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* Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * @author Alexander Rose \n */\n\nimport { Mat4 } from '../../../../mol-math/linear-algebra/3d/mat4.ts';\nimport type { StateBuilder, StateObjectSelector } from '../../../../mol-state/index.ts';\nimport type { PluginContext } from '../../../../mol-plugin/context.ts';\nimport { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/representation/spacefill.ts';\nimport { Color } from '../../../../mol-util/color/index.ts';\nimport { utf8Read } from '../../../../mol-io/common/utf8.ts';\nimport { Mat3, Quat, Vec3 } from '../../../../mol-math/linear-algebra.ts';\nimport {\n getGraphicsModeProps,\n getMesoscaleGroupParams,\n type GraphicsMode,\n MesoscaleGroup,\n MesoscaleState,\n} from '../state.ts';\nimport { ColorNames } from '../../../../mol-util/color/names.ts';\nimport {\n ShapeRepresentation3D,\n StructureRepresentation3D,\n} from '../../../../mol-plugin-state/transforms/representation.ts';\nimport { ParseCif, ParsePly, ReadFile } from '../../../../mol-plugin-state/transforms/data.ts';\nimport {\n ModelFromTrajectory,\n ShapeFromPly,\n TrajectoryFromGRO,\n TrajectoryFromMmCif,\n TrajectoryFromMOL,\n TrajectoryFromMOL2,\n TrajectoryFromPDB,\n TrajectoryFromSDF,\n TrajectoryFromXYZ,\n} from '../../../../mol-plugin-state/transforms/model.ts';\nimport { Euler } from '../../../../mol-math/linear-algebra/3d/euler.ts';\nimport { Asset } from '../../../../mol-util/assets.ts';\nimport type { Clip } from '../../../../mol-util/clip.ts';\nimport { StructureFromGeneric } from './model.ts';\nimport { getFileNameInfo } from '../../../../mol-util/file-info.ts';\nimport type { NumberArray } from '../../../../mol-util/type-helpers.ts';\nimport { BaseGeometry } from '../../../../mol-geo/geometry/base.ts';\nimport { ParamDefinition as PD } from '../../../../mol-util/param-definition.ts';\n\nfunction getSpacefillParams(color: Color, sizeFactor: number, graphics: GraphicsMode, clipVariant: Clip.Variant) {\n const gmp = getGraphicsModeProps(graphics === 'custom' ? 'quality' : graphics);\n return {\n type: {\n name: 'spacefill',\n params: {\n ...SpacefillRepresentationProvider.defaultValues,\n ignoreHydrogens: true,\n instanceGranularity: true,\n ignoreLight: true,\n lodLevels: gmp.lodLevels.map((l) => {\n return {\n ...l,\n stride: Math.max(1, Math.round(l.stride / Math.pow(sizeFactor, l.scaleBias))),\n };\n }),\n quality: 'lowest', // avoid 'auto', triggers boundary calc\n sizeFactor,\n clip: {\n variant: clipVariant,\n objects: [],\n },\n clipPrimitive: true,\n approximate: gmp.approximate,\n alphaThickness: gmp.alphaThickness,\n },\n },\n colorTheme: {\n name: 'uniform',\n params: {\n value: color,\n saturation: 0,\n lightness: 0,\n },\n },\n sizeTheme: {\n name: 'physical',\n params: {\n scale: 1,\n },\n },\n };\n}\n\nfunction getPlyShapeParams(color: Color, clipVariant: Clip.Variant) {\n return {\n ...PD.getDefaultValues(BaseGeometry.Params),\n instanceGranularity: true,\n ignoreLight: true,\n clip: {\n variant: clipVariant,\n objects: [],\n },\n quality: 'custom',\n doubleSided: true,\n coloring: {\n name: 'uniform',\n params: { color },\n },\n grouping: {\n name: 'none',\n params: {},\n },\n material: {\n metalness: 0.0,\n roughness: 1.0,\n bumpiness: 1.0,\n },\n bumpAmplitude: 0.1,\n bumpFrequency: 0.1 / 10,\n };\n}\n\nexport async function createGenericHierarchy(plugin: PluginContext, file: