[{"_1":2,"_175":-5,"_176":-5},"loaderData",{"_3":4,"_91":92},"root",{"_5":6,"_34":35,"_64":65},"ctx",{"_7":8,"_23":-5,"_24":25,"_26":27,"_28":20,"_29":20,"_30":20,"_31":32,"_33":20},"auth",{"_9":-5,"_10":-5,"_11":-5,"_12":-5,"_13":-5,"_14":-5,"_15":-5,"_16":-5,"_17":-5,"_18":-5,"_19":20,"_21":22},"sessionClaims","sessionId","sessionStatus","userId","actor","orgId","orgRole","orgSlug","orgPermissions","factorVerificationAge","isAuthenticated",false,"tokenType","session_token","user","preferencesKeybindings","default","preferencesTheme","light","preferencesFixers","preferencesCopilot","preferencesSelectionAi","notificationCount",0,"flagDenols","ENV",{"_36":37,"_38":39,"_40":41,"_42":43,"_44":45,"_46":47,"_48":49,"_50":51,"_52":53,"_54":55,"_56":57,"_58":59,"_60":61,"_62":63},"REACT_APP_SENTRY_DSN","https://586020d86f05489db63a554690acf1e9@o1398359.ingest.sentry.io/6724499","VAL_RUNTIME_NAME","prod","RENDER_GIT_COMMIT","7f439e1a7c8854d0a3e79c4918a7c5fa89d43a5d","RENDER_GIT_BRANCH","main","CLERK_PUBLISHABLE_KEY","pk_live_Y2xlcmsudmFsLnRvd24k","POSTHOG_API_TOKEN","phc_nmoyuAkStEZuUp69rYlg1DZgrIt19Gx0Y4Hwf8tGgJP","POSTHOG_API_HOST","https://wart.val.town","WEB_API_TEMPLATE","https://{val}.web.val.run","APP_URL","https://www.val.town","MODULE_URL","https://esm.town","VANITY_WEB_API_TEMPLATE","https://{label}.val.run/","DENOLS_URL","https://lsp.val.town","NODE_ENV","production","API_URL","https://api.val.town","clerkState",{"_66":67},"__internal_clerk_state",{"_68":69,"_70":45,"_71":72,"_73":72,"_74":20,"_75":72,"_76":72,"_77":72,"_78":72,"_79":80,"_89":20,"_90":20},"__clerk_ssr_state",{"_21":22,"_9":-5,"_10":-5,"_11":-5,"_12":-5,"_13":-5,"_14":-5,"_15":-5,"_16":-5,"_17":-5,"_18":-5,"_19":20},"__publishableKey","__proxyUrl","","__domain","__isSatellite","__signInUrl","__signUpUrl","__afterSignInUrl","__afterSignUpUrl","__clerk_debug",{"_81":20,"_19":20,"_82":72,"_83":84,"_85":72,"_86":45,"_87":20,"_88":72},"isSignedIn","proxyUrl","reason","session-token-and-uat-missing","message","publishableKey","isSatellite","domain","__telemetryDisabled","__telemetryDebug","routes/embed.x.$handle.$name.$",{"_93":94,"_95":96,"_97":98,"_99":100,"_146":147,"_172":173,"_174":-5},"handle","zcpbx","name","MolstarViewer","path","frontend/mesoscale-explorer/data/cellpack/preset.ts","project",{"_101":102,"_95":96,"_103":104,"_105":-5,"_106":20,"_107":108,"_109":-5,"_110":-5,"_12":111,"_112":-5,"_113":20,"_114":-5,"_115":32,"_14":116,"_117":118,"_119":118,"_120":121,"_122":121,"_123":121,"_124":118,"_125":118,"_23":126,"_129":130,"_132":133,"_145":20},"id","4a052a4e-a843-11f0-a0f8-0224a6c84d84","createdAt",["D",1760366740657],"deletedAt","legacyEnvVars","privacy","public","description","imageUrl","3da541a0-40a4-11f0-a359-812261733f73","pinnedFileId","pinPreview","screenshotVersion","likeCount","0942d0eb-af3b-49c4-9f38-74e044019762","userPerm","r","valPerm","blobPerm","rw","emailPerm","sqlitePerm","projectPerm","telemetryPerm",{"_93":94,"_127":128},"profileImageUrl","https://img.clerk.com/eyJ0eXBlIjoicHJveHkiLCJzcmMiOiJodHRwczovL2ltYWdlcy5jbGVyay5kZXYvb2F1dGhfZ2l0aHViL2ltZ18yeTBaUXNBY2E1VVg5MFllM3dISTM5aHV4akUifQ","org",{"_93":94,"_131":128,"_12":111},"avatar","branch",{"_134":135,"_95":43,"_101":136,"_137":102,"_138":-5,"_139":-5,"_140":-5,"_141":-5,"_142":-5,"_143":96,"_144":94},"version",661,"4a057be8-a843-11f0-a0f8-0224a6c84d84","projectId","forkedBranchId","forkedBranchVersion","forkedProjectPrivacy","forkedProjectId","forkedProjectOrgId","projectName","userHandle","isOwned","file",{"_101":148,"_95":149,"_150":151,"_152":153,"_154":136,"_155":156,"_157":158,"_103":159,"_134":160,"_161":162,"_163":164,"_165":20,"_166":-5,"_97":167},"2c054aee-bdcc-11f0-ba0c-42dde27851f2","preset.ts","fileId","c7ae4390-bdb5-11f0-acd9-42dde27851f2","parentId","2b2b0be0-bdcc-11f0-b9bc-42dde27851f2","branchId","branchVersion",569,"latest",true,["D",1762734505155],5,"fileType","script","content","/**\n * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.