,22 @@ export type IndexPairBonds = { bonds: IndexPairs, maxDistance: number }
function getGraph(indexA: ArrayLike<ElementIndex>, indexB: ArrayLike<ElementIndex>, props: Partial<IndexPairsProps>, count: number): IndexPairs {
const builder = new IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
const key = new Int32Array(builder.slotCount);
+ const operatorA = new Array(builder.slotCount);
+ const operatorB = new Array(builder.slotCount);
const order = new Int8Array(builder.slotCount);
const distance = new Array(builder.slotCount);
const flag = new Array(builder.slotCount);
for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
builder.addNextEdge();
builder.assignProperty(key, props.key ? props.key[i] : -1);
+ builder.assignProperty(operatorA, props.operatorA ? props.operatorA[i] : -1);
+ builder.assignProperty(operatorB, props.operatorB ? props.operatorB[i] : -1);
builder.assignProperty(order, props.order ? props.order[i] : 1);
builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
builder.assignProperty(flag, props.flag ? props.flag[i] : BondType.Flag.Covalent);
}
- return builder.createGraph({ key, order, distance, flag });
+ return builder.createGraph({ key, operatorA, operatorB, order, distance, flag });
}
export namespace IndexPairBonds {
@@ -50,6 +56,10 @@ export namespace IndexPairBonds {
indexA: Column<number>,
indexB: Column<number>,
key?: Column<number>,
+ /** Operator key for indexA. Used in bond computation. */
+ operatorA?: Column<number>,
+ /** Operator key for indexB. Used in bond computation. */
+ operatorB?: Column<number>,
order?: Column<number>,
/**
* Useful for bonds in periodic cells. That is, only bonds within the given
@@ -83,12 +93,30 @@ export namespace IndexPairBonds {
const indexA = pairs.indexA.toArray() as ArrayLike<ElementIndex>;
const indexB = pairs.indexB.toArray() as ArrayLike<ElementIndex>;
const key = pairs.key && pairs.key.toArray();
+ const operatorA = pairs.operatorA && pairs.operatorA.toArray();
+ const operatorB = pairs.operatorB && pairs.operatorB.toArray();
const order = pairs.order && pairs.order.toArray();
const distance = pairs.distance && pairs.distance.toArray();
const flag = pairs.flag && pairs.flag.toArray();
return {
- bonds: getGraph(indexA, indexB, { key, order, distance, flag }, count),
+ bonds: getGraph(indexA, indexB, { key, operatorA, operatorB, order, distance, flag }, count),
maxDistance: p.maxDistance
};
}
+
+ /** Like `getEdgeIndex` but taking `edgeProps.operatorA` and `edgeProps.operatorB` into account */
+ export function getEdgeIndexForOperators(bonds: IndexPairs, i: ElementIndex, j: ElementIndex, opI: number, opJ: number): number {
+ let a, b, opA, opB;
+ if (i < j) {
+ a = i; b = j;
+ opA = opI; opB = opJ;
+ } else {
+ a = j; b = i;
+ opA = opJ; opB = opI;
+ }
+ for (let t = bonds.offset[a], _t = bonds.offset[a + 1]; t < _t; t++) {
+ if (bonds.b[t] === b && bonds.edgeProps.operatorA[t] === opA && bonds.edgeProps.operatorB[t] === opB) return t;
+ }
+ return -1;
+ }
}
\ No newline at end of file
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index c51b441a77da6cfffd623877b0734df8e87fc757..7cf7070a41db2e78ce0fbef36e706b873b872b98 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -155,6 +155,6 @@ class QueryContextBondInfo<U extends Unit = Unit> {
}
get length() {
- return StructureElement.Location.distance(this.a, this. b);
+ return StructureElement.Location.distance(this.a, this.b);
}
}
\ No newline at end of file
diff --git a/src/mol-model/structure/structure/properties.ts b/src/mol-model/structure/structure/properties.ts
index 1ee3110f99cea729f8561224c2056042774763ac..71e003b232d9dd679a624d9162f792b683dc993c 100644
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -173,6 +173,7 @@ const unit = {
multiChain: p(l => Unit.Traits.is(l.unit.traits, Unit.Trait.MultiChain)),
object_primitive: p(l => l.unit.objectPrimitive),
operator_name: p(l => l.unit.conformation.operator.name),
+ operator_key: p(l => l.unit.conformation.operator.key),
model_index: p(l => l.unit.model.modelNum),
model_label: p(l => l.unit.model.label),
