3.4.0

changelog
package updates
2026-06-06 06:34:23 +08:00 · 2022-03-13 13:12:32 -07:00 · 2022-03-13 12:50:44 -07:00 · 2022-03-13 12:49:03 -07:00 · 2022-03-13 12:19:04 -07:00 · 2022-03-13 12:16:12 -07:00
68 changed files with 3550 additions and 514 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,20 @@ Note that since we don't clearly distinguish between a public and private interf

 ## [Unreleased]

+## [v3.4.0] - 2022-03-13
+
+- Fix handling of mmcif with empty ``label_*`` fields
+- Improve saccharide detection (compare against list from CCD)
+- Fix legend label of hydrophobicity color theme
+- Add ``LoadTrajectory`` action
+- Add ``CustomImportControls`` to left panel
+- Add Zenodo import extension (load structures, trajectories, volumes, and zip files)
+- Fix loading of some compressed files within sessions
+- Fix wrong element assignment for atoms with Charmm ion names
+- Fix handling of empty symmetry cell data
+- Add support for ``trr`` and ``nctraj`` coordinates files
+- Add support for ``prmtop`` and ``top`` topology files
+
 ## [v3.3.1] - 2022-02-27

 - Fix issue with unit boundary reuse (do at visual level instead)
--- a/README.md
+++ b/README.md
@@ -120,6 +120,9 @@ and navigate to `build/viewer`