Asset.File) {\n const asset = await plugin.runTask(plugin.managers.asset.resolve(file, 'zip'));\n let manifest: GenericManifest;\n // TODO: remove special handling for martini prototype\n if (asset.data['instanced_structure.json']) {\n const d = asset.data['instanced_structure.json'];\n const t = utf8Read(d, 0, d.length);\n const martini = JSON.parse(t) as { model: string; positions: Vec3[]; rotations: Vec3[]; function: string }[];\n console.log(martini);\n manifest = martiniToGeneric(martini);\n } else if (asset.data['manifest.json']) {\n const d = asset.data['manifest.json'];\n const t = utf8Read(d, 0, d.length);\n manifest = JSON.parse(t) as GenericManifest;\n } else {\n throw new Error('no manifest found');\n }\n console.log(manifest);\n\n const state = plugin.state.data;\n const graphicsMode = MesoscaleState.get(plugin).graphics;\n const groupParams = getMesoscaleGroupParams(graphicsMode);\n\n async function addGroup(g: GenericGroup, cell: StateObjectSelector, parent: string) {\n const group = await state.build()\n .to(cell)\n .apply(MesoscaleGroup, {\n ...groupParams,\n index: undefined,\n tag: `${g.root}:${g.id}`,\n label: g.label || g.id,\n description: g.description,\n color: {\n type: 'custom',\n illustrative: false,\n value: ColorNames.white,\n variability: 20,\n shift: 0,\n lightness: 0,\n alpha: 1,\n emissive: 0,\n },\n }, {\n tags: [`group:${g.root}:${g.id}`, g.root === parent ? `${g.root}:` : `${g.root}:${parent}`],\n state: { isCollapsed: true, isHidden: groupParams.hidden },\n })\n .commit();\n\n if (g.children) {\n for (const c of g.children) {\n await addGroup(c, group, g.id);\n }\n }\n }\n\n for (const r of manifest.roots) {\n const root = await state.build()\n .toRoot()\n .apply(MesoscaleGroup, {\n ...groupParams,\n root: true,\n index: -1,\n tag: `${r.id}:`,\n label: r.label || r.id,\n description: r.description,\n color: {\n type: 'custom',\n illustrative: false,\n value: ColorNames.white,\n variability: 20,\n shift: 0,\n lightness: 0,\n alpha: 1,\n emissive: 0,\n },\n }, { tags: `group:${r.id}:`, state: { isCollapsed: false, isHidden: groupParams.hidden } })\n .commit();\n\n if (r.children) {\n for (const c of r.children!) {\n await addGroup(c, root, r.id);\n }\n }\n }\n\n const transformAssets = new Map();\n const getTransformAsset = (file: string) => {\n if (!transformAssets.has(file)) {\n const d = asset.data[file];\n transformAssets.set(file, Asset.File(new File([d], file)));\n }\n return transformAssets.get(file)!;\n };\n\n const getAssetInstances = (instances: GenericInstances): GenericInstances => {\n return {\n positions: {\n data: Array.isArray(instances.positions.data) ? instances.positions.data : {\n file: getTransformAsset(instances.positions.data.file),\n view: instances.positions.data.view,\n },\n type: instances.positions.type,\n },\n rotations: {\n data: Array.isArray(instances.rotations.data) ? instances.rotations.data : {\n file: getTransformAsset(instances.rotations.data.file),\n view: instances.rotations.data.view,\n },\n variant: instances.rotations.variant,\n type: instances.rotations.type,\n },\n };\n };\n\n await state.transaction(async () => {\n try {\n plugin.animationLoop.stop({ noDraw: true });\n let build: StateBuilder.Root | StateBuilder.To = state.build();\n for (const ent of manifest.entities) {\n const d = asset.data[ent.file];\n const info = getFileNameInfo(ent.file);\n const isBinary = ['bcif'].includes(info.ext);\n\n const t = isBinary ? d : utf8Read(d, 0, d.length);\n const file = Asset.File(new File([t], ent.file));\n\n const color = (ent.color)\n ? Color.fromRgb(ent.color[0], ent.color[1], ent.color[2])\n : ColorNames.skyblue;\n\n const sizeFactor = ent.sizeFactor || 1;\n const tags = ent.groups.map(({ id, root }) => `${root}:${id}`);\n const instances = ent.instances && getAssetInstances(ent.instances);\n const description = ent.description;\n\n const label = ent.label || ent.file.split('.')