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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 { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif.ts';\nimport type { PluginStateObject } from '../../../../mol-plugin-state/objects.ts';\nimport { StructureRepresentation3D } from '../../../../mol-plugin-state/transforms/representation.ts';\nimport type { PluginContext } from '../../../../mol-plugin/context.ts';\nimport { SpacefillRepresentationProvider } from '../../../../mol-repr/structure/representation/spacefill.ts';\nimport type { StateBuilder, StateObjectRef, StateObjectSelector } from '../../../../mol-state/index.ts';\nimport type { Clip } from '../../../../mol-util/clip.ts';\nimport type { Color } from '../../../../mol-util/color/index.ts';\nimport { ColorNames } from '../../../../mol-util/color/names.ts';\nimport {\n getDistinctBaseColors,\n getDistinctGroupColors,\n getGraphicsModeProps,\n getMesoscaleGroupParams,\n type GraphicsMode,\n MesoscaleGroup,\n MesoscaleState,\n} from '../state.ts';\nimport { MmcifAssembly, MmcifStructure } from './model.ts';\n\nfunction getSpacefillParams(color: Color, scaleFactor: 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: false,\n instanceGranularity: false,\n ignoreLight: true,\n lodLevels: gmp.lodLevels.map((l) => {\n return {\n ...l,\n stride: Math.max(1, Math.round(l.stride / Math.pow(scaleFactor, l.scaleBias))),\n };\n }),\n quality: 'lowest', // avoid 'auto', triggers boundary calc\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 value: 1,\n },\n },\n };\n}\n\nexport async function createMmcifHierarchy(\n plugin: PluginContext,\n trajectory: StateObjectRef,\n) {\n const builder = plugin.builders.structure;\n const state = plugin.state.data;\n\n const model = await builder.createModel(trajectory, { modelIndex: 0 });\n const { data: entities, subtype } = model.data!.entities;\n\n const sd = model.data?.sourceData;\n if (MmcifFormat.is(sd)) {\n const pdbId = sd.data.db.struct.entry_id.value(0);\n MesoscaleState.set(plugin, {\n description: sd.data.db.struct.title.value(0),\n link: pdbId ? `https://www.rcsb.org/structure/${pdbId}` : '',\n });\n }\n\n const spheresAvgRadius = new Map();\n if (model.data!.coarseHierarchy.isDefined) {\n const spheresCount = new Map();\n const spheresEntity_id = model.data!.coarseHierarchy.spheres.entity_id;\n const spheresRadius = model.data!.coarseConformation.spheres.radius;\n for (let i = 0, il = spheresEntity_id.rowCount; i < il; ++i) {\n const entitiId = spheresEntity_id.value(i);\n const radius = spheresRadius[i];\n if (!spheresCount.has(entitiId)) {\n spheresCount.set(entitiId, 1);\n spheresAvgRadius.set(entitiId, radius);\n } else {\n spheresCount.set(entitiId, spheresCount.get(entitiId)! + 1);\n spheresAvgRadius.set(entitiId, spheresAvgRadius.get(entitiId)! + radius);\n }\n }\n spheresAvgRadius.forEach((v, k) => {\n spheresAvgRadius.set(k, v / spheresCount.get(k)!);\n });\n }\n\n const entGroups = new Map();\n const entIds = new Map }>();\n const entColors = new Map();\n\n const graphicsMode = MesoscaleState.get(plugin).graphics;\n const groupParams = getMesoscaleGroupParams(graphicsMode);\n\n const base = await state.build()\n .to(model)\n .apply(MmcifAssembly, { id: '' })\n .commit();\n\n const units = base.data!.units;\n const willBeMerged = units.length > 1 && units.every((u) => u.conformation.operator.isIdentity);\n const clipVariant = willBeMerged ? 'pixel' : 'instance';\n\n const entRoot = await state.build()\n .toRoot()\n .apply(MesoscaleGroup, {\n ...groupParams,\n root: true,\n index: -1,\n tag: 'ent:',\n label: 'entity',\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:ent:', state: { isCollapsed: false, isHidden: groupParams.hidden } })\n .commit();\n\n const getEntityType = (i: number) => {\n if (entities.type.value(i) === 'water') return 'water' as const;\n return subtype.value(i) || 'unknown type';\n };\n\n for (let i = 0; i < entities._rowCount; i++) {\n const t = getEntityType(i);\n if (!entIds.has(t)) {\n entIds.set(t, { idx: entIds.size, members: new Map() });\n }\n const cm = entIds.get(t)!;\n cm.members.set(i, cm.members.size);\n }\n\n //\n\n const baseEntColors = getDistinctBaseColors(entIds.size, 0);\n const entIdEntries = Array.from(entIds.entries());\n for (let i = 0; i < entIdEntries.length; ++i) {\n const [t, m] = entIdEntries[i];\n const groupColors = getDistinctGroupColors(m.members.size, baseEntColors[i], 20, 0);\n entColors.set(t, groupColors);\n }\n\n for (let i = 0; i < entities._rowCount; i++) {\n const t = getEntityType(i);\n if (!entGroups.has(t)) {\n const colorIdx = entIds.get(t)?.idx;\n const color = colorIdx !== undefined ? baseEntColors[colorIdx] : ColorNames.white;\n const group = await state.build()\n .to(entRoot)\n .applyOrUpdateTagged(`group:ent:${t}`, MesoscaleGroup, {\n ...groupParams,\n index: colorIdx,\n tag: `ent:${t}`,\n label: t,\n color: {\n type: 'generate',\n illustrative: false,\n value: color,\n variability: 20,\n shift: 0,\n lightness: 0,\n alpha: 1,\n emissive: 0,\n },\n }, { tags: `ent:`, state: { isCollapsed: true, isHidden: groupParams.hidden } })\n .commit({ revertOnError: true });\n entGroups.set(t, group);\n }\n }\n\n //\n\n await state.transaction(async () => {\n try {\n const dependsOn = [base.ref];\n plugin.animationLoop.stop({ noDraw: true });\n let build: StateBuilder.Root | StateBuilder.To = state.build();\n for (let i = 0; i < entities._rowCount; i++) {\n const t = getEntityType(i);\n const color = entColors.get(t)![entIds.get(t)!.members.get(i)!];\n const scaleFactor = spheresAvgRadius.get(entities.id.value(i)) || 1;\n\n build = build\n .toRoot()\n .apply(MmcifStructure, { structureRef: base.ref, entityId: entities.id.value(i) }, { dependsOn })\n .apply(\n StructureRepresentation3D,\n getSpacefillParams(color, scaleFactor, graphicsMode, clipVariant),\n { tags: [`ent:${t}`] },\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","deleted","label",[168,169,170,171,149],"frontend","mesoscale-explorer","data","mmcif","permalink","https://www.val.town/x/zcpbx/MolstarViewer/code/frontend/mesoscale-explorer/data/mmcif/preset.ts","extension","actionData","errors"]