    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts

+**Saccharide names**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts

 **GraphQL schemas**

--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
  "name": "molstar",
-  "version": "3.3.1",
+  "version": "3.4.0",
  "lockfileVersion": 2,
  "requires": true,
  "packages": {
    "": {
      "name": "molstar",
-      "version": "3.3.1",
+      "version": "3.4.0",
      "license": "MIT",
      "dependencies": {
        "@types/argparse": "^2.0.10",
@@ -15,8 +15,8 @@
        "@types/express": "^4.17.13",
        "@types/node": "^16.11.26",
        "@types/node-fetch": "^2.6.1",
-        "@types/react": "^17.0.39",
-        "@types/react-dom": "^17.0.11",
+        "@types/react": "^17.0.40",
+        "@types/react-dom": "^17.0.13",
        "@types/swagger-ui-dist": "3.30.1",
        "argparse": "^2.0.1",
        "body-parser": "^1.19.2",
@@ -27,8 +27,8 @@
        "immer": "^9.0.12",
        "immutable": "^4.0.0",
        "node-fetch": "^2.6.7",
-        "rxjs": "^7.5.4",
-        "swagger-ui-dist": "^4.5.2",
+        "rxjs": "^7.5.5",
+        "swagger-ui-dist": "^4.6.2",
        "tslib": "^2.3.1",
        "util.promisify": "^1.1.1",
        "xhr2": "^0.2.1"
@@ -47,38 +47,38 @@
        "@graphql-codegen/add": "^3.1.1",
        "@graphql-codegen/cli": "^2.6.2",
        "@graphql-codegen/time": "^3.1.1",
-        "@graphql-codegen/typescript": "^2.4.5",
+        "@graphql-codegen/typescript": "^2.4.7",
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-        "@graphql-codegen/typescript-graphql-request": "^4.3.7",
-        "@graphql-codegen/typescript-operations": "^2.3.2",
+        "@graphql-codegen/typescript-graphql-request": "^4.4.2",
+        "@graphql-codegen/typescript-operations": "^2.3.4",
        "@types/cors": "^2.8.12",
        "@types/gl": "^4.1.0",
        "@types/jest": "^27.4.1",
-        "@typescript-eslint/eslint-plugin": "^5.12.1",
-        "@typescript-eslint/parser": "^5.12.1",
+        "@typescript-eslint/eslint-plugin": "^5.14.0",
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        "cpx2": "^4.2.0",
        "crypto-browserify": "^3.12.0",
-        "css-loader": "^6.6.0",
-        "eslint": "^8.10.0",
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        "fs-extra": "^10.0.1",
        "graphql": "^16.3.0",
        "http-server": "^14.1.0",
        "jest": "^27.5.1",
-        "mini-css-extract-plugin": "^2.5.3",
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        "sass": "^1.49.9",
        "sass-loader": "^12.6.0",
-        "simple-git": "^3.2.6",
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-        "typescript": "^4.5.5",
-        "webpack": "^5.69.1",
+        "typescript": "^4.6.2",
+        "webpack": "^5.70.0",
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@@ -1189,15 +1189,6 @@
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@@ -1397,14 +1388,14 @@
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@@ -1413,9 +1404,9 @@
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@@ -14761,26 +14746,26 @@
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+      "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-5.14.0.tgz",
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-        "@typescript-eslint/scope-manager": "5.12.1",
-        "@typescript-eslint/types": "5.12.1",
-        "@typescript-eslint/typescript-estree": "5.12.1",
+        "@typescript-eslint/scope-manager": "5.14.0",
+        "@typescript-eslint/types": "5.14.0",
+        "@typescript-eslint/typescript-estree": "5.14.0",
        "eslint-scope": "^5.1.1",
        "eslint-utils": "^3.0.0"
      }
    },
    "@typescript-eslint/visitor-keys": {
-      "version": "5.12.1",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.12.1.tgz",
-      "integrity": "sha512-l1KSLfupuwrXx6wc0AuOmC7Ko5g14ZOQ86wJJqRbdLbXLK02pK/DPiDDqCc7BqqiiA04/eAA6ayL0bgOrAkH7A==",
+      "version": "5.14.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.14.0.tgz",
+      "integrity": "sha512-yL0XxfzR94UEkjBqyymMLgCBdojzEuy/eim7N9/RIcTNxpJudAcqsU8eRyfzBbcEzGoPWfdM3AGak3cN08WOIw==",
      "dev": true,
      "requires": {
-        "@typescript-eslint/types": "5.12.1",
+        "@typescript-eslint/types": "5.14.0",
        "eslint-visitor-keys": "^3.0.0"
      }
    },
@@ -16282,13 +16267,13 @@
      }
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    "css-loader": {
-      "version": "6.6.0",
-      "resolved": "https://registry.npmjs.org/css-loader/-/css-loader-6.6.0.tgz",
-      "integrity": "sha512-FK7H2lisOixPT406s5gZM1S3l8GrfhEBT3ZiL2UX1Ng1XWs0y2GPllz/OTyvbaHe12VgQrIXIzuEGVlbUhodqg==",
+      "version": "6.7.1",
+      "resolved": "https://registry.npmjs.org/css-loader/-/css-loader-6.7.1.tgz",
+      "integrity": "sha512-yB5CNFa14MbPJcomwNh3wLThtkZgcNyI2bNMRt8iE5Z8Vwl7f8vQXFAzn2HDOJvtDq2NTZBUGMSUNNyrv3/+cw==",