[0];\n build = build\n .toRoot()\n .apply(ReadFile, { file, label, isBinary });\n\n if (\n ['gro', 'cif', 'mmcif', 'mcif', 'bcif', 'pdb', 'ent', 'xyz', 'mol', 'sdf', 'sd', 'mol2'].includes(\n info.ext,\n )\n ) {\n if (['gro'].includes(info.ext)) {\n build = build.apply(TrajectoryFromGRO);\n } else if (['cif', 'mmcif', 'mcif', 'bcif'].includes(info.ext)) {\n build = build.apply(ParseCif).apply(TrajectoryFromMmCif);\n } else if (['pdb', 'ent'].includes(info.ext)) {\n build = build.apply(TrajectoryFromPDB);\n } else if (['xyz'].includes(info.ext)) {\n build = build.apply(TrajectoryFromXYZ);\n } else if (['mol'].includes(info.ext)) {\n build = build.apply(TrajectoryFromMOL);\n } else if (['sdf', 'sd'].includes(info.ext)) {\n build = build.apply(TrajectoryFromSDF);\n } else if (['mol2'].includes(info.ext)) {\n build = build.apply(TrajectoryFromMOL2);\n }\n\n let clipVariant: Clip.Variant = 'pixel';\n if (ent.instances) {\n if (Array.isArray(ent.instances.positions.data)) {\n clipVariant = ent.instances.positions.data.length <= 3 ? 'pixel' : 'instance';\n } else {\n const byteLength = ent.instances.positions.data.view\n ? ent.instances.positions.data.view.byteLength\n : asset.data[ent.instances.positions.data.file].length;\n clipVariant = byteLength <= 3 * 4 ? 'pixel' : 'instance';\n }\n }\n\n build = build\n .apply(ModelFromTrajectory, { modelIndex: 0 })\n .apply(StructureFromGeneric, { instances, label, description })\n .apply(\n StructureRepresentation3D,\n getSpacefillParams(color, sizeFactor, graphicsMode, clipVariant),\n { tags },\n );\n } else if (['ply'].includes(info.ext)) {\n if (['ply'].includes(info.ext)) {\n const transforms = await getTransforms(plugin, instances);\n const clipVariant = transforms.length === 1 ? 'pixel' : 'instance';\n build = build\n .apply(ParsePly)\n .apply(ShapeFromPly, { label, transforms })\n .apply(ShapeRepresentation3D, getPlyShapeParams(color, clipVariant), { tags });\n }\n } else {\n console.warn(`unknown file format '${info.ext}'`);\n }\n }\n await build.commit();\n } catch (e) {\n console.error(e);\n plugin.log.error(e);\n } finally {\n plugin.animationLoop.start();\n }\n }).run();\n\n asset.dispose();\n}\n\n//\n\ntype GenericRoot = {\n id: string;\n label?: string;\n description?: string;\n children: GenericGroup[];\n};\n\ntype GenericGroup = {\n id: string;\n /** reference to `${GenericRoot.id}` */\n root: string;\n label?: string;\n description?: string;\n children?: GenericGroup[];\n};\n\ntype GenericEntity = {\n /**\n * the entity file name\n *\n * the following extensions/formats are supported\n *\n * structures\n * - gro\n * - cif, mmcif, mcif, bcif\n * - pdb, ent\n * - xyz\n * - mol\n * - sdf, sd\n * - mol2\n *\n * meshes\n * - ply\n */\n file: string;\n label?: string;\n description?: string;\n color?: number[];\n groups: {\n /** reference to `${GenericGroup.id}` */\n id: string;\n /** reference to `${GenericGroup.root}` */\n root: string;\n }[];\n /**\n * defaults to a single, untransformed