Merge branch 'master' of https://github.com/molstar/molstar-proto

.dockerignore

+.*
+node_modules
+npm-debug.log
+*.sublime-project
\ No newline at end of file

.gitignore

@@ -6,4 +6,5 @@ npm-debug.log
 
 *.sublime-workspace
 
-web/render-test/index.js
\ No newline at end of file
+web/render-test/index.js
+.idea

Dockerfile

+# This is to build a container that demos the Molstar Canvas prototype
+# Source material: https://nodejs.org/en/docs/guides/nodejs-docker-webapp/
+# Source material: https://derickbailey.com/2017/05/31/how-a-650mb-node-js-image-for-docker-uses-less-space-than-a-50mb-image/
+# Source material: https://hub.docker.com/_/node/
+
+# Use the slimed NodeJS source, yielding a space savings of 600MB (~66% of total)
+FROM node:alpine
+
+# Create app directory
+WORKDIR /usr/src/app
+
+# Install app dependencies
+# A wildcard is used to ensure both package.json AND package-lock.json AND tslint.json AND tsconfig.json are copied
+# where available (npm@5+)
+COPY *.json ./
+
+# Install all dependencies and copy results
+RUN npm install
+COPY . .
+
+# Build application and bundle results
+RUN npm run build
+COPY build/ build/
+
+# Build Canvas application and bundle results
+RUN npm run build-canvas
+COPY build/ build/
+
+# Open ports for HTTP
+EXPOSE 8080/tcp
+
+# Setup standalone simple webserver to run the demo
+RUN npm install http-server -g
+
+# Start NodeJS at container stand up
+CMD [ "http-server", "build/canvas/", "-p", "8080" ]
+
+# Developer helpers (what is inside this container?)
+RUN node -v
+RUN ls -alh

README.md

@@ -78,6 +78,19 @@ From the root of the project:
 
 and navigate to `build/viewer`
 
+
+**Run via Docker**
+
+Build the docker image
+
+    docker build -t molstar-proto .
+
+Run the image
+
+    docker run -p 8080:8080 molstar-proto
+
+
+
 ### Code generation
 **CIF schemas**
 

src/mol-math/geometry/symmetry-operator.ts

@@ -30,6 +30,17 @@ namespace SymmetryOperator {
         return { name, matrix, inverse: Mat4.invert(Mat4.zero(), matrix), isIdentity: false, hkl: _hkl };
     }
 
+    export function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3) {
+        const matrix = Mat4.identity();
+        for (let i = 0; i < 3; i++) {
+            for (let j = 0; j < 3; j++) {
+                Mat4.setValue(matrix, i, j, Mat3.getValue(rot, i, j));
+            }
+        }
+        Mat4.setTranslation(matrix, offset);
+        return Mat4.isRotationAndTranslation(matrix, RotationEpsilon);
+    }
+
     export function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3) {
         const t = Mat4.identity();
         for (let i = 0; i < 3; i++) {

src/mol-model/structure/model/formats/mmcif.ts

@@ -66,7 +66,8 @@ function getNcsOperators(format: mmCIF_Format) {
     for (let i = 0; i < struct_ncs_oper._rowCount; i++) {
         const m = Tensor.toMat3(matrixSpace, matrix.value(i));
         const v = Tensor.toVec3(vectorSpace, vector.value(i));
-        opers[i] = SymmetryOperator.ofRotationAndOffset(`ncs_${id.value(i)}`, m, v);
+        if (!SymmetryOperator.checkIfRotationAndTranslation(m, v)) continue;
+        opers[opers.length] = SymmetryOperator.ofRotationAndOffset(`ncs_${id.value(i)}`, m, v);
     }
     return opers;
 }

src/servers/model/preprocess.ts

@@ -4,28 +4,14 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import * as argparse from 'argparse'
-import { preprocessFile } from './preprocess/preprocess';
+import * as cluster from 'cluster'
+import { runChild } from './preprocess/parallel';
 