      "dev": true,
      "requires": {
        "icss-utils": "^5.1.0",
-        "postcss": "^8.4.5",
+        "postcss": "^8.4.7",
        "postcss-modules-extract-imports": "^3.0.0",
        "postcss-modules-local-by-default": "^4.0.0",
        "postcss-modules-scope": "^3.0.0",
@@ -16662,9 +16647,9 @@
      }
    },
    "enhanced-resolve": {
-      "version": "5.8.3",
-      "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.8.3.tgz",
-      "integrity": "sha512-EGAbGvH7j7Xt2nc0E7D99La1OiEs8LnyimkRgwExpUMScN6O+3x9tIWs7PLQZVNx4YD+00skHXPXi1yQHpAmZA==",
+      "version": "5.9.2",
+      "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.9.2.tgz",
+      "integrity": "sha512-GIm3fQfwLJ8YZx2smuHpBKkXC1yOk+OBEmKckVyL0i/ea8mqDEykK3ld5dgH1QYPNyT/lIllxV2LULnxCHaHkA==",
      "dev": true,
      "requires": {
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@@ -16814,12 +16799,12 @@
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    "eslint": {
-      "version": "8.10.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.10.0.tgz",
-      "integrity": "sha512-tcI1D9lfVec+R4LE1mNDnzoJ/f71Kl/9Cv4nG47jOueCMBrCCKYXr4AUVS7go6mWYGFD4+EoN6+eXSrEbRzXVw==",
+      "version": "8.11.0",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.11.0.tgz",
+      "integrity": "sha512-/KRpd9mIRg2raGxHRGwW9ZywYNAClZrHjdueHcrVDuO3a6bj83eoTirCCk0M0yPwOjWYKHwRVRid+xK4F/GHgA==",
      "dev": true,
      "requires": {
-        "@eslint/eslintrc": "^1.2.0",
+        "@eslint/eslintrc": "^1.2.1",
        "@humanwhocodes/config-array": "^0.9.2",
        "ajv": "^6.10.0",
        "chalk": "^4.0.0",
@@ -19789,9 +19774,9 @@
      "dev": true
    },
    "mini-css-extract-plugin": {
-      "version": "2.5.3",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.5.3.tgz",
-      "integrity": "sha512-YseMB8cs8U/KCaAGQoqYmfUuhhGW0a9p9XvWXrxVOkE3/IiISTLw4ALNt7JR5B2eYauFM+PQGSbXMDmVbR7Tfw==",
+      "version": "2.6.0",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.6.0.tgz",
+      "integrity": "sha512-ndG8nxCEnAemsg4FSgS+yNyHKgkTB4nPKqCOgh65j3/30qqC5RaSQQXMm++Y6sb6E1zRSxPkztj9fqxhS1Eo6w==",
      "dev": true,
      "requires": {
        "schema-utils": "^4.0.0"
@@ -19890,9 +19875,9 @@
      "dev": true
    },
    "nanoid": {
-      "version": "3.2.0",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.2.0.tgz",
-      "integrity": "sha512-fmsZYa9lpn69Ad5eDn7FMcnnSR+8R34W9qJEijxYhTbfOWzr22n1QxCMzXLK+ODyW2973V3Fux959iQoUxzUIA==",
+      "version": "3.3.1",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.1.tgz",
+      "integrity": "sha512-n6Vs/3KGyxPQd6uO0eH4Bv0ojGSUvuLlIHtC3Y0kEO23YRge8H9x1GCzLn28YX0H66pMkxuaeESFq4tKISKwdw==",
      "dev": true
    },
    "natural-compare": {
@@ -20408,14 +20393,14 @@
      }
    },
    "postcss": {
-      "version": "8.4.5",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.5.tgz",
-      "integrity": "sha512-jBDboWM8qpaqwkMwItqTQTiFikhs/67OYVvblFFTM7MrZjt6yMKd6r2kgXizEbTTljacm4NldIlZnhbjr84QYg==",
+      "version": "8.4.8",
+      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.4.8.tgz",
+      "integrity": "sha512-2tXEqGxrjvAO6U+CJzDL2Fk2kPHTv1jQsYkSoMeOis2SsYaXRO2COxTdQp99cYvif9JTXaAk9lYGc3VhJt7JPQ==",
      "dev": true,
      "requires": {
-        "nanoid": "^3.1.30",
+        "nanoid": "^3.3.1",
        "picocolors": "^1.0.0",
-        "source-map-js": "^1.0.1"
+        "source-map-js": "^1.0.2"
      }
    },
    "postcss-modules-extract-imports": {
@@ -20899,9 +20884,9 @@
      }
    },
    "rxjs": {
-      "version": "7.5.4",
-      "resolved": "https://registry.npmjs.org/rxjs/-/rxjs-7.5.4.tgz",
-      "integrity": "sha512-h5M3Hk78r6wAheJF0a5YahB1yRQKCsZ4MsGdZ5O9ETbVtjPcScGfrMmoOq7EBsCRzd4BDkvDJ7ogP8Sz5tTFiQ==",
+      "version": "7.5.5",
+      "resolved": "https://registry.npmjs.org/rxjs/-/rxjs-7.5.5.tgz",
+      "integrity": "sha512-sy+H0pQofO95VDmFLzyaw9xNJU4KTRSwQIGM6+iG3SypAtCiLDzpeG8sJrNCWn2Up9km+KhkvTdbkrdy+yzZdw==",
      "requires": {
        "tslib": "^2.1.0"
      }
@@ -21140,9 +21125,9 @@
      "dev": true
    },
    "simple-git": {
-      "version": "3.2.6",
-      "resolved": "https://registry.npmjs.org/simple-git/-/simple-git-3.2.6.tgz",
-      "integrity": "sha512-1AFxwgpFiqpBEKHhRC8lhZxtLPP6iuzw2SUN91gA4+Hi+kSfm/oOiUZ2YiT+sEZPP/77KWG7Ci47P9+OC7Dcaw==",
+      "version": "3.3.0",
+      "resolved": "https://registry.npmjs.org/simple-git/-/simple-git-3.3.0.tgz",
+      "integrity": "sha512-K9qcbbZwPHhk7MLi0k0ekvSFXJIrRoXgHhqMXAFM75qS68vdHTcuzmul1ilKI02F/4lXshVgBoDll2t++JK0PQ==",
      "dev": true,
      "requires": {
        "@kwsites/file-exists": "^1.1.1",
@@ -21420,9 +21405,9 @@
      "dev": true
    },
    "swagger-ui-dist": {
-      "version": "4.5.2",
-      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.5.2.tgz",
-      "integrity": "sha512-wV4w54eW9z+VKbYJBJfULfqO05otCbM9jwgRIkwRl9CrfTVKelDzyhhEvdUQkGUzro+Ir8TOZPiZgKIdIdolWQ=="