model_entry_id: p(l => l.unit.model.entryId),
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
index 74f5127df14aabdc3ba3ec71e6ca40ba1c92804c..ab11f3f7b8598817c9c0ed68a1c953c5395e1686 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -71,6 +71,8 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const testDistanceSq = (bRadius + maxRadius) * (bRadius + maxRadius);
builder.startUnitPair(unitA.id, unitB.id);
+ const opKeyA = unitA.conformation.operator.key;
+ const opKeyB = unitB.conformation.operator.key;
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atomsA[_aI];
@@ -80,7 +82,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
if (!props.forceCompute && indexPairs) {
const { maxDistance } = indexPairs;
- const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;
+ const { offset, b, edgeProps: { order, distance, flag, key, operatorA, operatorB } } = indexPairs.bonds;
const srcA = sourceIndex.value(aI);
const aeI = getElementIdx(type_symbolA.value(aI));
@@ -90,6 +92,11 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const _bI = SortedArray.indexOf(unitB.elements, bI) as StructureElement.UnitIndex;
if (_bI < 0) continue;
+ const opA = operatorA[i];
+ const opB = operatorB[i];
+ if ((opA >= 0 && opA !== opKeyA && opA !== opKeyB) ||
+ (opB >= 0 && opB !== opKeyB && opB !== opKeyA)) continue;
+
const beI = getElementIdx(type_symbolA.value(bI));
const d = distance[i];
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 29fd505381b21fd4791c49718f3900b8eeb001cb..71bef526e5b8e7c850c46e1c84f180fe907ea976 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -55,7 +55,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const { type_symbol } = unit.model.atomicHierarchy.atoms;
const atomCount = unit.elements.length;
const { maxDistance } = indexPairs;
- const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;
+ const { offset, b, edgeProps: { order, distance, flag, key, operatorA, operatorB } } = indexPairs.bonds;
const { atomSourceIndex: sourceIndex } = unit.model.atomicHierarchy;
const { invertedIndex } = Model.getInvertedAtomSourceIndex(unit.model);
@@ -66,6 +66,8 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const orders: number[] = [];
const keys: number[] = [];
+ const opKey = unit.conformation.operator.key;
+
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atoms[_aI];
const aeI = getElementIdx(type_symbol.value(aI));
@@ -80,6 +82,10 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const _bI = SortedArray.indexOf(unit.elements, bI) as StructureElement.UnitIndex;
if (_bI < 0) continue;
+ const opA = operatorA[i];
+ const opB = operatorB[i];
+ if ((opA >= 0 && opA !== opKey) || (opB >= 0 && opB !== opKey)) continue;
+
const beI = getElementIdx(type_symbol.value(bI));
const d = distance[i];
diff --git a/src/mol-plugin-state/transforms/representation.ts b/src/mol-plugin-state/transforms/representation.ts
index 32c564437b540369c43419285eb68e579a24a925..a6089db15deb00ce21368622784dfcadcb3731fc 100644
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -43,6 +43,7 @@ import { Box3D } from '../../mol-math/geometry';
import { PlaneParams, PlaneRepresentation } from '../../mol-repr/shape/loci/plane';
import { Substance } from '../../mol-theme/substance';
import { Material } from '../../mol-util/material';
+import { lerp } from '../../mol-math/interpolate';
export { StructureRepresentation3D };
export { ExplodeStructureRepresentation3D };
@@ -56,6 +57,7 @@ export { SubstanceStructureRepresentation3DFromScript };
export { SubstanceStructureRepresentation3DFromBundle };
export { ClippingStructureRepresentation3DFromScript };
export { ClippingStructureRepresentation3DFromBundle };
+export { ThemeStrengthRepresentation3D };
export { VolumeRepresentation3D };
type StructureRepresentation3D = typeof StructureRepresentation3D
@@ -745,6 +747,62 @@ const ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn
}
});
+type ThemeStrengthRepresentation3D = typeof ThemeStrengthRepresentation3D
+const ThemeStrengthRepresentation3D = PluginStateTransform.BuiltIn({
+ name: 'theme-strength-representation-3d',