-const cmdParser = new argparse.ArgumentParser({
-    addHelp: true,
-    description: 'Preprocess CIF files to include custom properties and convert them to BinaryCIF format.'
-});
-cmdParser.addArgument(['--input', '-i'], { help: 'Input filename', required: true });
-cmdParser.addArgument(['--outCIF', '-oc'], { help: 'Output CIF filename', required: false });
-cmdParser.addArgument(['--outBCIF', '-ob'], { help: 'Output BinaryCIF filename', required: false });
-
-// TODO: "bulk" mode
-
-interface CmdArgs {
-    input: string,
-    outCIF?: string,
-    outBCIF?: string
+if (cluster.isMaster) {
+    require('./preprocess/master');
+} else {
+    runChild();
 }
 
-const cmdArgs = cmdParser.parseArgs() as CmdArgs;
-
-if (cmdArgs.input) preprocessFile(cmdArgs.input, cmdArgs.outCIF, cmdArgs.outBCIF);
-
 // example:
 // node build\node_modules\servers\model\preprocess -i e:\test\Quick\1cbs_updated.cif -oc e:\test\mol-star\model\1cbs.cif -ob e:\test\mol-star\model\1cbs.bcif
\ No newline at end of file

src/servers/model/preprocess/converter.ts

@@ -7,7 +7,7 @@
 import { CifCategory, CifField, CifFrame, getCifFieldType } from 'mol-io/reader/cif';
 import { CifWriter } from 'mol-io/writer/cif';
 import { Task } from 'mol-task';
-import { showProgress } from './util';
+// import { showProgress } from './util';
 
 function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
     return {
@@ -47,5 +47,5 @@ export function classifyCif(frame: CifFrame) {
             ret.push(getCategoryInstanceProvider(cat, fields));
         }
         return ret;
-    }).run(showProgress, 250);
+    }).run();
 }
\ No newline at end of file

src/servers/model/preprocess/master.ts

+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as fs from 'fs'
+import * as path from 'path'
+import * as argparse from 'argparse'
+import { preprocessFile } from './preprocess';
+import { ParallelPreprocessConfig, runMaster } from './parallel';
+
+const cmdParser = new argparse.ArgumentParser({
+    addHelp: true,
+    description: 'Preprocess CIF files to include custom properties and convert them to BinaryCIF format.'
+});
+cmdParser.addArgument(['--input', '-i'], { help: 'Input filename', required: false });
+cmdParser.addArgument(['--outCIF', '-oc'], { help: 'Output CIF filename', required: false });
+cmdParser.addArgument(['--outBCIF', '-ob'], { help: 'Output BinaryCIF filename', required: false });
+cmdParser.addArgument(['--bulk', '-b'], { help: 'Bulk JSON ({ numProcesses?: number, entries: { source: string, cif?: string, bcif?: string }[] })', required: false });
+cmdParser.addArgument(['--folderIn', '-f'], { help: 'Convert folder', required: false });
+cmdParser.addArgument(['--folderOutCIF', '-foc'], { help: 'Convert folder text output', required: false });
+cmdParser.addArgument(['--folderOutBCIF', '-fob'], { help: 'Convert folder binary output', required: false });
+cmdParser.addArgument(['--folderNumProcesses', '-fp'], { help: 'Convert folder num processes', required: false });
+
+interface CmdArgs {
+    bulk?: string,
+    input?: string,
+    outCIF?: string,
+    outBCIF?: string,
+    folderIn?: string,
+    folderOutCIF?: string,
+    folderOutBCIF?: string,
+    folderNumProcesses?: string
+}
+
+const cmdArgs = cmdParser.parseArgs() as CmdArgs;
+
+if (cmdArgs.input) preprocessFile(cmdArgs.input, cmdArgs.outCIF, cmdArgs.outBCIF);
+else if (cmdArgs.bulk) runBulk(cmdArgs.bulk);
+else if (cmdArgs.folderIn) runFolder(cmdArgs);
+
+function runBulk(input: string) {
+    const config = JSON.parse(fs.readFileSync(input, 'utf8')) as ParallelPreprocessConfig;
+    runMaster(config);
+}
+
+function runFolder(args: CmdArgs) {
+    const files = fs.readdirSync(args.folderIn!);
+    const config: ParallelPreprocessConfig = { numProcesses: +args.folderNumProcesses! || 1, entries: [] };
+    const cifTest = /\.cif$/;
+    for (const f of files) {
+        if (!cifTest.test(f)) continue;
+
+        config.entries.push({
+            source: path.join(args.folderIn!, f),
+            cif: cmdArgs.folderOutCIF ? path.join(args.folderOutCIF!, f) : void 0,
+            bcif: cmdArgs.folderOutBCIF ? path.join(args.folderOutBCIF!, path.parse(f).name + '.bcif') : void 0,
+        });
+    }
+    runMaster(config);
+}
+
+// example:
+// node build\node_modules\servers\model\preprocess -i e:\test\Quick\1cbs_updated.cif -oc e:\test\mol-star\model\1cbs.cif -ob e:\test\mol-star\model\1cbs.bcif
\ No newline at end of file