+      "version": "4.6.2",
+      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.6.2.tgz",
+      "integrity": "sha512-BSt+ukOGkGZ2uHV4jyyCAzt60ysyQpGZAAhtIh7AMHT4MH1xXGkoXm2tfr1oRqO1N4IEY6qqNAlmcfMo/dAYuw=="
    },
    "swap-case": {
      "version": "2.0.2",
@@ -21733,9 +21718,9 @@
      }
    },
    "typescript": {
-      "version": "4.5.5",
-      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz",
-      "integrity": "sha512-TCTIul70LyWe6IJWT8QSYeA54WQe8EjQFU4wY52Fasj5UKx88LNYKCgBEHcOMOrFF1rKGbD8v/xcNWVUq9SymA==",
+      "version": "4.6.2",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.6.2.tgz",
+      "integrity": "sha512-HM/hFigTBHZhLXshn9sN37H085+hQGeJHJ/X7LpBWLID/fbc2acUMfU+lGD98X81sKP+pFa9f0DZmCwB9GnbAg==",
      "dev": true
    },
    "ua-parser-js": {
@@ -21979,9 +21964,9 @@
      "dev": true
    },
    "webpack": {
-      "version": "5.69.1",
-      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.69.1.tgz",
-      "integrity": "sha512-+VyvOSJXZMT2V5vLzOnDuMz5GxEqLk7hKWQ56YxPW/PQRUuKimPqmEIJOx8jHYeyo65pKbapbW464mvsKbaj4A==",
+      "version": "5.70.0",
+      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.70.0.tgz",
+      "integrity": "sha512-ZMWWy8CeuTTjCxbeaQI21xSswseF2oNOwc70QSKNePvmxE7XW36i7vpBMYZFAUHPwQiEbNGCEYIOOlyRbdGmxw==",
      "dev": true,
      "requires": {
        "@types/eslint-scope": "^3.7.3",
@@ -21993,7 +21978,7 @@
        "acorn-import-assertions": "^1.7.6",
        "browserslist": "^4.14.5",
        "chrome-trace-event": "^1.0.2",
-        "enhanced-resolve": "^5.8.3",
+        "enhanced-resolve": "^5.9.2",
        "es-module-lexer": "^0.9.0",
        "eslint-scope": "5.1.1",
        "events": "^3.2.0",
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
  "name": "molstar",
-  "version": "3.3.1",
+  "version": "3.4.0",
  "description": "A comprehensive macromolecular library.",
  "homepage": "https://github.com/molstar/molstar#readme",
  "repository": {
@@ -94,38 +94,38 @@
    "@graphql-codegen/add": "^3.1.1",
    "@graphql-codegen/cli": "^2.6.2",
    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.5",
+    "@graphql-codegen/typescript": "^2.4.7",
    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.7",
-    "@graphql-codegen/typescript-operations": "^2.3.2",
+    "@graphql-codegen/typescript-graphql-request": "^4.4.2",
+    "@graphql-codegen/typescript-operations": "^2.3.4",
    "@types/cors": "^2.8.12",
    "@types/gl": "^4.1.0",
    "@types/jest": "^27.4.1",
-    "@typescript-eslint/eslint-plugin": "^5.12.1",
-    "@typescript-eslint/parser": "^5.12.1",
+    "@typescript-eslint/eslint-plugin": "^5.14.0",
+    "@typescript-eslint/parser": "^5.14.0",
    "benchmark": "^2.1.4",
    "concurrently": "^7.0.0",
    "cpx2": "^4.2.0",
    "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.6.0",
-    "eslint": "^8.10.0",
+    "css-loader": "^6.7.1",
+    "eslint": "^8.11.0",
    "extra-watch-webpack-plugin": "^1.0.3",
    "file-loader": "^6.2.0",
    "fs-extra": "^10.0.1",
    "graphql": "^16.3.0",
    "http-server": "^14.1.0",
    "jest": "^27.5.1",
-    "mini-css-extract-plugin": "^2.5.3",
+    "mini-css-extract-plugin": "^2.6.0",
    "path-browserify": "^1.0.1",
    "raw-loader": "^4.0.2",
    "sass": "^1.49.9",
    "sass-loader": "^12.6.0",
-    "simple-git": "^3.2.6",
+    "simple-git": "^3.3.0",
    "stream-browserify": "^3.0.0",
    "style-loader": "^3.3.1",
    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.5",
-    "webpack": "^5.69.1",
+    "typescript": "^4.6.2",
+    "webpack": "^5.70.0",
    "webpack-cli": "^4.9.2"
  },
  "dependencies": {
@@ -135,8 +135,8 @@
    "@types/express": "^4.17.13",
    "@types/node": "^16.11.26",
    "@types/node-fetch": "^2.6.1",
-    "@types/react": "^17.0.39",
-    "@types/react-dom": "^17.0.11",
+    "@types/react": "^17.0.40",
+    "@types/react-dom": "^17.0.13",
    "@types/swagger-ui-dist": "3.30.1",
    "argparse": "^2.0.1",
    "body-parser": "^1.19.2",
@@ -147,8 +147,8 @@
    "immer": "^9.0.12",
    "immutable": "^4.0.0",
    "node-fetch": "^2.6.7",
-    "rxjs": "^7.5.4",
-    "swagger-ui-dist": "^4.5.2",
+    "rxjs": "^7.5.5",
+    "swagger-ui-dist": "^4.6.2",
    "tslib": "^2.3.1",
    "util.promisify": "^1.1.1",
    "xhr2": "^0.2.1"
--- a/src/apps/viewer/app.ts
+++ b/src/apps/viewer/app.ts
@@ -17,13 +17,15 @@ import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { ZenodoImport } from '../../extensions/zenodo';
 import { Volume } from '../../mol-model/volume';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
 import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
@@ -63,6 +65,7 @@ const Extensions = {
    'mp4-export': PluginSpec.Behavior(Mp4Export),
    'geo-export': PluginSpec.Behavior(GeometryExport),
    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+    'zenodo-import': PluginSpec.Behavior(ZenodoImport),
 };