instance\n */\n instances?: GenericInstances;\n /**\n * defaults to 1 (assuming fully atomic structures)\n * for C-alpha only structures set to 2\n * for Martini coarse-grained set to 1.5\n */\n sizeFactor?: number;\n};\n\ntype BinaryData = {\n file: T;\n view?: {\n byteOffset: number;\n byteLength: number;\n };\n};\n\nexport type GenericInstances = {\n /**\n * translation vectors in Angstrom\n * [x0, y0, z0, ..., xn, yn, zn] with n = count - 1\n */\n positions: {\n /**\n * either the data itself or a pointer to binary data\n */\n data: number[] | BinaryData;\n /**\n * how to interpret the data\n * defaults to `{ kind: 'Array', type: 'Float32' }`\n */\n type?: { kind: 'Array'; type: 'Float32' };\n // TODO: maybe worthwhile in the future, mirroring encoders from BinaryCIF\n // | { kind: 'IntegerPackedFixedPoint', byteCount: number, srcSize: number, factor: number, srcType: 'Float32' }\n };\n /**\n * euler angles in XYZ order\n * [x0, y0, z0, ..., xn, yn, zn] with n = count - 1\n *\n * quaternion rotations in XYZW order\n * [x0, y0, z0, w0, ..., xn, yn, zn, wn] with n = count - 1\n *\n * rotation matrices in row-major order\n * [m00_0, m01_0, m02_0, ..., m20_n, m21_n, m22_n] with n = count - 1\n */\n rotations: {\n variant: 'euler' | 'quaternion' | 'matrix';\n /**\n * either the data itself or a pointer to binary data\n */\n data: number[] | BinaryData;\n /**\n * how to interpret the data\n * defaults to `{ kind: 'Array', type: 'Float32' }`\n */\n type?: { kind: 'Array'; type: 'Float32' };\n };\n};\n\ntype GenericFrame = {\n time: number;\n entities: {\n file: string;\n instances: GenericInstances;\n }[];\n};\n\ntype GenericTrajectory = {\n label?: string;\n description?: string;\n frames: GenericFrame[];\n};\n\ntype GenericManifest = {\n label?: string;\n description?: string;\n roots: GenericRoot[];\n entities: GenericEntity[];\n trajectories?: GenericTrajectory[];\n};\n\n//\n\nconst p = Vec3();\nconst q = Quat();\nconst m = Mat3();\nconst e = Euler();\n\nasync function getPositions(plugin: PluginContext, p: GenericInstances['positions']): Promise {\n if (Array.isArray(p.data)) {\n return p.data;\n } else {\n const a = await plugin.runTask(plugin.managers.asset.resolve(p.data.file, 'binary'));\n const o = p.data.view?.byteOffset || 0;\n const l = p.data.view?.byteLength || a.data.byteLength;\n return new Float32Array(a.data.buffer, o + a.data.byteOffset, l / 4);\n }\n}\n\nasync function getRotations(plugin: PluginContext, r: GenericInstances['rotations']): Promise {\n if (Array.isArray(r.data)) {\n return r.data;\n } else {\n const a = await plugin.runTask(plugin.managers.asset.resolve(r.data.file, 'binary'));\n const o = r.data.view?.byteOffset || 0;\n const l = r.data.view?.byteLength || a.data.byteLength;\n return new Float32Array(a.data.buffer, o + a.data.byteOffset, l / 4);\n }\n}\n\nexport async function getTransforms(plugin: PluginContext, instances?: GenericInstances) {\n const transforms: Mat4[] = [];\n if (instances) {\n const positions = await getPositions(plugin, instances.positions);\n const rotations = await getRotations(plugin, instances.rotations);\n\n for (let i = 0, il = positions.length / 3; i < il; ++i) {\n Vec3.fromArray(p, positions, i * 3);\n if (instances.rotations.variant === 'matrix') {\n Mat3.fromArray(m, rotations, i * 9);\n const t = Mat4.fromMat3(Mat4(), m);\n Mat4.setTranslation(t, p);\n transforms.push(t);\n } else if (instances.rotations.variant === 