+ display: 'Theme Strength 3D Representation',
+ from: SO.Molecule.Structure.Representation3D,
+ to: SO.Molecule.Structure.Representation3DState,
+ params: () => ({
+ overpaintStrength: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+ transparencyStrength: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+ substanceStrength: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
+ })
+})({
+ canAutoUpdate() {
+ return true;
+ },
+ apply({ a, params }) {
+ return new SO.Molecule.Structure.Representation3DState({
+ state: {
+ themeStrength: {
+ overpaint: params.overpaintStrength,
+ transparency: params.transparencyStrength,
+ substance: params.substanceStrength
+ },
+ },
+ initialState: {
+ themeStrength: { overpaint: 1, transparency: 1, substance: 1 },
+ },
+ info: { },
+ repr: a.data.repr
+ }, { label: 'Theme Strength', description: `${params.overpaintStrength.toFixed(2)}, ${params.transparencyStrength.toFixed(2)}, ${params.substanceStrength.toFixed(2)}` });
+ },
+ update({ a, b, newParams, oldParams }) {
+ if (newParams.overpaintStrength === b.data.state.themeStrength?.overpaint &&
+ newParams.transparencyStrength === b.data.state.themeStrength?.transparency &&
+ newParams.substanceStrength === b.data.state.themeStrength?.substance
+ ) return StateTransformer.UpdateResult.Unchanged;
+
+ b.data.state.themeStrength = {
+ overpaint: newParams.overpaintStrength,
+ transparency: newParams.transparencyStrength,
+ substance: newParams.substanceStrength,
+ };
+ b.data.repr = a.data.repr;
+ b.label = 'Theme Strength';
+ b.description = `${newParams.overpaintStrength.toFixed(2)}, ${newParams.transparencyStrength.toFixed(2)}, ${newParams.substanceStrength.toFixed(2)}`;
+ return StateTransformer.UpdateResult.Updated;
+ },
+ interpolate(src, tar, t) {
+ return {
+ overpaintStrength: lerp(src.overpaintStrength, tar.overpaintStrength, t),
+ transparencyStrength: lerp(src.transparencyStrength, tar.transparencyStrength, t),
+ substanceStrength: lerp(src.substanceStrength, tar.substanceStrength, t),
+ };
+ }
+});
+
//
export namespace VolumeRepresentation3DHelpers {
diff --git a/src/mol-plugin-ui/skin/base/components/viewport.scss b/src/mol-plugin-ui/skin/base/components/viewport.scss
index 2ca2872ace8a899d7e3eaf86ddbdbca392a27935..b5e2098c53ff67916f8295a43a0dee463b35de26 100644
--- a/src/mol-plugin-ui/skin/base/components/viewport.scss
+++ b/src/mol-plugin-ui/skin/base/components/viewport.scss
@@ -4,7 +4,7 @@
top: 0;
right: 0;
bottom: 0;
- background: black;
+ background: $default-background;
.msp-btn-link {
background: rgba(0,0,0,0.2);
diff --git a/src/mol-plugin/spec.ts b/src/mol-plugin/spec.ts
index 48f3c3fabfcd02942150caf224fafe0b696e3e4b..e0792376d11cca76f6c624226bb77047a368f62a 100644
--- a/src/mol-plugin/spec.ts
+++ b/src/mol-plugin/spec.ts
@@ -104,6 +104,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
PluginSpec.Action(StateTransforms.Representation.ClippingStructureRepresentation3DFromScript),
PluginSpec.Action(StateTransforms.Representation.SubstanceStructureRepresentation3DFromScript),
+ PluginSpec.Action(StateTransforms.Representation.ThemeStrengthRepresentation3D),
PluginSpec.Action(AssignColorVolume),
PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
diff --git a/src/mol-repr/representation.ts b/src/mol-repr/representation.ts
index 17da5156448dd9e75ff88ae586a1106c9386825d..33b452e766d5d80467d38d2582cfdcbce22f9462 100644
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/representation.ts
@@ -191,6 +191,8 @@ namespace Representation {
substance: Substance
/** Bit mask of per group clipping applied to the representation's renderobjects */
clipping: Clipping
+ /** Strength of the representations overpaint, transparency, substance*/
+ themeStrength: { overpaint: number, transparency: number, substance: number }
/** Controls if the representation's renderobjects are synced automatically with GPU or not */
syncManually: boolean
/** A transformation applied to the representation's renderobjects */
@@ -199,7 +201,20 @@ namespace Representation {
markerActions: MarkerActions
}
export function createState(): State {