src/servers/model/preprocess/parallel.ts

+/**
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as path from 'path'
+import * as cluster from 'cluster'
+import { now } from 'mol-task';
+import { PerformanceMonitor } from 'mol-util/performance-monitor';
+import { preprocessFile } from './preprocess';
+
+export interface PreprocessEntry {
+    source: string,
+    cif?: string,
+    bcif?: string
+}
+
+export interface ParallelPreprocessConfig {
+    numProcesses?: number,
+    entries: PreprocessEntry[]
+}
+
+export function runMaster(config: ParallelPreprocessConfig) {
+    const parts = partitionArray(config.entries, config.numProcesses || 1);
+    // const numForks = Math.min(parts.length, config.numProcesses);
+
+    const started = now();
+    let progress = 0;
+    const onMessage = (msg: any) => {
+        if (msg.type === 'tick') {
+            progress++;
+            const elapsed = now() - started;
+            console.log(`[${progress}/${config.entries.length}] in ${PerformanceMonitor.format(elapsed)} (avg ${PerformanceMonitor.format(elapsed / progress)}).`);
+        } else if (msg.type === 'error') {
+            console.error(`${msg.id}: ${msg.error}`)
+        }
+    }
+
+    for (const _ of parts) {
+        const worker = cluster.fork();
+        worker.on('message', onMessage);
+    }
+
+    let i = 0;
+    for (const id in cluster.workers) {
+        cluster.workers[id]!.send(parts[i++]);
+    }
+}
+
+export function runChild() {
+    process.on('message', async (entries: PreprocessEntry[]) => {
+        for (const entry of entries) {
+            try {
+                await preprocessFile(entry.source, entry.cif, entry.bcif);
+            } catch (e) {
+                process.send!({ type: 'error', id: path.parse(entry.source).name, error: '' + e });
+            }
+            process.send!({ type: 'tick' });
+        }
+        process.exit();
+    });
+}
+
+function partitionArray<T>(xs: T[], count: number): T[][] {
+    const ret: T[][] = [];
+    const s = Math.ceil(xs.length / count);
+    for (let i = 0; i < xs.length; i += s) {
+        const bucket: T[] = [];
+        for (let j = i, _j = Math.min(xs.length, i + s); j < _j; j++) {
+            bucket.push(xs[j]);
+        }
+        ret.push(bucket);
+    }
+    return ret;
+}
+

src/servers/model/preprocess/preprocess.ts

@@ -6,58 +6,62 @@
 
 import { readStructure } from '../server/structure-wrapper';
 import { classifyCif } from './converter';
-import { ConsoleLogger } from 'mol-util/console-logger';
+// import { ConsoleLogger } from 'mol-util/console-logger';
 import { Structure } from 'mol-model/structure';
 import { CifWriter } from 'mol-io/writer/cif';
 import Writer from 'mol-io/writer/writer';
 import { wrapFileToWriter } from '../server/api-local';
-import { Task } from 'mol-task';
-import { showProgress, clearLine } from './util';
+import { Task/*, now*/ } from 'mol-task';
+import { /*showProgress, clearLine */ } from './util';
 import { encode_mmCIF_categories, CifExportContext } from 'mol-model/structure/export/mmcif';
 