 const DefaultViewerOptions = {
@@ -453,11 +456,11 @@ export interface VolumeIsovalueInfo {
 export interface LoadTrajectoryParams {
    model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
    | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
-    | { kind: 'topology-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    | { kind: 'topology-url', url: string, format: BuiltInTopologyFormat, isBinary?: boolean }
+    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInTopologyFormat },
    modelLabel?: string,
-    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    coordinates: { kind: 'coordinates-url', url: string, format: BuiltInCoordinatesFormat, isBinary?: boolean }
+    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInCoordinatesFormat },
    coordinatesLabel?: string,
    preset?: keyof PresetTrajectoryHierarchy
 }
--- a/src/cli/chem-comp-dict/create-saccharides.ts
+++ b/src/cli/chem-comp-dict/create-saccharides.ts
@@ -0,0 +1,77 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+const writeFile = util.promisify(fs.writeFile);
+
+import { DatabaseCollection } from '../../mol-data/db';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { ensureDataAvailable, readCCD } from './util';
+
+function extractSaccharideNames(ccd: DatabaseCollection<CCD_Schema>) {
+    const saccharideNames: string[] = [];
+    for (const k in ccd) {
+        const { chem_comp } = ccd[k];
+        const type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push(
+        'UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+        'SQD', // SULFOQUINOVOSYLDIACYLGLYCEROL, via GlyFinder
+    );
+    return saccharideNames;
+}
+
+function writeSaccharideNamesFile(filePath: string, ionNames: string[]) {
+    const output = `/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+
+export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+    writeFile(filePath, output);
+}
+
+async function run(out: string, forceDownload = false) {
+    await ensureDataAvailable(forceDownload);
+    const ccd = await readCCD();
+    const saccharideNames = extractSaccharideNames(ccd);
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeSaccharideNamesFile(out, saccharideNames);
+}
+
+const parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
+    help: 'Force download of CCD and PVCD.'
+});
+interface Args {
+    out: string,
+    forceDownload?: boolean,
+}
+const args: Args = parser.parse_args();
+
+run(args.out, args.forceDownload);
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -32,6 +32,7 @@ import { Color } from '../../mol-util/color';
 import { objectForEach } from '../../mol-util/object';
 import { readFromFile } from '../../mol-util/data-source';
 import { ColorNames } from '../../mol-util/color/names';
+import { createBasic } from '../../mol-model-formats/structure/basic/schema';