- return { visible: true, alphaFactor: 1, pickable: true, colorOnly: false, syncManually: false, transform: Mat4.identity(), overpaint: Overpaint.Empty, transparency: Transparency.Empty, substance: Substance.Empty, clipping: Clipping.Empty, markerActions: MarkerActions.All };
+ return {
+ visible: true,
+ alphaFactor: 1,
+ pickable: true,
+ colorOnly: false,
+ syncManually: false,
+ transform: Mat4.identity(),
+ overpaint: Overpaint.Empty,
+ transparency: Transparency.Empty,
+ substance: Substance.Empty,
+ clipping: Clipping.Empty,
+ themeStrength: { overpaint: 1, transparency: 1, substance: 1 },
+ markerActions: MarkerActions.All
+ };
}
export function updateState(state: State, update: Partial<State>) {
if (update.visible !== undefined) state.visible = update.visible;
@@ -210,6 +225,7 @@ namespace Representation {
if (update.transparency !== undefined) state.transparency = update.transparency;
if (update.substance !== undefined) state.substance = update.substance;
if (update.clipping !== undefined) state.clipping = update.clipping;
+ if (update.themeStrength !== undefined) state.themeStrength = update.themeStrength;
if (update.syncManually !== undefined) state.syncManually = update.syncManually;
if (update.transform !== undefined) Mat4.copy(state.transform, update.transform);
if (update.markerActions !== undefined) state.markerActions = update.markerActions;
@@ -432,6 +448,7 @@ namespace Representation {
if (state.substance !== undefined) {
// TODO
}
+ if (state.themeStrength !== undefined) Visual.setThemeStrength(renderObject, state.themeStrength);
if (state.transform !== undefined) Visual.setTransform(renderObject, state.transform);
Representation.updateState(currentState, state);
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index a50d04ae0c47bda3e592bfd93e2aa2b25dcc4de3..e959f918968aaaed200bac13a026db2b64dc6b1d 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -127,6 +127,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
const remappedClipping = Clipping.remap(state.clipping, _structure);
visual.setClipping(remappedClipping);
}
+ if (state.themeStrength !== undefined && visual) visual.setThemeStrength(state.themeStrength);
if (state.transform !== undefined && visual) visual.setTransform(state.transform);
if (state.unitTransforms !== undefined && visual) {
// Since ComplexVisuals always renders geometries between units, the application
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 71f5314e921092800bf3a916e11bf2f480776687..526c5be397c93d512b344424b5015d7c8779a68c 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -299,6 +299,9 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
setClipping(clipping: Clipping) {
Visual.setClipping(renderObject, clipping, lociApply, true);
},
+ setThemeStrength(strength: { overpaint: number, transparency: number, substance: number }) {
+ Visual.setThemeStrength(renderObject, strength);
+ },
destroy() {
dispose?.(geometry);
if (renderObject) {
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index d7a2b6e0634e71156342aff34217ec67b23ac55b..b713ede00253e42f34151a19bd149f1157fd7e06 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -222,7 +222,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
}
function setVisualState(visual: UnitsVisual<P>, group: Unit.SymmetryGroup, state: Partial<StructureRepresentationState>) {
- const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, transform, unitTransforms } = state;
+ const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, themeStrength, transform, unitTransforms } = state;
if (visible !== undefined) visual.setVisibility(visible);
if (alphaFactor !== undefined) visual.setAlphaFactor(alphaFactor);
@@ -231,6 +231,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
if (transparency !== undefined) visual.setTransparency(transparency, webgl);
if (substance !== undefined) visual.setSubstance(substance, webgl);
if (clipping !== undefined) visual.setClipping(clipping);
+ if (themeStrength !== undefined) visual.setThemeStrength(themeStrength);
if (transform !== undefined) visual.setTransform(transform);
if (unitTransforms !== undefined) {
