Merge pull request #1040 from papillot/1015-Binary-Cif-support

1015 binary cif support

examples/js/gui.js

@@ -524,7 +524,9 @@ NGL.MenubarFileWidget = function (stage) {
 
   function onPdbInputKeyDown (e) {
     if (e.keyCode === 13) {
-      stage.loadFile('rcsb://' + e.target.value.trim(), {
+      const val = e.target.value.trim()
+      const protocol = val.startsWith('AF_') ? 'rcsb://' : 'pdbe://'
+      stage.loadFile(protocol + val, {
         defaultRepresentation: true
       })
       e.target.value = ''

examples/scripts/showcase/viruses.js

@@ -14,7 +14,7 @@ function createElement (name, properties, style) {
   return el
 }
 
-var pdbs = [ '1stm', '3nap', '1sid', '2ft1', '4cwu' ]
+var pdbs = [ '1stm', '3nap', '1sid', '2ft1', '6cgv' ]
 var colors = [ 'red', 'yellow', 'green', 'lightblue', 'violet' ]
 
 Promise.all(pdbs.map(function (id) {

package.json

@@ -14,7 +14,7 @@
     "prebuild": "npm run lint",
     "build": "npm run dts && rollup -c",
     "postbuild": "node ./scripts/makeScriptsList.js",
-    "test": "jest",
+    "test": "vitest --globals",
     "preversion": "npm test",
     "version": "npm run build-min && git add -A dist",
     "postversion": "git push && git push --tags",
@@ -27,17 +27,6 @@
     "prerelease": "./scripts/release.sh prerelease",
     "build-min": "npm run lint && npm run dts && rollup -c rollup.config.dist.js"
   },
-  "jest": {
-    "moduleFileExtensions": [
-      "ts",
-      "js"
-    ],
-    "transform": {
-      "\\.ts$": "ts-jest",
-      "\\.es6\\.js": "babel-jest"
-    },
-    "testRegex": "\\.spec\\.ts|kin.*test.ts$"
-  },
   "homepage": "https://github.com/arose/ngl#readme",
   "repository": {
     "type": "git",
@@ -67,24 +56,23 @@
     "@rollup/plugin-typescript": "^8.1.1",
     "@types/chroma-js": "^1.3.5",
     "@types/jest": "^27.5.1",
-    "@types/node": "^10.17.9",
     "@types/offscreencanvas": "^2019.6.4",
     "@types/signals": "1.0.1",
     "@types/sprintf-js": "^1.1.2",
     "@types/three": "^0.158.2",
     "@yushijinhun/three-minifier-rollup": "^0.3.1",
     "babel-plugin-array-includes": "^2.0.3",
-    "jest": "^29.7.0",
-    "jest-environment-jsdom": "^29.7.0",
+    "jsdom": "^24.0.0",
     "rollup": "^2.38.5",
-    "standard": "^17.1.0",
-    "ts-jest": "^29.1.1",
+    "standard": "^11.0.1",
     "tslib": "^2.3.1",
     "typedoc": "^0.22.15",
-    "typescript": "^4.5.4"
+    "typescript": "^4.5.4",
+    "vitest": "^1.5.2"
   },
   "dependencies": {
     "chroma-js": "^1.3.7",
+    "molstar": "^4.1.0",
     "signals": "^1.0.0",
     "sprintf-js": "^1.1.2",
     "three": "^0.158.0"

src/datasource/alphafold-datasource.ts

@@ -5,12 +5,11 @@
  */
 
 import { Log, DatasourceRegistry } from '../globals'
-import { getProtocol } from '../utils'
 import { getFileInfo } from '../loader/loader-utils'
 import Datasource from './datasource'
 
 const baseUrl = '//alphafold.ebi.ac.uk/files/AF-'
-const suffixURL = '-F1-model_v2.pdb'
+const suffixURL = '-F1-model_v4.pdb'
 
 class AlphafoldDatasource extends Datasource {
     getUrl (src: string) {
@@ -23,7 +22,7 @@ class AlphafoldDatasource extends Datasource {
             Log.warn('unsupported AF ext', info.ext)
             url = baseUrl + uniprotid + suffixURL
         }
-        return getProtocol() + url
+        return 'https://' + url
     }
 