 function getCellPackModelUrl(fileName: string, baseUrl: string) {
    return `${baseUrl}/results/${fileName}`;
@@ -310,7 +311,8 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
    const cif = getCifCurve(name, transforms, model);
    const curveModelTask = Task.create('Curve Model', async ctx => {
        const format = MmcifFormat.fromFrame(cif);
-        const models = await createModels(format.data.db, format, ctx);
+        const basic = createBasic(format.data.db, true);
+        const models = await createModels(basic, format, ctx);
        return models.representative;
    });

--- a/src/extensions/zenodo/index.ts
+++ b/src/extensions/zenodo/index.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { ZenodoImportUI } from './ui';
+
+export const ZenodoImport = PluginBehavior.create<{ }>({
+    name: 'extension-zenodo-import',
+    category: 'misc',
+    display: {
+        name: 'Zenodo Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.customImportControls.set('zenodo-import', ZenodoImportUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customImportControls.delete('zenodo-import');
+        }
+    },
+    params: () => ({ })
+});
--- a/src/extensions/zenodo/ui.tsx
+++ b/src/extensions/zenodo/ui.tsx
@@ -0,0 +1,302 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { DownloadFile } from '../../mol-plugin-state/actions/file';
+import { DownloadStructure, LoadTrajectory } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { CoordinatesFormatCategory } from '../../mol-plugin-state/formats/coordinates';
+import { TopologyFormatCategory } from '../../mol-plugin-state/formats/topology';
+import { TrajectoryFormatCategory } from '../../mol-plugin-state/formats/trajectory';
+import { VolumeFormatCategory } from '../../mol-plugin-state/formats/volume';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { OpenInBrowserSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { PluginContext } from '../../mol-plugin/context';
+import { formatBytes } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+type ZenodoFile = {
+    bucket: string
+    checksum: string
+    key: string
+    links: {
+        [key: string]: string
+        self: string
+    }
+    size: number
+    type: string
+}
+
+type ZenodoRecord = {
+    id: number
+    conceptdoi: string
+    conceptrecid: string
+    created: string
+    doi: string
+    files: ZenodoFile[]
+    revision: number
+    updated: string
+    metadata: {
+        title: string
+    }
+}
+
+interface State {
+    busy?: boolean
+    recordValues: PD.Values<typeof ZenodoImportParams>
+    importValues?: PD.Values<ImportParams>
+    importParams?: ImportParams
+    record?: ZenodoRecord
+    files?: ZenodoFile[]
+}
+
+const ZenodoImportParams = {
+    record: PD.Text('', { description: 'Zenodo ID.' })
+};
+
+function createImportParams(files: ZenodoFile[], plugin: PluginContext) {
+    const modelOpts: [string, string][] = [];
+    const topologyOpts: [string, string][] = [];
+    const coordinatesOpts: [string, string][] = [];
+    const volumeOpts: [string, string][] = [];
+    const compressedOpts: [string, string][] = [];
+
+    const structureExts = new Map<string, { format: string, isBinary: boolean }>();
+    const coordinatesExts = new Map<string, { format: string, isBinary: boolean }>();
+    const topologyExts = new Map<string, { format: string, isBinary: boolean }>();
+    const volumeExts = new Map<string, { format: string, isBinary: boolean }>();
+
+    for (const { provider: { category, binaryExtensions, stringExtensions }, name } of plugin.dataFormats.list) {
+        if (category === TrajectoryFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) structureExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) structureExts.set(e, { format: name, isBinary: false });
+        } else if (category === VolumeFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) volumeExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) volumeExts.set(e, { format: name, isBinary: false });
+        } else if (category === CoordinatesFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) coordinatesExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) coordinatesExts.set(e, { format: name, isBinary: false });
+        } else if (category === TopologyFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) topologyExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) topologyExts.set(e, { format: name, isBinary: false });
+        }
+    }
+
+    for (const file of files) {
+        const label = `${file.key} (${formatBytes(file.size)})`;
+        if (structureExts.has(file.type)) {
+            const { format, isBinary } = structureExts.get(file.type)!;
+            modelOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+            topologyOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (volumeExts.has(file.type)) {
+            const { format, isBinary } = volumeExts.get(file.type)!;
+            volumeOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (topologyExts.has(file.type)) {
+            const { format, isBinary } = topologyExts.get(file.type)!;
+            topologyOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (coordinatesExts.has(file.type)) {
+            const { format, isBinary } = coordinatesExts.get(file.type)!;
+            coordinatesOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (file.type === 'zip') {
+            compressedOpts.push([`${file.links.self}|${file.type}|true`, label]);
+        }
+    }
+
+    const params: PD.Params = {};
+    let defaultType = '';
+
+    if (modelOpts.length) {
+        defaultType = 'structure';
+        params.structure = PD.Select(modelOpts[0][0], modelOpts);
+    }
+
+    if (topologyOpts.length && coordinatesOpts.length) {
+        if (!defaultType) defaultType = 'trajectory';
+        params.trajectory = PD.Group({
+            topology: PD.Select(topologyOpts[0][0], topologyOpts),
+            coordinates: PD.Select(coordinatesOpts[0][0], coordinatesOpts),
+        }, { isFlat: true });
+    }
+
+    if (volumeOpts.length) {
+        if (!defaultType) defaultType = 'volume';
+        params.volume = PD.Select(volumeOpts[0][0], volumeOpts);
+    }
+
+    if (compressedOpts.length) {
+        if (!defaultType) defaultType = 'compressed';
+        params.compressed = PD.Select(compressedOpts[0][0], compressedOpts);
+    }
+
+    return {
+        type: PD.MappedStatic(defaultType, Object.keys(params).length ? params : { '': PD.EmptyGroup() })
+    };
+}
+type ImportParams = ReturnType<typeof createImportParams>
+
+export class ZenodoImportUI extends CollapsableControls<{}, State> {
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Zenodo Import',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: OpenInBrowserSvg },
+            recordValues: PD.getDefaultValues(ZenodoImportParams),
+            importValues: undefined,
+            importParams: undefined,
+            record: undefined,
+            files: undefined,
+        };
+    }
+
+    private recordParamsOnChange = (values: any) => {
+        this.setState({ recordValues: values });
+    };
+
+    private importParamsOnChange = (values: any) => {
+        this.setState({ importValues: values });
+    };
+
+    private loadRecord = async () => {
+        try {
+            this.setState({ busy: true });
+            const record: ZenodoRecord = await this.plugin.runTask(this.plugin.fetch({ url: `https://zenodo.org/api/records/${this.state.recordValues.record}`, type: 'json' }));
+            const importParams = createImportParams(record.files, this.plugin);
+            this.setState({
+                record,
+                files: record.files,
+                busy: false,
+                importValues: PD.getDefaultValues(importParams),
+                importParams
+            });
+        } catch (e) {
+            console.error(e);
+            this.plugin.log.error(`Failed to load Zenodo record '${this.state.recordValues.record}'`);
+            this.setState({ busy: false });
+        }
+    };
+
+    private loadFile = async (values: PD.Values<ImportParams>) => {
+        try {
+            this.setState({ busy: true });
+
+            const t = values.type;
+            if (t.name === 'structure') {
+                const defaultParams = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            url,
+                            format: format as any,
+                            isBinary: isBinary === 'true',
+                            options: defaultParams.source.params.options,
+                        }
+                    }
+                }));
+            } else if (t.name === 'trajectory') {
+                const [topologyUrl, topologyFormat, topologyIsBinary] = t.params.topology.split('|');
+                const [coordinatesUrl, coordinatesFormat, coordinatesIsBinary] = t.params.coordinates.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(LoadTrajectory, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            model: {
+                                url: topologyUrl,
+                                format: topologyFormat as any,
+                                isBinary: topologyIsBinary === 'true',
+                            },
+                            coordinates: {
+                                url: coordinatesUrl,
+                                format: coordinatesFormat as any,
+                                isBinary: coordinatesIsBinary === 'true',
+                            },
+                        }
+                    }
+                }));
+            } else if (t.name === 'volume') {
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            url,
+                            format: format as any,
+                            isBinary: isBinary === 'true',
+                        }
+                    }
+                }));
+            } else if (t.name === 'compressed') {
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadFile, {
+                    url,
+                    format: format as any,
+                    isBinary: isBinary === 'true',
+                    visuals: true
+                }));
+            }
+        } catch (e) {
+            console.error(e);
+            this.plugin.log.error(`Failed to load Zenodo file`);
+        } finally {
+            this.setState({ busy: false });
+        }
+    };
+
+    private clearRecord = () => {
+        this.setState({
+            importValues: undefined,
+            importParams: undefined,
+            record: undefined,
+            files: undefined
+        });
+    };
+
+    private renderLoadRecord() {
+        return <div style={{ marginBottom: 10 }}>
+            <ParameterControls params={ZenodoImportParams} values={this.state.recordValues} onChangeValues={this.recordParamsOnChange} isDisabled={this.state.busy} />
+            <Button onClick={this.loadRecord} style={{ marginTop: 1 }} disabled={this.state.busy || !this.state.recordValues.record}>
+                Load Record
+            </Button>
+        </div>;
+    }
+
+    private renderRecordInfo(record: ZenodoRecord) {
+        return <div style={{ marginBottom: 10 }}>
+            <div className='msp-help-text'>
+                <div>Record {`${record.id}`}: <i>{`${record.metadata.title}`}</i></div>
+            </div>
+            <Button onClick={this.clearRecord} style={{ marginTop: 1 }} disabled={this.state.busy}>
+                Clear
+            </Button>
+        </div>;
+    }
+
+    private renderImportFile(params: ImportParams, values: PD.Values<ImportParams>) {
+        return values.type.name ? <div style={{ marginBottom: 10 }}>
+            <ParameterControls params={params} values={this.state.importValues} onChangeValues={this.importParamsOnChange} isDisabled={this.state.busy} />
+            <Button onClick={() => this.loadFile(values)} style={{ marginTop: 1 }} disabled={this.state.busy}>
+                Import File
+            </Button>
+        </div> : <div className='msp-help-text' style={{ marginBottom: 10 }}>
+            <div>No supported files</div>
+        </div>;
+    }
+
+    protected renderControls(): JSX.Element | null {
+        return <>
+            {!this.state.record ? this.renderLoadRecord() : null}
+            {this.state.record ? this.renderRecordInfo(this.state.record) : null}
+            {this.state.importParams && this.state.importValues ? this.renderImportFile(this.state.importParams, this.state.importValues) : null}
+        </>;
+    }
+}
--- a/src/mol-canvas3d/camera.ts
+++ b/src/mol-canvas3d/camera.ts
@@ -10,6 +10,7 @@ import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 import { Scene } from '../mol-gl/scene';
+import { assertUnreachable } from '../mol-util/type-helpers';