if (unitTransforms) {
@@ -243,7 +244,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
}
function setState(state: Partial<StructureRepresentationState>) {
- const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, transform, unitTransforms, syncManually, markerActions } = state;
+ const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, themeStrength, transform, unitTransforms, syncManually, markerActions } = state;
const newState: Partial<StructureRepresentationState> = {};
if (visible !== _state.visible) newState.visible = visible;
@@ -261,6 +262,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
if (clipping !== undefined && _structure) {
newState.clipping = Clipping.remap(clipping, _structure);
}
+ if (themeStrength !== undefined) newState.themeStrength = themeStrength;
if (transform !== undefined && !Mat4.areEqual(transform, _state.transform, EPSILON)) {
newState.transform = transform;
}
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 8c0e3a1d8b7e25488410100f02594b508ed4367a..cd5e898e7501affaa640e1b083bf543ebc30cc23 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -381,6 +381,9 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
setClipping(clipping: Clipping) {
Visual.setClipping(renderObject, clipping, lociApply, true);
},
+ setThemeStrength(strength: { overpaint: number, transparency: number, substance: number }) {
+ Visual.setThemeStrength(renderObject, strength);
+ },
destroy() {
dispose?.(geometry);
if (renderObject) {
diff --git a/src/mol-repr/visual.ts b/src/mol-repr/visual.ts
index 924e0fb81fa141c54b0b3e001f4b4fafeb02a3c2..4a3f41ebb38bef03cf66c8ec2d0f4ae026f0ba8b 100644
--- a/src/mol-repr/visual.ts
+++ b/src/mol-repr/visual.ts
@@ -55,6 +55,7 @@ interface Visual<D, P extends PD.Params> {
setTransparency: (transparency: Transparency, webgl?: WebGLContext) => void
setSubstance: (substance: Substance, webgl?: WebGLContext) => void
setClipping: (clipping: Clipping) => void
+ setThemeStrength: (strength: { overpaint: number, transparency: number, substance: number }) => void
destroy: () => void
mustRecreate?: (data: D, props: PD.Values<P>, webgl?: WebGLContext) => boolean
}
@@ -349,6 +350,14 @@ namespace Visual {
ValueCell.updateIfChanged(dClipping, clipping.layers.length > 0);
}
+ export function setThemeStrength(renderObject: GraphicsRenderObject | undefined, strength: { overpaint: number, transparency: number, substance: number }) {
+ if (renderObject) {
+ ValueCell.updateIfChanged(renderObject.values.uOverpaintStrength, strength.overpaint);
+ ValueCell.updateIfChanged(renderObject.values.uTransparencyStrength, strength.transparency);
+ ValueCell.updateIfChanged(renderObject.values.uSubstanceStrength, strength.substance);
+ }
+ }
+
export function setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array | null) {
if (!renderObject || (!transform && !instanceTransforms)) return;
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index c6de383731b5f36a097cd321d19660c7e4502651..aa2f336d6208bc5524dff06f74278084c9cdf983 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -252,6 +252,9 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
setClipping(clipping: Clipping) {
return Visual.setClipping(renderObject, clipping, lociApply, true);
},
+ setThemeStrength(strength: { overpaint: number, transparency: number, substance: number }) {
+ Visual.setThemeStrength(renderObject, strength);
+ },
destroy() {
dispose?.(geometry);
if (renderObject) {
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 209da4376e81c413caada96b2a2b544146e3de48..e7125a35814c22831970ee0571f198158e9df89a 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -273,6 +273,7 @@ const atomProperty = {
sourceIndex: atomProp(Type.Num, 'Index of the atom/element in the input file.'),
operatorName: atomProp(Type.Str, 'Name of the symmetry operator applied to this element.'),
+ operatorKey: atomProp(Type.Num, 'Key of the symmetry operator applied to this element.'),
modelIndex: atomProp(Type.Num, 'Index of the model in the input file.'),
modelLabel: atomProp(Type.Str, 'Label/header of the model in the input file.')
