From 904e9b869c4f735d0576d6726fd2ef5ee6c47039 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 30 Jul 2019 12:03:26 -0700
Subject: [PATCH] wip, cellpack loader improvements
---
src/apps/viewer/extensions/cellpack/model.ts | 81 +++++++++++++-------
1 file changed, 54 insertions(+), 27 deletions(-)
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index a192a9955..faa230b51 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -10,7 +10,7 @@ import { PluginStateObject as PSO } from '../../../../mol-plugin/state/objects';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
import { Ingredient, Packing } from './data';
import { getFromPdb, getFromCellPackDB } from './util';
-import { Model, Structure, StructureSymmetry, StructureSelection, Queries, QueryContext, StructureProperties as SP } from '../../../../mol-model/structure';
+import { Model, Structure, StructureSymmetry, StructureSelection, Queries, QueryContext } from '../../../../mol-model/structure';
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';
@@ -22,6 +22,8 @@ import { distinctColors } from '../../../../mol-util/color/distinct';
import { ModelIndexColorThemeProvider } from '../../../../mol-theme/color/model-index';
import { Hcl } from '../../../../mol-util/color/spaces/hcl';
import { ParseCellPack, StructureFromCellpack } from './state';
+import { formatMolScript } from '../../../../mol-script/language/expression-formatter';
+import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/cellPACK_database_1.1.0/results/${fileName}`
@@ -40,23 +42,14 @@ async function getModel(id: string, baseUrl: string) {
return model
}
-async function getStructure(model: Model, props: { assembly?: string, trace?: boolean }) {
+async function getStructure(model: Model, props: { assembly?: string }) {
let structure = Structure.ofModel(model)
- const { assembly, trace } = props
+ const { assembly } = props
if (assembly) {
structure = await StructureSymmetry.buildAssembly(structure, assembly).run()
}
- if (trace === true) {
- const query = Queries.generators.atoms({ atomTest: ctx => {
- const atomId = SP.atom.label_atom_id(ctx.element)
- return atomId === 'CA' || atomId === 'P'
- }})
- const result = query(new QueryContext(structure))
- structure = StructureSelection.unionStructure(result)
- }
-
const query = Queries.internal.atomicSequence()
const result = query(new QueryContext(structure))
structure = StructureSelection.unionStructure(result)
@@ -107,7 +100,7 @@ async function getIngredientStructure(ingredient: Ingredient, baseUrl: string) {
const model = await getModel(source.pdb || name, baseUrl)
if (!model) return
- const structure = await getStructure(model, { trace: true, assembly: source.biomt ? '1' : undefined })
+ const structure = await getStructure(model, { assembly: source.biomt ? '1' : undefined })
const transforms = getTransforms(results)
const assembly = getAssembly(transforms, structure)
return assembly
@@ -152,7 +145,15 @@ export const LoadCellPackModel = StateAction.build({
['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
['NM_Analysis_FigureC1.4.cpr.json', 'NM_Analysis_FigureC1.4']
]),
- baseUrl: PD.Text('https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master/')
+ baseUrl: PD.Text('https://cdn.jsdelivr.net/gh/mesoscope/cellPACK_data@master/'),
+ preset: PD.Group({
+ traceOnly: PD.Boolean(false),
+ representation: PD.Select('spacefill', [
+ ['spacefill', 'Spacefill'],
+ ['gaussian-surface', 'Gaussian Surface'],
+ ['point', 'Point'],
+ ])
+ }, { isExpanded: true })
},
from: PSO.Root
})(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
@@ -174,20 +175,23 @@ export const LoadCellPackModel = StateAction.build({
for (let i = 0, il = packings.length; i < il; ++i) {
const hcl = Hcl.fromColor(Hcl(), colors[i])
const hue = [Math.max(0, hcl[0] - 35), Math.min(360, hcl[0] + 35)] as [number, number]
-
- tree.apply(StructureFromCellpack, { packing: i, baseUrl: params.baseUrl })
+ const p = { packing: i, baseUrl: params.baseUrl }
+
+ const expression = params.preset.traceOnly
+ ? MS.struct.generator.atomGroups({
+ 'atom-test': MS.core.logic.or([
+ MS.core.rel.eq([MS.ammp('label_atom_id'), 'CA']),
+ MS.core.rel.eq([MS.ammp('label_atom_id'), 'P'])
+ ])
+ })
+ : MS.struct.generator.all()
+ const query = { language: 'mol-script' as const, expression: formatMolScript(expression) }
+
+ tree.apply(StructureFromCellpack, p)
+ .apply(StateTransforms.Model.UserStructureSelection, { query })
.apply(StateTransforms.Representation.StructureRepresentation3D,
StructureRepresentation3DHelpers.createParams(ctx, Structure.Empty, {
- // repr: ctx.structureRepresentation.registry.get('point'),
- repr: [
- ctx.structureRepresentation.registry.get('gaussian-surface'),
- (c, ctx) => {
- return {
- quality: 'custom', resolution: 10, radiusOffset: 2,
- alpha: 1.0, flatShaded: false, doubleSided: false,
- }
- }
- ],
+ repr: getReprParams(ctx, params.preset),
color: [
ModelIndexColorThemeProvider,
(c, ctx) => {
@@ -206,4 +210,27 @@ export const LoadCellPackModel = StateAction.build({
}
await state.updateTree(tree).runInContext(taskCtx);
-}));
\ No newline at end of file
+}));
+
+function getReprParams(ctx: PluginContext, params: { representation: 'spacefill' | 'gaussian-surface' | 'point', traceOnly: boolean }) {
+ const { representation, traceOnly } = params
+ switch (representation) {
+ case 'spacefill':
+ return traceOnly
+ ? [
+ ctx.structureRepresentation.registry.get('spacefill'),
+ () => ({ sizeFactor: 2 })
+ ] as [any, any]
+ : ctx.structureRepresentation.registry.get('spacefill')
+ case 'gaussian-surface':
+ return [
+ ctx.structureRepresentation.registry.get('gaussian-surface'),
+ () => ({
+ quality: 'custom', resolution: 10, radiusOffset: 2,
+ alpha: 1.0, flatShaded: false, doubleSided: false,
+ })
+ ] as [any, any]
+ case 'point':
+ return ctx.structureRepresentation.registry.get('point')
+ }
+}
\ No newline at end of file
--
GitLab