diff --git a/README.md b/README.md
index 5b5ead33d2cf3cd0239daa67e14d2cc5833bc64d..4da71bf2ef54c6129134af1d0474ba794ba7be3d 100644
--- a/README.md
+++ b/README.md
@@ -114,9 +114,9 @@ and navigate to `build/viewer`
**Convert any CIF to BinaryCIF**
- node build/model-server/preprocess -i file.cif -ob file.bcif
-
-To see all available commands, use ``node build/model-server/preprocess -h``.
+ node lib/servers/model/preprocess -i file.cif -ob file.bcif
+
+To see all available commands, use ``node lib/servers/model/preprocess -h``.
Or
diff --git a/src/apps/viewer/extensions/cellpack/curve.ts b/src/apps/viewer/extensions/cellpack/curve.ts
index 011d2dd15037fde20679e0b55ccf71fa0a03513e..4b789f7a5cb1755033270839266762a1686da4eb 100644
--- a/src/apps/viewer/extensions/cellpack/curve.ts
+++ b/src/apps/viewer/extensions/cellpack/curve.ts
@@ -191,19 +191,14 @@ function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
const rpTmpVec1 = Vec3()
-export function getMatFromResamplePoints(points: NumberArray) {
- const segmentLength = 3.4
- const new_points = ResampleControlPoints(points, 3.4)
+export function getMatFromResamplePoints(points: NumberArray, segmentLength: number) {
+ const new_points = ResampleControlPoints(points, segmentLength)
const npoints = new_points.length
const new_normal = GetSmoothNormals(new_points)
const frames = GetMiniFrame(new_points, new_normal)
const limit = npoints
const transforms: Mat4[] = []
const pti = Vec3.copy(rpTmpVec1, new_points[0]);
- // console.log(new_points.length)
- // console.log(points.length/3)
- // console.log(limit)
- // console.log(segmentLength)
for (let i = 0; i<npoints-2; ++i) {
const pti1: Vec3 = new_points[i+1] // Vec3.create(points[(i+1)*3],points[(i+1)*3+1],points[(i+1)*3+2]);
const d = Vec3.distance(pti, pti1)
diff --git a/src/apps/viewer/extensions/cellpack/data.ts b/src/apps/viewer/extensions/cellpack/data.ts
index 183dfab4f62ac37bc8d87d65773c14fd4b7fbf05..ff393fac6d2e8526608b6f50af7d9aa763b37de9 100644
--- a/src/apps/viewer/extensions/cellpack/data.ts
+++ b/src/apps/viewer/extensions/cellpack/data.ts
@@ -27,8 +27,7 @@ export interface Cell {
export interface Recipe {
setupfile: string
- /** First entry is name, secound is path: [name: string, path: string][] */
- paths: [string, string][]
+ paths: [string, string][] // [name: string, path: string][]
version: string
name: string
}
@@ -42,21 +41,40 @@ export interface Packing {
ingredients: { [key: string]: Ingredient }
}
-export interface Ingredient {
- source: IngredientSource
- results: [Vec3, Quat][]
- name: string
- positions?: [Vec3[]] // why wrapped in an extra array?
- radii?: [number[]] // why wrapped in an extra array?
+export interface Positions {
+ coords?: Vec3[];
+}
+export interface Radii {
+ radii?: number[];
+}
+
+export interface Ingredient {
+ source: IngredientSource;
+ results: [Vec3, Quat][];
+ name: string;
+ /** Vec3[]];CoarseGraind Beads coordinates LOD */
+ positions?: [Positions];
+ /** number[]];CoarseGraind Beads radii LOD */
+ radii?: [Radii];
/** Number of `curveX` properties in the object where `X` is a 0-indexed number */
- nbCurve?: number
+ nbCurve?: number;
/** Curve properties are Vec3[] but that is not expressable in TypeScript */
- [curveX: string]: unknown
+ [curveX: string]: unknown;
+ /** the orientation in the membrane */
+ principalAxis?: Vec3;
+ /** offset along membrane */
+ offset?: Vec3;
}
export interface IngredientSource {
- pdb: string
- transform: { center: boolean, translate?: Vec3 }
- biomt?: boolean
-}
+ pdb: string;
+ bu?: string; /** biological unit e.g AU,BU1,etc.. */
+ selection?: string; /** NGL selection or :A or :B etc.. */
+ model?: string; /** model number e.g 0,1,2... */
+ transform: {
+ center: boolean;
+ translate?: Vec3;
+ };
+ biomt?: boolean;
+}
\ No newline at end of file
diff --git a/src/apps/viewer/extensions/cellpack/model.ts b/src/apps/viewer/extensions/cellpack/model.ts
index e43e7e5144c8472d01c49cef7f6ef8b7d86d647a..5ef48f02eff4e741a53a8b8f59350e9f5c413b96 100644
--- a/src/apps/viewer/extensions/cellpack/model.ts
+++ b/src/apps/viewer/extensions/cellpack/model.ts
@@ -8,7 +8,7 @@ import { StateAction, StateBuilder, StateTransformer, State } from '../../../../
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 } from './data';
+import { Ingredient, IngredientSource, CellPacking } from './data';
import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile } from './util';