},
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index deab2d4baa0c10ab7fc3641b258ef8a1c7a0cce2..a87b23c7e6509c4324585904548578e9f8f10dd6 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -299,6 +299,7 @@ const symbols = [
D(MolScript.structureQuery.atomProperty.core.z, atomProp(StructureProperties.atom.z)),
D(MolScript.structureQuery.atomProperty.core.sourceIndex, atomProp(StructureProperties.atom.sourceIndex)),
D(MolScript.structureQuery.atomProperty.core.operatorName, atomProp(StructureProperties.unit.operator_name)),
+ D(MolScript.structureQuery.atomProperty.core.operatorKey, atomProp(StructureProperties.unit.operator_key)),
D(MolScript.structureQuery.atomProperty.core.modelIndex, atomProp(StructureProperties.unit.model_index)),
D(MolScript.structureQuery.atomProperty.core.modelLabel, atomProp(StructureProperties.unit.model_label)),
D(MolScript.structureQuery.atomProperty.core.atomKey, (ctx, xs) => {
diff --git a/src/mol-script/script/mol-script/symbols.ts b/src/mol-script/script/mol-script/symbols.ts
index c4bd1cfe251bba567bfdd89eabc319cea26ece99..feb891928cd41da4977ee58ffee8132a15ed0601 100644
--- a/src/mol-script/script/mol-script/symbols.ts
+++ b/src/mol-script/script/mol-script/symbols.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 Mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 Mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { UniqueArray } from '../../../mol-data/generic';
@@ -205,6 +206,7 @@ export const SymbolTable = [
Alias(MolScript.structureQuery.atomProperty.core.z, 'atom.z'),
Alias(MolScript.structureQuery.atomProperty.core.sourceIndex, 'atom.src-index'),
Alias(MolScript.structureQuery.atomProperty.core.operatorName, 'atom.op-name'),
+ Alias(MolScript.structureQuery.atomProperty.core.operatorKey, 'atom.op-key'),
Alias(MolScript.structureQuery.atomProperty.core.modelIndex, 'atom.model-index'),
Alias(MolScript.structureQuery.atomProperty.core.modelLabel, 'atom.model-label'),
Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
@@ -253,6 +255,7 @@ export const SymbolTable = [
'Bond Properties',
Alias(MolScript.structureQuery.bondProperty.order, 'bond.order'),
Alias(MolScript.structureQuery.bondProperty.length, 'bond.length'),
+ Alias(MolScript.structureQuery.bondProperty.key, 'bond.key'),
Alias(MolScript.structureQuery.bondProperty.atomA, 'bond.atom-a'),
Alias(MolScript.structureQuery.bondProperty.atomB, 'bond.atom-b'),
Macro(MSymbol('bond.is', Arguments.List(StructureQueryTypes.BondFlag), Type.Bool,