From eb196a41b51bedbfe7a96c5d10eb171e04c753c4 Mon Sep 17 00:00:00 2001
From: ludovic autin <autin@scripps.edu>
Date: Tue, 14 Sep 2021 11:25:15 -0700
Subject: [PATCH] change variables names to avoid confusion with other types.
Added the xrayshading for the compartment geometry
---
src/extensions/cellpack/data.ts | 16 ++++++++------
src/extensions/cellpack/model.ts | 38 ++++++++++++++++++--------------
src/extensions/cellpack/state.ts | 21 ++++++++++--------
3 files changed, 42 insertions(+), 33 deletions(-)
diff --git a/src/extensions/cellpack/data.ts b/src/extensions/cellpack/data.ts
index f415040fc..6764ddc7f 100644
--- a/src/extensions/cellpack/data.ts
+++ b/src/extensions/cellpack/data.ts
@@ -15,13 +15,15 @@ export interface CellPacking {
name: string,
location: 'surface' | 'interior' | 'cytoplasme'
ingredients: Packing['ingredients']
+ compartment?: CellCompartment
+}
+
+export interface CellCompartment {
filename?: string
geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None'
- primitives?: Primitives
+ compartment_primitives?: CompartmentPrimitives
}
-//
-
export interface Cell {
recipe: Recipe
options?: RecipeOptions
@@ -46,11 +48,11 @@ export interface Compartment {
interior?: Packing
geom?: unknown
geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None'
- mb?: Primitives
+ mb?: CompartmentPrimitives
}
// Primitives discribing a compartment
-export const enum PrimitiveType {
+export const enum CompartmentPrimitiveType {
MetaBall = 0,
Sphere = 1,
Cube = 2,
@@ -60,10 +62,10 @@ export const enum PrimitiveType {
None = 6
}
-export interface Primitives{
+export interface CompartmentPrimitives{
positions?: number[];
radii?: number[];
- types?: PrimitiveType[];
+ types?: CompartmentPrimitiveType[];
}
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 1a55ed03f..5715ce080 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -9,7 +9,7 @@ import { StateAction, StateBuilder, StateTransformer, State } from '../../mol-st
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, Primitives } from './data';
+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';
@@ -31,6 +31,7 @@ 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';
function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`;
@@ -524,7 +525,8 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
} else if (geometry_membrane) {
await b.apply(StateTransforms.Data.ParsePly, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.ShapeFromPly)
- .apply(StateTransforms.Representation.ShapeRepresentation3D)
+ .apply(StateTransforms.Representation.ShapeRepresentation3D, { xrayShaded: true,
+ doubleSided: true, coloring: { name: 'uniform', params: { color: ColorNames.orange } } })
.commit({ revertOnError: true });
} else {
const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
@@ -539,7 +541,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
}
}
-async function handleMembraneSpheres(state: State, primitives: Primitives) {
+async function handleMembraneSpheres(state: State, primitives: CompartmentPrimitives) {
const nSpheres = primitives.positions!.length / 3;
// console.log('ok mb ', nSpheres);
// TODO : take in account the type of the primitives.
@@ -619,16 +621,14 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
representation: params.preset.representation,
};
await CellpackPackingPreset.apply(packing, packingParams, plugin);
- if (packings[i].location === 'surface') {
- // console.log('ok surface ' + params.membrane);
+ if (packings[i].compartment) {
if (params.membrane === 'lipids') {
- // console.log('ok packings[i].geom_type ' + packings[i].geom_type);
- if (packings[i].geom_type) {
- if (packings[i].geom_type === 'file') {
+ if (packings[i].compartment!.geom_type) {
+ if (packings[i].compartment!.geom_type === 'file') {
// TODO: load mesh files or vertex,faces data
- await loadMembrane(plugin, packings[i].filename!, state, params);
- } else if (packings[i].primitives) {
- await handleMembraneSpheres(state, packings[i].primitives!);
+ await loadMembrane(plugin, packings[i].compartment!.filename!, state, params);
+ } else if (packings[i].compartment!.compartment_primitives) {
+ await handleMembraneSpheres(state, packings[i].compartment!.compartment_primitives!);
}
} else {
// try loading membrane from repo as a bcif file or from the given list of files.