 export { ICamera, Camera };

@@ -84,7 +85,7 @@ class Camera implements ICamera {
        switch (this.state.mode) {
            case 'orthographic': updateOrtho(this); break;
            case 'perspective': updatePers(this); break;
-            default: throw new Error('unknown camera mode');
+            default: assertUnreachable(this.state.mode);
        }

        const changed = !Mat4.areEqual(this.projection, this.prevProjection, EPSILON) || !Mat4.areEqual(this.view, this.prevView, EPSILON);
--- a/src/mol-geo/geometry/text/text-builder.ts
+++ b/src/mol-geo/geometry/text/text-builder.ts
@@ -8,6 +8,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { ChunkedArray } from '../../../mol-data/util';
 import { Text } from './text';
 import { getFontAtlas } from './font-atlas';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 const quadIndices = new Uint16Array([
    0, 1, 2,
@@ -237,7 +238,7 @@ export namespace TextBuilder {
                            yBaseCenter = yTop;
                            break;
                        default:
-                            throw new Error('unsupported attachment');
+                            assertUnreachable(attachment);
                    }
                    caAdd2(mappings, xTip, yTip); // tip
                    caAdd2(mappings, xBaseA, yBaseA); // base A
--- a/src/mol-gl/shader-code.ts
+++ b/src/mol-gl/shader-code.ts
@@ -202,6 +202,7 @@ export const DirectVolumeShaderCode = ShaderCode('direct-volume', directVolume_v

 import { image_vert } from './shader/image.vert';
 import { image_frag } from './shader/image.frag';
+import { assertUnreachable } from '../mol-util/type-helpers';
 export const ImageShaderCode = ShaderCode('image', image_vert, image_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);

