diff --git a/CHANGELOG.md b/CHANGELOG.md
index 63fbb66684769dccddcf28a9abee8717bdf532b7..c5667a79c9f84710336247e681f434786a578286 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,25 +6,8 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
-## [v3.10.2] - 2022-06-26
-
-- Fix superfluous shader varying
-- Improve use of gl_VertexID when possible
-
-## [v3.10.1] - 2022-06-26
-
-- Fix groupCount when updating TextureMesh-based visuals
-
-## [v3.10.0] - 2022-06-24
-
-- Add support for Glycam saccharide names
-- Add ``PluginConfig.Viewport.ShowTrajectoryControls`` config option
-
-## [v3.9.1] - 2022-06-19
-
-- Fix missing ``super.componentWillUnmount()`` calls (@simeonborko)
-- Fix missing ``uGroupCount`` update for visuals
-- Fix missing aromatic bond display
+- CellPack extension tweaks
+ - Use instancing to create DNA/RNA curves to save memory
## [v3.9.0] - 2022-05-30
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 02ce77cc07c4acb829ec4daf0a1e7b83167162e5..3bab461ff5be6c4db129491d5663a7ff3396ce50 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.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>
* @author Ludovic Autin <ludovic.autin@gmail.com>
@@ -12,7 +12,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
import { Ingredient, CellPacking, CompartmentPrimitives } from './data';
import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit, Trajectory } from '../../mol-model/structure';
-import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { trajectoryFromMmCIF } from '../../mol-model-formats/structure/mmcif';
import { trajectoryFromPDB } from '../../mol-model-formats/structure/pdb';
import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
import { SymmetryOperator } from '../../mol-math/geometry';
@@ -22,17 +22,12 @@ import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, Structure
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { getMatFromResamplePoints } from './curve';
import { compile } from '../../mol-script/runtime/query/compiler';
-import { CifCategory, CifField } from '../../mol-io/reader/cif';
-import { mmCIF_Schema } from '../../mol-io/reader/cif/schema/mmcif';
-import { Column } from '../../mol-data/db';
-import { createModels } from '../../mol-model-formats/structure/basic/parser';
import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
import { Asset } from '../../mol-util/assets';
import { Color } from '../../mol-util/color';
import { objectForEach } from '../../mol-util/object';
import { readFromFile } from '../../mol-util/data-source';
import { ColorNames } from '../../mol-util/color/names';
-import { createBasic } from '../../mol-model-formats/structure/basic/schema';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`;
@@ -142,7 +137,7 @@ async function getStructure(plugin: PluginContext, model: Model, source: Ingredi
function getTransformLegacy(trans: Vec3, rot: Quat) {
const q: Quat = Quat.create(-rot[3], rot[0], rot[1], rot[2]);
- const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+ const m: Mat4 = Mat4.fromQuat(Mat4(), q);
Mat4.transpose(m, m);
Mat4.scale(m, m, Vec3.create(-1.0, 1.0, -1.0));
Mat4.setTranslation(m, trans);
@@ -151,7 +146,7 @@ function getTransformLegacy(trans: Vec3, rot: Quat) {
function getTransform(trans: Vec3, rot: Quat) {
const q: Quat = Quat.create(-rot[0], rot[1], rot[2], -rot[3]);
- const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+ const m: Mat4 = Mat4.fromQuat(Mat4(), q);
const p: Vec3 = Vec3.create(-trans[0], trans[1], trans[2]);
Mat4.setTranslation(m, p);
return m;
@@ -214,111 +209,10 @@ function getAssembly(name: string, transforms: Mat4[], structure: Structure) {
return builder.getStructure();
}
-function getCifCurve(name: string, transforms: Mat4[], model: Model) {
- if (!MmcifFormat.is(model.sourceData)) throw new Error('mmcif source data needed');
-
- const { db } = model.sourceData.data;
- const d = db.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', db.entity),
- chem_comp: CifCategory.ofTable('chem_comp', db.chem_comp),
- atom_site: CifCategory.ofFields('atom_site', _atom_site)
- };
-
- return {
- header: name,
- categoryNames: Object.keys(categories),
- categories
- };
-}
-
-async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
- const cif = getCifCurve(name, transforms, model);
- const curveModelTask = Task.create('Curve Model', async ctx => {
- const format = MmcifFormat.fromFrame(cif);
