diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index a548ba6f4057d1b5254152b09dc167fe1ea2bfb9..88f381c18ea6f61a63646cd789af2317ae5e02ae 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -8,7 +8,7 @@ import { StateAction } from '../../../../mol-state';
import { PluginContext } from '../../../../mol-plugin/context';
import { PluginStateObject as PSO } from '../../../../mol-plugin/state/objects';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { Ingredient, CellPacking } from './data';
+import { Ingredient, CellPacking, Cell } from './data';
import { getFromPdb, getFromCellPackDB } from './util';
import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext } from '../../../../mol-model/structure';
import { trajectoryFromMmCIF } from '../../../../mol-model-formats/structure/mmcif';
@@ -28,6 +28,11 @@ import { compile } from '../../../../mol-script/runtime/query/compiler';
import { UniformColorThemeProvider } from '../../../../mol-theme/color/uniform';
import { ThemeRegistryContext } from '../../../../mol-theme/theme';
import { ColorTheme } from '../../../../mol-theme/color';
+import { _parse_mmCif } from '../../../../mol-model-formats/structure/mmcif/parser';
+import { ModelFormat } from '../../../../mol-model-formats/structure/format';
+import { CifCategory, CifField } from '../../../../mol-io/reader/cif';
+import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
+import { Column } from '../../../../mol-data/db';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`
@@ -118,6 +123,109 @@ function getAssembly(transforms: Mat4[], structure: Structure) {
return builder.getStructure();
}
+function getCifCurve(name: string, transforms: Mat4[], model: Model) {
+ const d = model.sourceData.data.atom_site
+ const n = d._rowCount
+ const rowCount = n * transforms.length
+
+ const { offsets, count } = model.atomicHierarchy.chainAtomSegments
+
+ const x = d.Cartn_x.toArray()
+ const y = d.Cartn_y.toArray()
+ const z = d.Cartn_z.toArray()
+
+ const Cartn_x = new Float32Array(rowCount)
+ const Cartn_y = new Float32Array(rowCount)
+ const Cartn_z = new Float32Array(rowCount)
+ const map = new Uint32Array(rowCount)
+ const seq = new Int32Array(rowCount)
+ let offset = 0
+ for (let c = 0; c < count; ++c) {
+ const cStart = offsets[c]
+ const cEnd = offsets[c + 1]
+ const cLength = cEnd - cStart
+ for (let t = 0, tl = transforms.length; t < tl; ++t) {
+ const m = transforms[t]
+ for (let j = cStart; j < cEnd; ++j) {
+ const i = offset + j - cStart
+ const xj = x[j], yj = y[j], zj = z[j]
+ Cartn_x[i] = m[0] * xj + m[4] * yj + m[8] * zj + m[12]
+ Cartn_y[i] = m[1] * xj + m[5] * yj + m[9] * zj + m[13]
+ Cartn_z[i] = m[2] * xj + m[6] * yj + m[10] * zj + m[14]
+ map[i] = j
+ seq[i] = t + 1
+ }
+ offset += cLength
+ }
+ }
+
+ function multColumn<T>(column: Column<T>) {
+ const array = column.toArray()
+ return Column.ofLambda({
+ value: row => array[map[row]],
+ areValuesEqual: (rowA, rowB) => map[rowA] === map[rowB] || array[map[rowA]] === array[map[rowB]],
+ rowCount, schema: column.schema
+ })
+ }
+
+ const _atom_site: CifCategory.SomeFields<mmCIF_Schema['atom_site']> = {
+ auth_asym_id: CifField.ofColumn(multColumn(d.auth_asym_id)),
+ auth_atom_id: CifField.ofColumn(multColumn(d.auth_atom_id)),
+ auth_comp_id: CifField.ofColumn(multColumn(d.auth_comp_id)),
+ auth_seq_id: CifField.ofNumbers(seq),
+
+ B_iso_or_equiv: CifField.ofColumn(Column.ofConst(0, rowCount, Column.Schema.float)),
+ Cartn_x: CifField.ofNumbers(Cartn_x),
+ Cartn_y: CifField.ofNumbers(Cartn_y),
+ Cartn_z: CifField.ofNumbers(Cartn_z),
+ group_PDB: CifField.ofColumn(Column.ofConst('ATOM', rowCount, Column.Schema.str)),
+ id: CifField.ofColumn(Column.ofLambda({