     getExt (src: string) {

src/datasource/pdbe-datasource.ts

@@ -0,0 +1,58 @@
+/**
+ * @file PDB Europe Datasource
+ * @author Paul Pillot <[email protected]>
+ * @private
+ */
+
+import { Log, DatasourceRegistry } from '../globals'
+import { getFileInfo } from '../loader/loader-utils'
+import Datasource from './datasource'
+
+const baseUrl = '//www.ebi.ac.uk/pdbe/entry-files/download/'
+
+// Examples:
+//https://www.ebi.ac.uk/pdbe/entry-files/download/5z6y_updated.cif
+//https://www.ebi.ac.uk/pdbe/entry-files/download/pdb5z6y.ent
+//https://www.ebi.ac.uk/pdbe/entry-files/download/5z6y.bcif
+
+class PDBeDatasource extends Datasource {
+  getUrl (src: string) {
+    // valid path are
+    // XXXX.pdb, XXXX.ent, XXXX.cif, XXXX.bcif
+    // XXXX defaults to XXXX.bcif
+    const info = getFileInfo(src)
+    let pdbid = info.name.indexOf('_') > -1 ? info.name : info.name.substring(0, 4) // Allow extended pdb codes
+    let url
+    switch (info.ext) {
+        case 'cif':
+            url = baseUrl + pdbid + '_updated.cif'  // "Updated mmcif" files contain connectivity
+            break
+        case 'pdb':
+        case 'ent':
+            if (!pdbid.startsWith('pdb')) {
+                pdbid = 'pdb' + pdbid
+            }
+            url = baseUrl + pdbid + '.ent'
+            break
+        case 'bcif':
+            url = baseUrl + info.path
+            break
+        case '':
+            url = baseUrl + pdbid + '.bcif'
+            break
+        default:
+            Log.warn('unsupported ext', info.ext)
+            url = baseUrl + pdbid + '.bcif'
+    }
+    return 'https://' + url
+  }
+
+  getExt (src: string) {
+    const ext = getFileInfo(src).ext
+    return ext ? ext : 'mmtf'
+  }
+}
+
+DatasourceRegistry.add('pdbe', new PDBeDatasource())
+
+export default PDBeDatasource

src/datasource/rcsb-datasource.ts

@@ -13,30 +13,37 @@ const baseUrl = '//files.rcsb.org/download/'
 const mmtfBaseUrl = '//mmtf.rcsb.org/v1.0/'
 const mmtfFullUrl = mmtfBaseUrl + 'full/'
 const mmtfReducedUrl = mmtfBaseUrl + 'reduced/'
+const bcifBaseUrl = '//models.rcsb.org/'
 
 class RcsbDatasource extends Datasource {
   getUrl (src: string) {
     // valid path are
     // XXXX.pdb, XXXX.pdb.gz, XXXX.cif, XXXX.cif.gz, XXXX.mmtf, XXXX.bb.mmtf
     // XXXX defaults to XXXX.cif
     const info = getFileInfo(src)
-    const pdbid = info.name.substr(0, 4)
+    const pdbid = info.name.indexOf('_') > -1 ? info.name : info.name.substring(0, 4) // Allow extended pdb codes and alphafold codes
     let url
     if ([ 'pdb', 'cif' ].includes(info.ext) &&
         (info.compressed === false || info.compressed === 'gz')
     ) {
       url = baseUrl + info.path
     } else if (info.ext === 'mmtf') {
+      Log.warn('MMTF files distribution is discontinued by RCSB PDB as of July 2, 2024.\n Consider using bcif format instead. See https://www.rcsb.org/news/65a1af31c76ca3abcc925d0c for the deprecation notice')
       if (info.base.endsWith('.bb')) {
         url = mmtfReducedUrl + pdbid
       } else {
         url = mmtfFullUrl + pdbid
       }
+    } else if (info.ext === 'bcif' &&
+        (info.compressed === false || info.compressed === 'gz')
+    ) {
+      url = bcifBaseUrl + info.path
     } else if (!info.ext) {
-      url = mmtfFullUrl + pdbid
+      Log.warn('mmCif files available from RCSB PDB lack connectivity information.\n Consider using PDBe as the data provider for using "Updated mmCif files" that contain residues connectivity records.')
+      url = bcifBaseUrl + pdbid + '.bcif.gz'
     } else {
       Log.warn('unsupported ext', info.ext)
-      url = mmtfFullUrl + pdbid
+      url = bcifBaseUrl + pdbid + '.bcif.gz'
     }
     return getProtocol() + url
   }

src/ngl.ts

@@ -181,6 +181,7 @@ import './utils/gzip-decompressor'
 //
 
 import './datasource/rcsb-datasource'
+import './datasource/pdbe-datasource'
 import './datasource/pubchem-datasource'
 import './datasource/passthrough-datasource'
 import './datasource/alphafold-datasource'