'quaternion') {\n Quat.fromArray(q, rotations, i * 4);\n const t = Mat4.fromQuat(Mat4(), q);\n Mat4.setTranslation(t, p);\n transforms.push(t);\n } else if (instances.rotations.variant === 'euler') {\n Euler.fromArray(e, rotations, i * 3);\n Quat.fromEuler(q, e, 'XYZ');\n const t = Mat4.fromQuat(Mat4(), q);\n Mat4.setTranslation(t, p);\n transforms.push(t);\n }\n }\n } else {\n transforms.push(Mat4.identity());\n }\n\n return transforms;\n}\n\n//\n\ntype MartiniManifest = {\n model: string;\n positions: Vec3[];\n rotations: Vec3[];\n function: string;\n}[];\n\nfunction martiniToGeneric(martini: MartiniManifest): GenericManifest {\n const functionRoot: GenericRoot = {\n id: 'function',\n label: 'Function',\n description: 'Functional classification',\n children: [],\n };\n const entities: GenericEntity[] = [];\n\n const seenGroups = new Set();\n\n const membraneGroup = {\n id: 'membane',\n root: 'function',\n label: 'Membrane',\n children: [] as GenericGroup[],\n };\n functionRoot.children!.push(membraneGroup);\n seenGroups.add(membraneGroup.id);\n\n const lipidsGroup = {\n id: 'lipid',\n root: 'function',\n label: 'Lipid',\n children: [] as GenericGroup[],\n };\n membraneGroup.children!.push(lipidsGroup);\n seenGroups.add(lipidsGroup.id);\n\n const upperGroup = {\n id: 'upper',\n root: 'function',\n label: 'Upper Leaflet',\n };\n lipidsGroup.children!.push(upperGroup);\n seenGroups.add(upperGroup.id);\n\n const lowerGroup = {\n id: 'lower',\n root: 'function',\n label: 'Lower Leaflet',\n };\n lipidsGroup.children!.push(lowerGroup);\n seenGroups.add(lowerGroup.id);\n\n const memprotGroup = {\n id: 'memprot',\n root: 'function',\n label: 'Transmembrane Protein',\n };\n membraneGroup.children!.push(memprotGroup);\n seenGroups.add(memprotGroup.id);\n\n for (const e of martini) {\n const label = e.model.split('.')[0];\n const group = e.function || 'Metabolite';\n\n const positions = {\n data: e.positions.flat().map((x) => Math.round((x * 10) * 100) / 100),\n };\n const rotations = {\n data: e.rotations.flat().map((x) => Math.round(x * 100) / 100),\n variant: 'euler' as const,\n };\n\n if (group.includes('lower leaflet')) {\n entities.push({\n file: e.model,\n label: label.substring(15),\n groups: [{ root: 'function', id: 'lower' }],\n instances: { positions, rotations },\n sizeFactor: 1.5,\n });\n } else if (group.includes('upper leaflet')) {\n entities.push({\n file: e.model,\n label: label.substring(15),\n groups: [{ root: 'function', id: 'upper' }],\n instances: { positions, rotations },\n sizeFactor: 1.5,\n });\n } else if (group.length === 4) {\n entities.push({\n file: e.model,\n label: label.substring(17),\n groups: [{ root: 'function', id: 'memprot' }],\n instances: { positions, rotations },\n sizeFactor: 1.5,\n });\n } else {\n if (!seenGroups.has(group)) {\n functionRoot.children!.push({\n id: group,\n root: 'function',\n label: group,\n });\n seenGroups.add(group);\n }\n entities.push({\n file: e.model,\n label,\n groups: [{ root: 'function', id: group }],\n instances: { positions, rotations },\n sizeFactor: 1.5,\n });\n }\n }\n\n return {\n label: 'Martini',\n description: 'Martini coarse-grained model',\n roots: [functionRoot],\n entities,\n };\n}\n","deleted","label",[168,169,170,171,149],"frontend","mesoscale-explorer","data","generic","permalink","https://www.val.town/x/zcpbx/MolstarViewer/code/frontend/mesoscale-explorer/data/generic/preset.ts","extension","actionData","errors"]