From 4e6e8fed82e90525cf5e6325d3dc6f0d55f08361 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 25 Aug 2019 21:04:40 -0700
Subject: [PATCH] add rna in hiv cellpack models
---
src/apps/viewer/extensions/cellpack/model.ts | 96 +++++++++++++++-----
src/apps/viewer/extensions/cellpack/state.ts | 22 -----
src/mol-plugin/state/transforms/model.ts | 12 +--
3 files changed, 78 insertions(+), 52 deletions(-)
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index d7e144071..6bf9db7a1 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -26,6 +26,9 @@ import { formatMolScript } from '../../../../mol-script/language/expression-form
import { MolScriptBuilder as MS } from '../../../../mol-script/language/builder';
import { getMatFromResamplePoints } from './curve';
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';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/cellPACK_database_1.1.0/results/${fileName}`
@@ -44,7 +47,7 @@ async function getModel(id: string, baseUrl: string) {
return model
}
-async function getStructure(model: Model, props: { assembly?: string }) {
+async function getStructure(model: Model, props: { assembly?: string } = {}) {
let structure = Structure.ofModel(model)
const { assembly } = props
@@ -170,14 +173,11 @@ export const LoadCellPackModel = StateAction.build({
id: PD.Select('influenza_model1.json', [
['blood_hiv_immature_inside.json', 'blood_hiv_immature_inside'],
['BloodHIV1.0_mixed_fixed_nc1.cpr', 'BloodHIV1.0_mixed_fixed_nc1'],
- // ['BloodPlasma1.2.apr.json', 'BloodPlasma1.2'],
- // ['BloodSerumfillResult.apr', 'BloodSerumfillResult'],
['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'],
- // ['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', [
@@ -194,14 +194,41 @@ export const LoadCellPackModel = StateAction.build({
const root = state.build().toRoot();
const cellPackBuilder = root
- .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.id })
- .apply(StateTransforms.Data.ParseJson)
+ .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 isHiv = (
+ params.id === 'BloodHIV1.0_mixed_fixed_nc1.cpr' ||
+ params.id === 'HIV-1_0.1.6-8_mixed_radii_pdb.cpr'
+ )
+
+ if (isHiv) {
+ for (let i = 0, il = packings.length; i < il; ++i) {
+ if (packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0') {
+ const url = `${params.baseUrl}/cellPACK_database_1.1.0/extras/rna_allpoints.json`
+ const data = await ctx.fetch({ url, type: 'string' }).runInContext(taskCtx);
+ const { points } = await (new Response(data)).json() as { points: number[] }
+
+ const curve0: Vec3[] = []
+ for (let j = 0, jl = points.length; j < jl; j += 3) {
+ curve0.push(Vec3.fromArray(Vec3(), points, j))
+ }
+ packings[i].ingredients['RNA'] = {
+ source: { pdb: 'RNA_U_Base.pdb', transform: { center: false } },
+ results: [],
+ name: 'RNA',
+ nbCurve: 1,
+ curve0
+ }
+ }
+ }
+ }
+
const colors = distinctColors(packings.length)
for (let i = 0, il = packings.length; i < il; ++i) {
@@ -224,23 +251,26 @@ export const LoadCellPackModel = StateAction.build({
.apply(StateTransforms.Representation.StructureRepresentation3D,
StructureRepresentation3DHelpers.createParams(ctx, Structure.Empty, {
repr: getReprParams(ctx, params.preset),
- color: [
- ModelIndexColorThemeProvider,
- (c, ctx) => {
- return {
- palette: {
- name: 'generate',
- params: {
- hue, chroma: [30, 80], luminance: [15, 85],
- clusteringStepCount: 50, minSampleCount: 800,
- maxCount: 75
- }
- }
- }
- }
- ]
- }))
- }
+ color: getColorParams(hue)
+ })
+ )
+ }
+
+ if (isHiv) {
+ const url = `${params.baseUrl}/cellPACK_database_1.1.0/membranes/hiv_lipids.bcif`
+ tree.apply(StateTransforms.Data.Download, { url }, { state: { isGhost: true } })
+ .apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
+ .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
+ .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
+ .apply(StateTransforms.Model.StructureFromModel, undefined, { state: { isGhost: true } })
+ .apply(StateTransforms.Misc.CreateGroup, { label: 'HIV1_envelope_Membrane' })
+ .apply(StateTransforms.Representation.StructureRepresentation3D,