- const basic = createBasic(format.data.db, true);
- const models = await createModels(basic, format, ctx);
- return models.representative;
- });
-
- const curveModel = await plugin.runTask(curveModelTask);
- // ingredient.source.selection = undefined;
- return getStructure(plugin, curveModel, ingredient);
+async function getCurve(name: string, transforms: Mat4[], model: Model) {
+ const structure = Structure.ofModel(model);
+ const assembly = getAssembly(name, transforms, structure);
+ return assembly;
}
async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache, location: 'surface' | 'interior' | 'cytoplasme') {
@@ -339,7 +233,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
if (!model) return;
let structure: Structure;
if (nbCurve) {
- structure = await getCurve(plugin, name, ingredient, getCurveTransforms(ingredient), model);
+ structure = await getCurve(name, getCurveTransforms(ingredient), model);
} else {
if ((!results || results.length === 0)) return;
let bu: string|undefined = source.bu ? source.bu : undefined;
@@ -363,7 +257,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
structure = Structure.transform(structure, m1);
if (ingredient.offset) {
const o: Vec3 = Vec3.create(ingredient.offset[0], ingredient.offset[1], ingredient.offset[2]);
- if (!Vec3.exactEquals(o, Vec3.zero())) { // -1, 1, 4e-16 ??
+ if (!Vec3.exactEquals(o, Vec3())) { // -1, 1, 4e-16 ??
if (location !== 'surface') {
Vec3.negate(o, o);
}
@@ -377,7 +271,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
if (!Vec3.exactEquals(p, Vec3.unitZ)) {
const q: Quat = Quat.identity();
Quat.rotationTo(q, p, Vec3.unitZ);
- const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
+ const m: Mat4 = Mat4.fromQuat(Mat4(), q);
structure = Structure.transform(structure, m);
}
}
@@ -671,7 +565,7 @@ const LoadCellPackModelParams = {
ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredient files' }),
preset: PD.Group({
traceOnly: PD.Boolean(false),
- representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))
+ representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation'] as const))
}, { isExpanded: true })
};
type LoadCellPackModelParams = PD.Values<typeof LoadCellPackModelParams>
diff --git a/src/extensions/cellpack/preset.ts b/src/extensions/cellpack/preset.ts
index 895f2fb1ab7d085a297bcdfe5cc350dcd06e1e43..6fbfe6ca8c271a0ec3a2728e511c23d3dd2165db 100644
--- a/src/extensions/cellpack/preset.ts
+++ b/src/extensions/cellpack/preset.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>
* @author Ludovic Autin <ludovic.autin@gmail.com>
@@ -13,7 +13,7 @@ import { CellPackGenerateColorThemeProvider } from './color/generate';
export const CellpackPackingPresetParams = {
traceOnly: PD.Boolean(true),
- representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
+ representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'] as const)),
};
export type CellpackPackingPresetParams = PD.ValuesFor<typeof CellpackPackingPresetParams>
@@ -37,8 +37,8 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
Object.assign(reprProps, {
quality: 'custom', resolution: 10, radiusOffset: 2, doubleSided: false
});
- } else if (params.representation === 'spacefill' && params.traceOnly) {
- Object.assign(reprProps, { sizeFactor: 2 });
+ } else if (params.representation === 'spacefill') {
+ Object.assign(reprProps, { sizeFactor: params.traceOnly ? 2 : 1 });
}
// default is generated
@@ -57,7 +57,7 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
//
export const CellpackMembranePresetParams = {
- representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
+ representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'] as const)),
};
export type CellpackMembranePresetParams = PD.ValuesFor<typeof CellpackMembranePresetParams>
@@ -84,7 +84,7 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({
const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, {});
const representations = {
- membrane: builder.buildRepresentation(update, components.membrane, { type: 'gaussian-surface', typeParams: { ...typeParams, ...reprProps }, color: 'uniform', colorParams: { value: ColorNames.lightgrey } }, { tag: 'all' })
+ membrane: builder.buildRepresentation(update, components.membrane, { type: params.representation, typeParams: { ...typeParams, ...reprProps }, color: 'uniform', colorParams: { value: ColorNames.lightgrey } }, { tag: 'all' })
};
await update.commit({ revertOnError: true });