@@ -636,9 +636,13 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
await loadMembrane(plugin, packings[i].name, state, params);
}
}
- } else if (params.membrane === 'spheres') {
- if (packings[i].primitives) {
- await handleMembraneSpheres(state, packings[i].primitives!);
+ } else if (params.membrane === 'geometry') {
+ if (packings[i].compartment!.compartment_primitives) {
+ await handleMembraneSpheres(state, packings[i].compartment!.compartment_primitives!);
+ } else if (packings[i].compartment!.geom_type === 'file') {
+ if (packings[i].compartment!.filename!.toLowerCase().endsWith('.ply')) {
+ await loadMembrane(plugin, packings[i].compartment!.filename!, state, params);
+ }
}
}
}
@@ -650,10 +654,10 @@ const LoadCellPackModelParams = {
'id': PD.Select('InfluenzaModel2.json', [
['blood_hiv_immature_inside.json', 'Blood HIV immature'],
['HIV_immature_model.json', 'HIV immature'],
- ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'Blood HIV'],
+ ['Blood_HIV.json', 'Blood HIV'],
['HIV-1_0.1.6-8_mixed_radii_pdb.json', 'HIV'],
['influenza_model1.json', 'Influenza envelope'],
- ['InfluenzaModel2.json', 'Influenza Complete'],
+ ['InfluenzaModel2.json', 'Influenza complete'],
['ExosomeModel.json', 'Exosome Model'],
['MycoplasmaGenitalium.json', 'Mycoplasma Genitalium curated model'],
] as const, { description: 'Download the model definition with `id` from the server at `baseUrl.`' }),
@@ -661,7 +665,7 @@ const LoadCellPackModelParams = {
}, { options: [['id', 'Id'], ['file', 'File']] }),
baseUrl: PD.Text(DefaultCellPackBaseUrl),
results: PD.File({ accept: '.bin', description: 'open results file in binary format from cellpackgpu for the specified recipe', label: 'Results file' }),
- membrane: PD.Select('lipids', PD.arrayToOptions(['lipids', 'spheres', 'none'])),
+ membrane: PD.Select('lipids', PD.arrayToOptions(['lipids', 'geometry', 'none'])),
ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredient files' }),
preset: PD.Group({
traceOnly: PD.Boolean(false),
diff --git a/src/extensions/cellpack/state.ts b/src/extensions/cellpack/state.ts
index 948f0e0cb..c06979fad 100644
--- a/src/extensions/cellpack/state.ts
+++ b/src/extensions/cellpack/state.ts
@@ -66,12 +66,13 @@ const ParseCellPack = PluginStateTransform.BuiltIn({
if (compartments) {
for (const name in compartments) {
const { surface, interior } = compartments[name];
+ let filename = '';
+ if (compartments[name].geom_type === 'file') {
+ filename = (compartments[name].geom) ? compartments[name].geom as string : '';
+ }
+ const compartment = { filename: filename, geom_type: compartments[name].geom_type, compartment_primitives: compartments[name].mb };
if (surface) {
- let filename = '';
- if (compartments[name].geom_type === 'file') {
- filename = (compartments[name].geom) ? compartments[name].geom as string : '';
- }
- packings.push({ name, location: 'surface', ingredients: surface.ingredients, filename: filename, geom_type: compartments[name].geom_type, primitives: compartments[name].mb });
+ packings.push({ name, location: 'surface', ingredients: surface.ingredients, compartment: compartment });
for (const iName in surface.ingredients) {
if (surface.ingredients[iName].ingtype === 'fiber') {
cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
@@ -86,7 +87,8 @@ const ParseCellPack = PluginStateTransform.BuiltIn({
comp_counter++;
}
if (interior) {
- packings.push({ name, location: 'interior', ingredients: interior.ingredients });
+ if (!surface) packings.push({ name, location: 'interior', ingredients: interior.ingredients, compartment: compartment });
+ else packings.push({ name, location: 'interior', ingredients: interior.ingredients });
for (const iName in interior.ingredients) {
if (interior.ingredients[iName].ingtype === 'fiber') {
cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
@@ -306,7 +308,8 @@ export const CreateCompartmentSphere = CreateTransformer({
to: PSO.Shape.Representation3D,
params: {
center: PD.Vec3(Vec3()),
- radius: PD.Numeric(1)
+ radius: PD.Numeric(1),
+ label: PD.Text(`Compartment Sphere`)
}
})({
canAutoUpdate({ oldParams, newParams }) {
@@ -316,8 +319,8 @@ export const CreateCompartmentSphere = CreateTransformer({
return Task.create('Compartment Sphere', async ctx => {
const data = params;
const repr = MBRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => (MBParams));
- await repr.createOrUpdate({ ...params, quality: 'custom', doubleSided: true }, data).runInContext(ctx);
- return new PSO.Shape.Representation3D({ repr, sourceData: a }, { label: `Compartment Sphere` });
+ await repr.createOrUpdate({ ...params, quality: 'custom', xrayShaded: true, doubleSided: true }, data).runInContext(ctx);
+ return new PSO.Shape.Representation3D({ repr, sourceData: a }, { label: data.label });
});
}
});
\ No newline at end of file
--
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