+ StructureRepresentation3DHelpers.createParams(ctx, Structure.Empty, {
+ repr: getReprParams(ctx, params.preset),
+ color: UniformColorThemeProvider
+ })
+ )
+ }
await state.updateTree(tree).runInContext(taskCtx);
}));
@@ -266,4 +296,22 @@ function getReprParams(ctx: PluginContext, params: { representation: 'spacefill'
case 'point':
return ctx.structureRepresentation.registry.get('point')
}
+}
+
+function getColorParams(hue: [number, number]) {
+ return [
+ ModelIndexColorThemeProvider,
+ (c: ColorTheme.Provider<any>, ctx: ThemeRegistryContext) => {
+ return {
+ palette: {
+ name: 'generate',
+ params: {
+ hue, chroma: [30, 80], luminance: [15, 85],
+ clusteringStepCount: 50, minSampleCount: 800,
+ maxCount: 75
+ }
+ }
+ }
+ }
+ ] as [any, any]
}
\ No newline at end of file
diff --git a/src/apps/viewer/extensions/cellpack/state.ts b/src/apps/viewer/extensions/cellpack/state.ts
index 79a992a96..105ed330d 100644
--- a/src/apps/viewer/extensions/cellpack/state.ts
+++ b/src/apps/viewer/extensions/cellpack/state.ts
@@ -6,7 +6,6 @@
import { PluginStateObject as PSO, PluginStateTransform } from '../../../../mol-plugin/state/objects';
import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
-import { Structure } from '../../../../mol-model/structure';
import { Task } from '../../../../mol-task';
import { CellPack as _CellPack, Cell, CellPacking } from './data';
import { createStructureFromCellPack } from './model';
@@ -69,25 +68,4 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
return new PSO.Molecule.Structure(structure, { label: packing.name })
});
}
-});
-
-export { AddStructure }
-type AddStructure = typeof AddStructure
-const AddStructure = PluginStateTransform.BuiltIn({
- name: 'add-structure',
- display: { name: 'Add Structure', description: 'Add existing molecular structure.' },
- from: PSO.Root,
- to: PSO.Molecule.Structure,
- params: {
- structure: PD.Value<Structure>(Structure.Empty),
- label: PD.Text('Structure')
- }
-})({
- apply({ a, params }) {
- return Task.create('Build Structure', async ctx => {
- const s = params.structure
- const props = { label: params.label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
- return new PSO.Molecule.Structure(s, props);
- })
- }
});
\ No newline at end of file
diff --git a/src/mol-plugin/state/transforms/model.ts b/src/mol-plugin/state/transforms/model.ts
index 261f70da6..3ac616e72 100644
--- a/src/mol-plugin/state/transforms/model.ts
+++ b/src/mol-plugin/state/transforms/model.ts
@@ -162,6 +162,10 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
}
});
+function structureDesc(s: Structure) {
+ return s.elementCount === 1 ? '1 element' : `${s.elementCount} elements`
+}
+
type StructureFromTrajectory = typeof StructureFromTrajectory
const StructureFromTrajectory = PluginStateTransform.BuiltIn({
name: 'structure-from-trajectory',
@@ -172,7 +176,7 @@ const StructureFromTrajectory = PluginStateTransform.BuiltIn({
apply({ a }) {
return Task.create('Build Structure', async ctx => {
const s = Structure.ofTrajectory(a.data);
- const props = { label: s.label, description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
+ const props = { label: 'Ensemble', description: structureDesc(s) };
return new SO.Molecule.Structure(s, props);
})
}
@@ -189,16 +193,12 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
return Task.create('Build Structure', async ctx => {
const s = Structure.ofModel(a.data);
await ensureSecondaryStructure(s)
- const props = { label: 'Deposited', description: s.elementCount === 1 ? '1 element' : `${s.elementCount} elements` };
+ const props = { label: 'Deposited', description: structureDesc(s) };
return new SO.Molecule.Structure(s, props);
})
}
});
-function structureDesc(s: Structure) {
- return s.elementCount === 1 ? '1 element' : `${s.elementCount} elements`;
-}
-
type StructureAssemblyFromModel = typeof StructureAssemblyFromModel
const StructureAssemblyFromModel = PluginStateTransform.BuiltIn({
name: 'structure-assembly-from-model',
--
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