From 35baaaf59442a6602b8f7ca8b6f1cc76df48e429 Mon Sep 17 00:00:00 2001
From: ludovic autin <autin@scripps.edu>
Date: Mon, 13 Sep 2021 11:46:27 -0700
Subject: [PATCH] support for compartment PLY file.
---
src/extensions/cellpack/data.ts | 30 +++++---
src/extensions/cellpack/model.ts | 48 +++++++-----
src/extensions/cellpack/representation.ts | 16 ----
src/extensions/cellpack/state.ts | 16 ++--
src/extensions/cellpack/util.ts | 89 +----------------------
5 files changed, 62 insertions(+), 137 deletions(-)
diff --git a/src/extensions/cellpack/data.ts b/src/extensions/cellpack/data.ts
index 51ad02365..f415040fc 100644
--- a/src/extensions/cellpack/data.ts
+++ b/src/extensions/cellpack/data.ts
@@ -13,11 +13,11 @@ export interface CellPack {
export interface CellPacking {
name: string,
- location: 'surface' | 'interior' | 'cytoplasme',
+ location: 'surface' | 'interior' | 'cytoplasme'
ingredients: Packing['ingredients']
- geom?: string
- geom_type?: string
- mb?: Membrane
+ filename?: string
+ geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None'
+ primitives?: Primitives
}
//
@@ -44,17 +44,29 @@ export interface Recipe {
export interface Compartment {
surface?: Packing
interior?: Packing
- geom?: string
- geom_type?: string
- mb?: Membrane
+ geom?: unknown
+ geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None'
+ mb?: Primitives
}
-export interface Membrane{
+// Primitives discribing a compartment
+export const enum PrimitiveType {
+ MetaBall = 0,
+ Sphere = 1,
+ Cube = 2,
+ Cylinder = 3,
+ Cone = 4,
+ Plane = 5,
+ None = 6
+}
+
+export interface Primitives{
positions?: number[];
radii?: number[];
- source?: string;
+ types?: PrimitiveType[];
}
+
export interface Packing {
ingredients: { [key: string]: Ingredient }
}
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 8b5dbe904..1a55ed03f 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, Membrane } from './data';
+import { Ingredient, CellPacking, Primitives } 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';
@@ -18,7 +18,7 @@ import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
import { SymmetryOperator } from '../../mol-math/geometry';
import { Task, RuntimeContext } from '../../mol-task';
import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, StructureFromAssemblies, CreateSphere } from './state';
+import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, StructureFromAssemblies, CreateCompartmentSphere } from './state';
import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
import { getMatFromResamplePoints } from './curve';
import { compile } from '../../mol-script/runtime/query/compiler';
@@ -186,7 +186,7 @@ function getCurveTransforms(ingredient: Ingredient) {
// test for resampling
const distance: number = Vec3.distance(_points[0], _points[1]);
if (distance >= segmentLength + 2.0) {
- console.info(distance);
+ // console.info(distance);
resampling = true;
}
const points = new Float32Array(_points.length * 3);
@@ -479,6 +479,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
}
}
let legacy_membrane: boolean = false; // temporary variable until all membrane are converted to the new correct cif format
+ let geometry_membrane: boolean = false; // membrane can be a mesh geometry
let b = state.build().toRoot();
if (file) {
if (file.name.endsWith('.cif')) {
@@ -493,6 +494,10 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
} else if (name.toLowerCase().endsWith('.cif')) {
const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}`);
b = b.apply(StateTransforms.Data.Download, { url, isBinary: false, label: name }, { state: { isGhost: true } });
+ } else if (name.toLowerCase().endsWith('.ply')) {
+ const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/geometries/${name}`);
+ b = b.apply(StateTransforms.Data.Download, { url, isBinary: false, label: name }, { state: { isGhost: true } });
+ geometry_membrane = true;
} else {
const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}.bcif`);
b = b.apply(StateTransforms.Data.Download, { url, isBinary: true, label: name }, { state: { isGhost: true } });
@@ -516,6 +521,11 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
representation: params.preset.representation,
};
await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
+ } else if (geometry_membrane) {
+ await b.apply(StateTransforms.Data.ParsePly, undefined, { state: { isGhost: true } })
+ .apply(StateTransforms.Model.ShapeFromPly)
+ .apply(StateTransforms.Representation.ShapeRepresentation3D)
+ .commit({ revertOnError: true });
} else {
const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
.apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
@@ -529,19 +539,20 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
}
}
-async function handleMembraneSpheres(state: State, mb: Membrane) {
- const nSpheres = mb.positions!.length / 3;
- console.log('ok mb ', nSpheres);
+async function handleMembraneSpheres(state: State, primitives: Primitives) {
+ const nSpheres = primitives.positions!.length / 3;
+ // console.log('ok mb ', nSpheres);
+ // TODO : take in account the type of the primitives.