\n *\n * @author Alexander Rose \n * @author Ludovic Autin \n */\n\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 { 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 { CellpackAssembly, CellpackStructure } from './model.ts';\n\nfunction getSpacefillParams(color: Color, sizeFactor: number, graphics: GraphicsMode, merge?: boolean) {\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: true,\n ignoreLight: true,\n lodLevels: gmp.lodLevels,\n quality: 'lowest', // avoid 'auto', triggers boundary calc\n sizeFactor,\n clip: {\n variant: merge ? 'pixel' : 'instance',\n objects: [],\n },\n clipPrimitive: true,\n approximate: gmp.approximate,\n alphaThickness: gmp.alphaThickness,\n visuals: [merge ? 'structure-element-sphere' : 'element-sphere'],\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\nfunction getSizeFactor(name: string): number {\n switch (name) {\n case 'dLDL':\n return 2.5;\n case 'iLDL':\n return 5;\n case 'NP_CA':\n case 'POL_CA':\n case 'FactorH1':\n case 'iIgM_Antibody_5mer':\n // case 'MG_271_272_273_274_192MER': // has a coarse and an atomic part\n return 2;\n default:\n return 1;\n }\n}\n\nexport async function createCellpackHierarchy(\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 entities = model.data!.entities.data;\n\n const compGroups = new Map();\n const compIds = new Map }>();\n const compColors = new Map();\n\n const funcGroups = new Map();\n const funcIds = new Map();\n const funcColors = 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(CellpackAssembly, { id: '' })\n .commit();\n\n const compRoot = await state.build()\n .toRoot()\n .apply(MesoscaleGroup, {\n ...groupParams,\n root: true,\n index: -1,\n tag: 'comp:',\n label: 'compartment',\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:comp:', state: { isCollapsed: false, isHidden: groupParams.hidden } })\n .commit();\n\n const funcRoot = await state.build()\n .toRoot()\n .apply(MesoscaleGroup, {\n ...groupParams,\n root: true,\n index: -1,\n tag: 'func:',\n label: 'function',\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:func:', state: { isCollapsed: false, isHidden: groupParams.hidden } })\n .commit();\n\n if (entities._rowCount > 1) {\n for (let i = 0; i < entities._rowCount; i++) {\n const description = entities.pdbx_description.value(i)[0] || 'unknown compartment';\n const d = description.split('.');\n const n = d.slice(0, -1).join('.');\n const l = d.at(-1)!;\n if (!compIds.has(n)) {\n compIds.set(n, { idx: compIds.size, members: new Map() });\n }\n const cm = compIds.get(n)!;\n cm.members.set(l, cm.members.size);\n\n const f = entities.details.value(i) || 'unknown function';\n if (!funcIds.has(f)) {\n funcIds.set(f, { idx: funcIds.size, size: 0 });\n }\n funcIds.get(f)!.size += 1;\n }\n\n //\n\n const baseCompColors = getDistinctBaseColors(compIds.size, 0);\n const compIdEntries = Array.from(compIds.entries());\n for (let i = 0; i < compIdEntries.length; ++i) {\n const [n, m] = compIdEntries[i];\n const groupColors = getDistinctGroupColors(m.members.size, baseCompColors[i], 20, 0);\n