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 <paul.pillot@tandemai.com>
+ * @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'