import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit } from '../../../../mol-model/structure';
import { trajectoryFromMmCIF, MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
@@ -34,44 +34,55 @@ function getCellPackModelUrl(fileName: string, baseUrl: string) {
return `${baseUrl}/results/${fileName}`
}
-async function getModel(id: string, baseUrl: string, file?: File) {
+async function getModel(id: string, model_id: number, baseUrl: string, file?: File) {
let model: Model;
if (file) {
const text = await file.text()
if (file.name.endsWith('.cif')) {
const cif = (await parseCif(text)).blocks[0]
- model = (await trajectoryFromMmCIF(cif).run())[0]
+ model = (await trajectoryFromMmCIF(cif).run())[model_id]
} else if (file.name.endsWith('.pdb')) {
const pdb = await parsePDBfile(text, id)
- model = (await trajectoryFromPDB(pdb).run())[0]
+ model = (await trajectoryFromPDB(pdb).run())[model_id]
} else {
throw new Error(`unsupported file type '${file.name}'`)
}
} else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
// return
const cif = await getFromPdb(id)
- model = (await trajectoryFromMmCIF(cif).run())[0]
+ model = (await trajectoryFromMmCIF(cif).run())[model_id]
} else {
const pdb = await getFromCellPackDB(id, baseUrl)
- model = (await trajectoryFromPDB(pdb).run())[0]
+ model = (await trajectoryFromPDB(pdb).run())[model_id]
}
return model
}
-async function getStructure(model: Model, props: { assembly?: string } = {}) {
+async function getStructure(model: Model, source: IngredientSource, props: { assembly?: string } = {}) {
let structure = Structure.ofModel(model)
const { assembly } = props
if (assembly) {
structure = await StructureSymmetry.buildAssembly(structure, assembly).run()
}
+ let query;
+ if (source.selection){
+ const asymIds: string[] = source.selection.replace(' :','').split(' or')
+ query = MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+ 'chain-test': MS.core.set.has([MS.set(...asymIds), MS.ammp('auth_asym_id')])
+ })
+ ])
+ } else {
+ query = MS.struct.modifier.union([
+ MS.struct.generator.atomGroups({
+ 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
+ })
+ ])
+ }
- const query = MS.struct.modifier.union([
- MS.struct.generator.atomGroups({
- 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer'])
- })
- ])
const compiled = compile<StructureSelection>(query)
const result = compiled(new QueryContext(structure))
structure = StructureSelection.unionStructure(result)
@@ -79,7 +90,7 @@ async function getStructure(model: Model, props: { assembly?: string } = {}) {
return structure
}
-function getTransform(trans: Vec3, rot: Quat) {
+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)
Mat4.transpose(m, m)
@@ -88,14 +99,24 @@ function getTransform(trans: Vec3, rot: Quat) {
return m
}
-function getResultTransforms(results: Ingredient['results']) {
- return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]))
+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 p: Vec3 = Vec3.create(trans[0],trans[1],trans[2])
+ Mat4.setTranslation(m, p)
+ return m
+}
+
+
+function getResultTransforms(results: Ingredient['results'], legacy: boolean) {
+ if (legacy) return results.map((r: Ingredient['results'][0]) => getTransformLegacy(r[0], r[1]))
+ else return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]))
}
function getCurveTransforms(ingredient: Ingredient) {
const n = ingredient.nbCurve || 0
const instances: Mat4[] = []
-
+ const segmentLength = (ingredient.radii)? ((ingredient.radii[0].radii)?ingredient.radii[0].radii[0]*2.0:3.4):3.4;
for (let i = 0; i < n; ++i) {
const cname = `curve${i}`
if (!(cname in ingredient)) {
@@ -109,7 +130,7 @@ function getCurveTransforms(ingredient: Ingredient) {
}
const points = new Float32Array(_points.length * 3)
for (let i = 0, il = _points.length; i < il; ++i) Vec3.toArray(_points[i], points, i * 3)
- const newInstances = getMatFromResamplePoints(points)
+ const newInstances = getMatFromResamplePoints(points,segmentLength)
instances.push(...newInstances)
}
@@ -224,7 +245,7 @@ function getCifCurve(name: string, transforms: Mat4[], model: Model) {
};
}
-async function getCurve(name: string, transforms: Mat4[], model: Model) {
+async function getCurve(name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
const cif = getCifCurve(name, transforms, model)
const curveModelTask = Task.create('Curve Model', async ctx => {