+ value: row => row,
+ areValuesEqual: (rowA, rowB) => rowA === rowB,
+ rowCount, schema: d.id.schema,
+ })),
+
+ label_alt_id: CifField.ofColumn(multColumn(d.label_alt_id)),
+
+ label_asym_id: CifField.ofColumn(multColumn(d.label_asym_id)),
+ label_atom_id: CifField.ofColumn(multColumn(d.label_atom_id)),
+ label_comp_id: CifField.ofColumn(multColumn(d.label_comp_id)),
+ label_seq_id: CifField.ofNumbers(seq),
+ label_entity_id: CifField.ofColumn(Column.ofConst('1', rowCount, Column.Schema.str)),
+
+ occupancy: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.float)),
+ type_symbol: CifField.ofColumn(multColumn(d.type_symbol)),
+
+ pdbx_PDB_ins_code: CifField.ofColumn(Column.ofConst('', rowCount, Column.Schema.str)),
+ pdbx_PDB_model_num: CifField.ofColumn(Column.ofConst(1, rowCount, Column.Schema.int)),
+ }
+
+ const categories = {
+ entity: CifCategory.ofTable('entity', model.sourceData.data.entity),
+ chem_comp: CifCategory.ofTable('chem_comp', model.sourceData.data.chem_comp),
+ atom_site: CifCategory.ofFields('atom_site', _atom_site)
+ }
+
+ return {
+ header: name,
+ categoryNames: Object.keys(categories),
+ categories
+ };
+}
+
+async function getCurve(name: string, transforms: Mat4[], model: Model) {
+ const cif = getCifCurve(name, transforms, model)
+
+ const curveModelTask = Task.create('Curve Model', async ctx => {
+ const format = ModelFormat.mmCIF(cif)
+ const models = await _parse_mmCif(format, ctx)
+ return models[0]
+ })
+
+ const curveModel = await curveModelTask.run()
+ return getStructure(curveModel)
+}
+
async function getIngredientStructure(ingredient: Ingredient, baseUrl: string) {
const { name, source, results, nbCurve } = ingredient
@@ -133,10 +241,12 @@ async function getIngredientStructure(ingredient: Ingredient, baseUrl: string) {
const model = await getModel(source.pdb || name, baseUrl)
if (!model) return
- const structure = await getStructure(model, { assembly: source.biomt ? '1' : undefined })
- const transforms = nbCurve ? getCurveTransforms(ingredient) : getResultTransforms(results)
- const assembly = getAssembly(transforms, structure)
- return assembly
+ if (nbCurve) {
+ return getCurve(name, getCurveTransforms(ingredient), model)
+ } else {
+ const structure = await getStructure(model, { assembly: source.biomt ? '1' : undefined })
+ return getAssembly(getResultTransforms(results), structure)
+ }
}
export function createStructureFromCellPack(packing: CellPacking, baseUrl: string) {
@@ -144,14 +254,16 @@ export function createStructureFromCellPack(packing: CellPacking, baseUrl: strin
const { ingredients, name } = packing
const structures: Structure[] = []
for (const iName in ingredients) {
- if (ctx.shouldUpdate) ctx.update(iName)
+ if (ctx.shouldUpdate) await ctx.update(iName)
const s = await getIngredientStructure(ingredients[iName], baseUrl)
if (s) structures.push(s)
}
+ if (ctx.shouldUpdate) await ctx.update(`${name} - units`)
const builder = Structure.Builder({ label: name })
let offsetInvariantId = 0
for (const s of structures) {
+ if (ctx.shouldUpdate) await ctx.update(`${s.label}`)
let maxInvariantId = 0
for (const u of s.units) {
const invariantId = u.invariantId + offsetInvariantId
@@ -161,6 +273,7 @@ export function createStructureFromCellPack(packing: CellPacking, baseUrl: strin
offsetInvariantId += maxInvariantId
}
+ if (ctx.shouldUpdate) await ctx.update(`${name} - structure`)
const s = builder.getStructure()
return s
})
@@ -175,6 +288,7 @@ export const LoadCellPackModel = StateAction.build({
['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV-1_0.1.6-8_mixed_radii_pdb'],
['influenza_model1.json', 'influenza_model1'],
['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