for (let j = 0; j < nSpheres; j++) {
await state.build()
.toRoot()
- .apply(CreateSphere, {
+ .apply(CreateCompartmentSphere, {
center: Vec3.create(
- mb.positions![j * 3 + 0],
- mb.positions![j * 3 + 1],
- mb.positions![j * 3 + 2]
+ primitives.positions![j * 3 + 0],
+ primitives.positions![j * 3 + 1],
+ primitives.positions![j * 3 + 2]
),
- radius: mb!.radii![j]
+ radius: primitives!.radii![j]
})
.commit();
}
@@ -609,14 +620,15 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
};
await CellpackPackingPreset.apply(packing, packingParams, plugin);
if (packings[i].location === 'surface') {
- console.log('ok surface ' + params.membrane);
+ // console.log('ok surface ' + params.membrane);
if (params.membrane === 'lipids') {
- console.log('ok packings[i].geom_type ' + packings[i].geom_type);
+ // console.log('ok packings[i].geom_type ' + packings[i].geom_type);
if (packings[i].geom_type) {
if (packings[i].geom_type === 'file') {
- await loadMembrane(plugin, packings[i].geom!, state, params);
- } else if (packings[i].mb) {
- await handleMembraneSpheres(state, packings[i].mb!);
+ // 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!);
}
} else {
// try loading membrane from repo as a bcif file or from the given list of files.
@@ -625,8 +637,8 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
}
}
} else if (params.membrane === 'spheres') {
- if (packings[i].mb) {
- await handleMembraneSpheres(state, packings[i].mb!);
+ if (packings[i].primitives) {
+ await handleMembraneSpheres(state, packings[i].primitives!);
}
}
}
diff --git a/src/extensions/cellpack/representation.ts b/src/extensions/cellpack/representation.ts
index 64dcbf096..261e3a3c4 100644
--- a/src/extensions/cellpack/representation.ts
+++ b/src/extensions/cellpack/representation.ts
@@ -49,11 +49,6 @@ export type UnitcellProps = PD.Values<MBParams>
function getMBMesh(data: MembraneSphereData, props: UnitcellProps, mesh?: Mesh) {
const state = MeshBuilder.createState(256, 128, mesh);
const radius = props.radius;
- // const p = DefaultPolyhedronProps;
- // p.detail = 3;
- // p.radius = radius;
- // const { vertices, indices } = Icosahedron();
- // const asphere = Polyhedron(vertices, indices, p);
const asphere = Sphere(3);
const trans: Mat4 = Mat4.identity();
Mat4.fromScaling(trans, Vec3.create(radius, radius, radius));
@@ -69,17 +64,6 @@ function getMBShape(ctx: RuntimeContext, data: MembraneSphereData, props: Unitce
return Shape.create(label, data, geo, () => props.cellColor, () => 1, () => label);
}
-//
-/*
-export function getMBData(model: Model, symmetry: Symmetry, props: UnitcellProps) {
- const ref = Vec3();
- if (props.ref === 'model') {
- Vec3.transformMat4(ref, Model.getCenter(model), symmetry.spacegroup.cell.toFractional);
- }
- return { symmetry, ref };
-}
-*/
-
export type MBRepresentation = Representation<MembraneSphereData, MBParams>
export function MBRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneSphereData, MBParams>): MBRepresentation {
return Representation.createMulti('MB', ctx, getParams, Representation.StateBuilder, MembraneSphereVisuals as unknown as Representation.Def<MembraneSphereData, MBParams>);
diff --git a/src/extensions/cellpack/state.ts b/src/extensions/cellpack/state.ts
index 7e6374156..948f0e0cb 100644
--- a/src/extensions/cellpack/state.ts
+++ b/src/extensions/cellpack/state.ts
@@ -67,7 +67,11 @@ const ParseCellPack = PluginStateTransform.BuiltIn({
for (const name in compartments) {
const { surface, interior } = compartments[name];
if (surface) {
- packings.push({ name, location: 'surface', ingredients: surface.ingredients, geom: compartments[name].geom, geom_type: compartments[name].geom_type, mb: compartments[name].mb });
+ 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 });
for (const iName in surface.ingredients) {
if (surface.ingredients[iName].ingtype === 'fiber') {
cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
@@ -295,9 +299,9 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
});
const CreateTransformer = StateTransformer.builderFactory('cellPACK');
-export const CreateSphere = CreateTransformer({
- name: 'create-sphere',
- display: 'Sphere',
+export const CreateCompartmentSphere = CreateTransformer({
+ name: 'create-compartment-sphere',
+ display: 'CompartmentSphere',
from: PSO.Root, // or whatever data source
to: PSO.Shape.Representation3D,
params: {
@@ -309,11 +313,11 @@ export const CreateSphere = CreateTransformer({
return true;
},
apply({ a, params }, plugin: PluginContext) {
- return Task.create('Custom Sphere', async ctx => {
+ 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: `My Sphere` });
+ return new PSO.Shape.Representation3D({ repr, sourceData: a }, { label: `Compartment Sphere` });
});
}
});
\ No newline at end of file
diff --git a/src/extensions/cellpack/util.ts b/src/extensions/cellpack/util.ts
index 452b4c4b5..b7c8aea30 100644
--- a/src/extensions/cellpack/util.ts
+++ b/src/extensions/cellpack/util.ts
@@ -38,7 +38,6 @@ async function downloadPDB(plugin: PluginContext, url: string, id: string, asset
}
export async function getFromPdb(plugin: PluginContext, pdbId: string, assetManager: AssetManager) {
- // ${pdbId.toUpperCase()}
const { cif, asset } = await downloadCif(plugin, `https://models.rcsb.org/${pdbId}.bcif`, true, assetManager);
return { mmcif: cif.blocks[0], asset };
}
@@ -107,90 +106,4 @@ export function getFloatValue(value: DataView, offset: number) {
}
return mantissa * Math.pow(10, exponent);
-}
-
-/*
-async function loadPackingResultsBinary(plugin: PluginContext, runtime: RuntimeContext, file: Asset.File, packing: CellPack){
- const model_data = await readFromFile(file.file!, 'binary').runInContext(runtime);// async ?