@@ -234,7 +255,7 @@ async function getCurve(name: string, transforms: Mat4[], model: Model) {
})
const curveModel = await curveModelTask.run()
- return getStructure(curveModel)
+ return getStructure(curveModel, ingredient.source)
}
async function getIngredientStructure(ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles) {
@@ -251,14 +272,51 @@ async function getIngredientStructure(ingredient: Ingredient, baseUrl: string, i
if (name === 'lypoglycane') return
}
- const model = await getModel(source.pdb || name, baseUrl, file)
+ // model id in case structure is NMR
+ const model_id = (ingredient.source.model)? parseInt(ingredient.source.model) : 0;
+ const model = await getModel(source.pdb || name,model_id, baseUrl, file)
if (!model) return
if (nbCurve) {
- return getCurve(name, getCurveTransforms(ingredient), model)
+ return getCurve(name, ingredient, getCurveTransforms(ingredient), model)
} else {
- const structure = await getStructure(model, { assembly: source.biomt ? '1' : undefined })
- return getAssembly(getResultTransforms(results), structure)
+ let bu: string|undefined = source.bu ? source.bu : undefined;
+ if (bu){
+ if (bu === 'AU') {
+ bu = undefined;
+ } else {
+ bu = bu.slice(2)
+ }
+ }
+ let structure = await getStructure(model,source, { assembly: bu })
+ // transform with offset and pcp
+ let legacy: boolean = true
+ if (ingredient.offset || ingredient.principalAxis){
+ // center the structure
+ legacy=false
+ const boundary = structure.boundary
+ let structureCenter: Vec3 = Vec3.zero()
+ Vec3.negate(structureCenter,boundary.sphere.center)
+ const m1: Mat4 = Mat4.identity()
+ Mat4.setTranslation(m1, structureCenter)
+ structure = Structure.transform(structure,m1)
+ if (ingredient.offset){
+ if (!Vec3.exactEquals(ingredient.offset,Vec3.zero())){
+ const m: Mat4 = Mat4.identity();
+ Mat4.setTranslation(m, ingredient.offset)
+ structure = Structure.transform(structure,m);
+ }
+ }
+ if (ingredient.principalAxis){
+ if (!Vec3.exactEquals(ingredient.principalAxis,Vec3.unitZ)){
+ const q: Quat = Quat.identity();
+ Quat.rotationTo(q,ingredient.principalAxis,Vec3.unitZ)
+ const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q)
+ structure = Structure.transform(structure,m);
+ }
+ }
+ }
+ return getAssembly(getResultTransforms(results,legacy), structure)
}
}
@@ -319,6 +377,44 @@ async function handleHivRna(ctx: { runtime: RuntimeContext, fetch: AjaxTask }, p
}
}
+async function loadMembrane(name: string, plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
+ const fname: string = `${name}.bcif`
+ let ingredientFiles: IngredientFiles = {}
+ if (params.ingredients.files !== null) {
+ for (let i = 0, il = params.ingredients.files.length; i < il; ++i) {
+ const file = params.ingredients.files.item(i)
+ if (file) ingredientFiles[file.name] = file
+ }
+ }
+ const url = `${params.baseUrl}/membranes/${name}.bcif`
+ //
+ const file = (ingredientFiles)?ingredientFiles[fname]:null;
+ // can we check if url exist
+ let membrane
+ if (!file) {
+ membrane = await state.build().toRoot()
+ .apply(StateTransforms.Data.Download, { label: name, url, isBinary: true }, { 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)
+ .commit()
+ } else {
+ membrane = await state.build().toRoot()
+ .apply(StateTransforms.Data.ReadFile, { file, isBinary: true, label: file.name }, { 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)
+ .commit()
+ }
+
+ const membraneParams = {
+ representation: params.preset.representation,
+ }
+ await CellpackMembranePreset.apply(membrane, membraneParams, plugin)
+}
+
async function loadHivMembrane(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
const url = `${params.baseUrl}/membranes/hiv_lipids.bcif`
const membrane = await state.build().toRoot()
@@ -381,6 +477,9 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
representation: params.preset.representation,
}
await CellpackPackingPreset.apply(packing, packingParams, plugin)
+ if ( packings[i].location === 'surface' ){
+ await loadMembrane(packings[i].name, plugin, runtime, state, params)
+ }
}
}
@@ -392,6 +491,7 @@ const LoadCellPackModelParams = {
['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV-1_0.1.6-8_mixed_radii_pdb'],
['hiv_lipids.bcif', 'hiv_lipids'],
['influenza_model1.json', 'influenza_model1'],
+ ['ExosomeModel.json', 'ExosomeModel'],
['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
] as const),
'file': PD.File({ accept: 'id' }),