compColors.set(n, groupColors);\n }\n\n //\n\n const baseFuncColors = getDistinctBaseColors(funcIds.size, 0);\n const funcIdEntries = Array.from(funcIds.entries());\n for (let i = 0; i < funcIdEntries.length; ++i) {\n const [n, m] = funcIdEntries[i];\n const groupColors = getDistinctGroupColors(m.size, baseFuncColors[i], 20, 0);\n funcColors.set(n, groupColors);\n }\n\n //\n\n for (let i = 0; i < entities._rowCount; i++) {\n const description = entities.pdbx_description.value(i)[0] || 'unknown compartment';\n const nodes = description.split('.');\n for (let j = 0, jl = nodes.length - 1; j < jl; ++j) {\n const n = nodes.slice(0, j + 1).join('.');\n const p = nodes.slice(0, j).join('.');\n if (!compGroups.has(n)) {\n const colorIdx = compIds.get(n)?.idx;\n const color = colorIdx !== undefined ? baseCompColors[colorIdx] : ColorNames.white;\n const label = nodes[j];\n const parent = compGroups.get(p) ?? compRoot;\n parent.cell!.state.isCollapsed = false;\n const group = await state.build()\n .to(parent)\n .apply(MesoscaleGroup, {\n ...groupParams,\n root: parent === compRoot,\n index: colorIdx,\n tag: `comp:${n}`,\n label,\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 }, {\n tags: [`group:comp:${n}`, `comp:${p}`],\n state: { isCollapsed: true, isHidden: groupParams.hidden },\n })\n .commit({ revertOnError: true });\n compGroups.set(n, group);\n }\n }\n\n const f = entities.details.value(i) || 'unknown function';\n if (!funcGroups.has(f)) {\n const colorIdx = funcIds.get(f)?.idx;\n const color = colorIdx !== undefined ? baseFuncColors[colorIdx] : ColorNames.white;\n const group = await state.build()\n .to(funcRoot)\n .apply(MesoscaleGroup, {\n ...groupParams,\n index: colorIdx,\n tag: `func:${f}`,\n label: f,\n color: {\n type: 'custom',\n illustrative: false,\n value: color,\n variability: 20,\n shift: 0,\n lightness: 0,\n alpha: 1,\n emissive: 0,\n },\n }, {\n tags: [`group:func:${f}`, 'func:'],\n state: { isCollapsed: true, isHidden: groupParams.hidden },\n })\n .commit({ revertOnError: true });\n funcGroups.set(f, 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 description = entities.pdbx_description.value(i)[0] || 'model';\n const d = description.split('.');\n const n = d.slice(0, -1).join('.');\n const l = d.at(-1)!;\n\n const f = entities.details.value(i) || 'unknown function';\n\n const color = compColors.get(n)![compIds.get(n)!.members.get(l)!];\n const sizeFactor = getSizeFactor(l);\n\n build = build\n .toRoot()\n .apply(CellpackStructure, { structureRef: base.ref, entityId: entities.id.value(i) }, {\n dependsOn,\n })\n .apply(StructureRepresentation3D, getSpacefillParams(color, sizeFactor, graphicsMode), {\n tags: [`comp:${n}`, `func:${f}`],\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 } else {\n const dependsOn = [base.ref];\n\n const merge = base.data &&\n base.data.model.entities.data._rowCount === 1 &&\n base.data.unitSymmetryGroups.length > 100 &&\n base.data.unitSymmetryGroups.some((usg) => usg.units.length > 1);\n\n await state.build()\n .toRoot()\n .apply(CellpackStructure, { structureRef: base.ref, entityId: entities.id.value(0) }, { dependsOn })\n .apply(StructureRepresentation3D, getSpacefillParams(ColorNames.lightgray, 1, graphicsMode, merge), {\n tags: [`comp:`, `func:`],\n })\n .commit();\n }\n}\n","deleted","label",[168,169,170,171,149],"frontend","mesoscale-explorer","data","cellpack","permalink","https://www.val.town/x/zcpbx/MolstarViewer/code/frontend/mesoscale-explorer/data/cellpack/preset.ts","extension","actionData","errors"]