-// TODO: error handling, bulk mode
+// TODO: error handling
+// let linearId = 0;
 
 export async function preprocessFile(filename: string, outputCif?: string, outputBcif?: string) {
-    ConsoleLogger.log('ModelServer', `Reading ${filename}...`);
+    // linearId++;
+
+    //const started = now();
+    //ConsoleLogger.log(`${linearId}`, `Reading '${filename}'...`);
     const input = await readStructure('entry', '_local_', filename);
-    ConsoleLogger.log('ModelServer', `Classifying CIF categories...`);
+    //ConsoleLogger.log(`${linearId}`, `Classifying CIF categories...`);
     const categories = await classifyCif(input.cifFrame);
-    clearLine();
+    //clearLine();
 
     const exportCtx = CifExportContext.create(input.structure, input.structure.models[0]);
 
     if (outputCif) {
-        ConsoleLogger.log('ModelServer', `Encoding CIF...`);
+        //ConsoleLogger.log(`${linearId}`, `Encoding CIF...`);
         const writer = wrapFileToWriter(outputCif);
         const encoder = CifWriter.createEncoder({ binary: false });
         await encode(input.structure, input.cifFrame.header, categories, encoder, exportCtx, writer);
-        clearLine();
+        // clearLine();
         writer.end();
     }
 
     if (outputBcif) {
-        ConsoleLogger.log('ModelServer', `Encoding BinaryCIF...`);
+        // ConsoleLogger.log(`${linearId}`, `Encoding BinaryCIF...`);
         const writer = wrapFileToWriter(outputBcif);
         const encoder = CifWriter.createEncoder({ binary: true, binaryAutoClassifyEncoding: true });
         await encode(input.structure, input.cifFrame.header, categories, encoder, exportCtx, writer);
-        clearLine();
+        //clearLine();
         writer.end();
     }
-    ConsoleLogger.log('ModelServer', `Done.`);
+    // ConsoleLogger.log(`${linearId}`, `Finished '${filename}' in ${Math.round(now() - started)}ms`);
 }
 
 function encode(structure: Structure, header: string, categories: CifWriter.Category[], encoder: CifWriter.Encoder, exportCtx: CifExportContext, writer: Writer) {
     return Task.create('Encode', async ctx => {
         const skipCategoryNames = new Set<string>(categories.map(c => c.name));
         encoder.startDataBlock(header);
-        let current = 0;
+        // let current = 0;
         for (const cat of categories){
             encoder.writeCategory(cat);
-            current++;
-            if (ctx.shouldUpdate) await ctx.update({ message: 'Encoding...', current, max: categories.length });
+            // current++;
+            // if (ctx.shouldUpdate) await ctx.update({ message: 'Encoding...', current, max: categories.length });
         }
         encode_mmCIF_categories(encoder, structure, { skipCategoryNames, exportCtx });
         encoder.encode();
         encoder.writeTo(writer);
-    }).run(showProgress, 250);
+    }).run();
 }
\ No newline at end of file

src/servers/model/properties.ts

@@ -6,14 +6,14 @@
  */
 
 import { Model } from 'mol-model/structure';
-import { PDBe_structureQualityReport } from './properties/pdbe';
-import { RCSB_assemblySymmetry } from './properties/rcsb';
+//import { PDBe_structureQualityReport } from './properties/pdbe';
+//import { RCSB_assemblySymmetry } from './properties/rcsb';
 
 export function attachModelProperties(model: Model): Promise<any>[] {
     // return a list of promises that start attaching the props in parallel
     // (if there are downloads etc.)
     return [
-        PDBe_structureQualityReport(model),
-        RCSB_assemblySymmetry(model)
+        //PDBe_structureQualityReport(model),
+        //RCSB_assemblySymmetry(model)
     ];
 }
\ No newline at end of file