+ ['curveTest', 'Curve Test'],
]),
baseUrl: PD.Text(DefaultCellPackBaseUrl),
preset: PD.Group({
@@ -192,14 +306,50 @@ export const LoadCellPackModel = StateAction.build({
const root = state.build().toRoot();
- const cellPackBuilder = root
- .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.id }, { state: { isGhost: true } })
- .apply(StateTransforms.Data.ParseJson, undefined, { state: { isGhost: true } })
- .apply(ParseCellPack)
+ let cellPackBuilder: any
+
+ if (params.id === 'curveTest') {
+ const url = `${params.baseUrl}/extras/rna_allpoints.json`
+ const data = await ctx.fetch({ url, type: 'string' }).runInContext(taskCtx);
+ const { points } = await (new Response(data)).json() as { points: number[] }
+ const curve0: Vec3[] = []
+ for (let j = 0, jl = Math.min(points.length, 3 * 100); j < jl; j += 3) {
+ curve0.push(Vec3.fromArray(Vec3(), points, j))
+ }
+ const cell: Cell = {
+ recipe: { setupfile: '', paths: [], version: '', name: 'Curve Test' },
+ compartments: {
+ 'CurveCompartment': {
+ interior: {
+ ingredients: {
+ 'CurveIngredient': {
+ source: { pdb: 'RNA_U_Base.pdb', transform: { center: false } },
+ results: [],
+ name: 'RNA',
+ nbCurve: 1,
+ curve0
+ }
+ }
+ }
+ }
+ }
+ }
+
+ cellPackBuilder = root
+ .apply(StateTransforms.Data.ImportJson, { data: cell }, { state: { isGhost: true } })
+ .apply(ParseCellPack)
+ } else {
+ cellPackBuilder = root
+ .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.id }, { state: { isGhost: true } })
+ .apply(StateTransforms.Data.ParseJson, undefined, { state: { isGhost: true } })
+ .apply(ParseCellPack)
+
+
+ }
const cellPackObject = await state.updateTree(cellPackBuilder).runInContext(taskCtx)
const { packings } = cellPackObject.data
- let tree = state.build().to(cellPackBuilder.ref);
+ const tree = state.build().to(cellPackBuilder.ref);
const isHiv = (
params.id === 'BloodHIV1.0_mixed_fixed_nc1.cpr' ||
@@ -270,7 +420,9 @@ export const LoadCellPackModel = StateAction.build({
)
}
+ console.time('cellpack')
await state.updateTree(tree).runInContext(taskCtx);
+ console.timeEnd('cellpack')
}));
function getReprParams(ctx: PluginContext, params: { representation: 'spacefill' | 'gaussian-surface' | 'point', traceOnly: boolean }) {
diff --git a/src/apps/viewer/extensions/cellpack/util.ts b/src/apps/viewer/extensions/cellpack/util.ts
index f71e107016e61dd4bf66966932906662d88f6cb6..6e64ed3dff740caea81d450a2d80286e800470a8 100644
--- a/src/apps/viewer/extensions/cellpack/util.ts
+++ b/src/apps/viewer/extensions/cellpack/util.ts
@@ -14,8 +14,8 @@ async function parseCif(data: string|Uint8Array) {
return parsed.result;
}
-async function parsePDBfile(data: string) {
- const comp = parsePDB(data);
+async function parsePDBfile(data: string, id: string) {
+ const comp = parsePDB(data, id);
const parsed = await comp.run();
if (parsed.isError) throw parsed;
return parsed.result;
@@ -26,9 +26,9 @@ async function downloadCif(url: string, isBinary: boolean) {
return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
}
-async function downloadPDB(url: string) {
+async function downloadPDB(url: string, id: string) {
const data = await fetch(url);
- return parsePDBfile(await data.text());
+ return parsePDBfile(await data.text(), id);
}
export async function getFromPdb(id: string) {
@@ -42,6 +42,7 @@ function getCellPackDataUrl(id: string, baseUrl: string) {
}
export async function getFromCellPackDB(id: string, baseUrl: string) {
- const parsed = await downloadPDB(getCellPackDataUrl(id, baseUrl));
+ const name = id.endsWith('.pdb') ? id.substring(0, id.length - 4) : id
+ const parsed = await downloadPDB(getCellPackDataUrl(id, baseUrl), name);
return parsed;
}
\ No newline at end of file