- let buffer = model_data.buffer;
- let {cell, packings } = packing;
- if (!IsNativeEndianLittle) {
- // flip the byte order
- buffer = flipByteOrder(model_data, 4);
- }
- const numbers = new DataView(buffer);
- const ninst = getFloatValue(numbers, 0);
- const npoints = getFloatValue(numbers, 4);
- const ncurve = getFloatValue(numbers, 8);
-
- let pos = new Float32Array();
- let quat = new Float32Array();
- let ctr_pos = new Float32Array();
- let ctr_info = new Float32Array();
- let curve_ids = new Float32Array();
-
- let offset = 12;
- if (ninst !== 0){
- pos = new Float32Array(buffer, offset, ninst * 4);offset += ninst * 4 * 4;
- quat = new Float32Array(buffer, offset, ninst * 4);offset += ninst * 4 * 4;
- }
- if ( npoints !== 0 ) {
- ctr_pos = new Float32Array(buffer, offset, npoints * 4);offset += npoints * 4 * 4;
- offset += npoints * 4 * 4;
- ctr_info = new Float32Array(buffer, offset, npoints * 4);offset += npoints * 4 * 4;
- curve_ids = new Float32Array(buffer, offset, ncurve * 4);offset += ncurve * 4 * 4;
- }
-
- for (let i = 0; i < ninst; i++) {
- const x: number = pos[i * 4 + 0];
- const y: number = pos[i * 4 + 1];
- const z: number = pos[i * 4 + 2];
- const ingr_id = pos[i * 4 + 3] as number;
- const pid = cell.mapping_ids![ingr_id];
- if (!packings[pid[0]].ingredients[pid[1]].results) {
- packings[pid[0]].ingredients[pid[1]].results = [];
- }
- packings[pid[0]].ingredients[pid[1]].results.push([Vec3.create(x, y, z),
- Quat.create(quat[i * 4 + 0], quat[i * 4 + 1], quat[i * 4 + 2], quat[i * 4 + 3])]);
- }
- let counter = 0;
- let ctr_points: Vec3[] = [];
- let prev_ctype = 0;
- let prev_cid = 0;
-
- for (let i = 0; i < npoints; i++) {
- const x: number = -ctr_pos[i * 4 + 0];
- const y: number = ctr_pos[i * 4 + 1];
- const z: number = ctr_pos[i * 4 + 2];
- const cid: number = ctr_info[i * 4 + 0];// curve id
- const ctype: number = curve_ids[cid * 4 + 0];// curve type
- // cid 148 165 -1 0
- // console.log("cid ",cid,ctype,prev_cid,prev_ctype);//165,148
- if (prev_ctype !== ctype){
- const pid = cell.mapping_ids![-prev_ctype - 1];
- const cname = `curve${counter}`;
- packings[pid[0]].ingredients[pid[1]].nbCurve = counter + 1;
- packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
- ctr_points = [];
- counter = 0;
- } else if (prev_cid !== cid){
- ctr_points = [];
- const pid = cell.mapping_ids![-prev_ctype - 1];
- const cname = `curve${counter}`;
- packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
- counter += 1;
- }
- ctr_points.push(Vec3.create(x, y, z));
- prev_ctype = ctype;
- prev_cid = cid;
- }
- // do the last one
- if ( npoints !== 0 ) {
- const pid = cell.mapping_ids![-prev_ctype - 1];
- const cname = `curve${counter}`;
- packings[pid[0]].ingredients[pid[1]].nbCurve = counter + 1;
- packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
- }
- return packings;
-}
-*/
\ No newline at end of file
+}
\ No newline at end of file
--
GitLab