 //
@@ -228,7 +229,7 @@ function getDefinesCode(defines: ShaderDefines, ignore?: IgnoreDefine) {
            } else if (typeof v === 'boolean') {
                if (v) lines.push(`#define ${name}`);
            } else {
-                throw new Error('unknown define type');
+                assertUnreachable(v);
            }
        }
    }
--- a/src/mol-gl/webgl/buffer.ts
+++ b/src/mol-gl/webgl/buffer.ts
@@ -8,7 +8,7 @@ import { WebGLContext } from './context';
 import { ValueCell } from '../../mol-util';
 import { RenderableSchema } from '../renderable/schema';
 import { idFactory } from '../../mol-util/id-factory';
-import { ValueOf } from '../../mol-util/type-helpers';
+import { assertUnreachable, ValueOf } from '../../mol-util/type-helpers';
 import { GLRenderingContext } from './compat';
 import { WebGLExtensions } from './extensions';
 import { WebGLState } from './state';
@@ -66,9 +66,8 @@ function dataTypeFromArray(gl: GLRenderingContext, array: ArrayType) {
        return gl.INT;
    } else if (array instanceof Float32Array) {
        return gl.FLOAT;
-    } else {
-        throw new Error('Should nevver happen');
    }
+    assertUnreachable(array);
 }

 export function getBufferType(gl: GLRenderingContext, bufferType: BufferType) {
--- a/src/mol-io/common/binary-cif/classifier.ts
+++ b/src/mol-io/common/binary-cif/classifier.ts
@@ -7,6 +7,7 @@

 import { ArrayEncoder, ArrayEncoding as E } from './array-encoder';
 import { getArrayDigitCount } from '../../../mol-util/number';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 export function classifyIntArray(xs: ArrayLike<number>) {
    return IntClassifier.classify(xs as number[]);
@@ -62,7 +63,7 @@ namespace IntClassifier {
        for (let i = 0, n = data.length; i < n; i++) {
            incSize(info, size, data[i]);
        }
-        return { ...byteSize(size), kind: 'pack' };
+        return { ...byteSize(size), kind: 'pack' as const };
    }

    function deltaSize(data: number[], info: IntColumnInfo) {
@@ -72,7 +73,7 @@ namespace IntClassifier {
            incSizeSigned(size, data[i] - prev);
            prev = data[i];
        }
-        return { ...byteSize(size), kind: 'delta' };
+        return { ...byteSize(size), kind: 'delta' as const };
    }

    function rleSize(data: number[], info: IntColumnInfo) {
@@ -90,7 +91,7 @@ namespace IntClassifier {
        incSize(info, size, data[data.length - 1]);
        incSize(info, size, run);

-        return { ...byteSize(size), kind: 'rle' };
+        return { ...byteSize(size), kind: 'rle' as const };
    }

    function deltaRleSize(data: number[], info: IntColumnInfo) {
@@ -111,7 +112,7 @@ namespace IntClassifier {
        incSizeSigned(size, prevValue);
        incSizeSigned(size, run);

-        return { ...byteSize(size), kind: 'delta-rle' };
+        return { ...byteSize(size), kind: 'delta-rle' as const };
    }

    export function getSize(data: number[]) {
@@ -132,9 +133,8 @@ namespace IntClassifier {
            case 'rle': return E.by(E.runLength).and(E.integerPacking);
            case 'delta': return E.by(E.delta).and(E.integerPacking);
            case 'delta-rle': return E.by(E.delta).and(E.runLength).and(E.integerPacking);
+            default: assertUnreachable(size);
        }
-
-        throw new Error('should not happen :)');
    }
 }

@@ -169,9 +169,8 @@ namespace FloatClassifier {
            case 'rle': return fp.and(E.runLength).and(E.integerPacking);
            case 'delta': return fp.and(E.delta).and(E.integerPacking);
            case 'delta-rle': return fp.and(E.delta).and(E.runLength).and(E.integerPacking);
+            default: assertUnreachable(size);
        }
-
-        throw new Error('should not happen :)');
    }

    function getMultiplier(mantissaDigits: number) {
--- a/src/mol-io/common/binary-cif/decoder.ts
+++ b/src/mol-io/common/binary-cif/decoder.ts
@@ -7,6 +7,7 @@

 import { Encoding, EncodedData } from './encoding';
 import { IsNativeEndianLittle, flipByteOrder } from '../binary';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 /**
 * Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/
@@ -33,7 +34,7 @@ function decodeStep(data: any, encoding: Encoding): any {
                case Encoding.IntDataType.Uint32: return uint32(data);
                case Encoding.FloatDataType.Float32: return float32(data);
                case Encoding.FloatDataType.Float64: return float64(data);
-                default: throw new Error('Unsupported ByteArray type.');
+                default: assertUnreachable(encoding.type);
            }
        }
        case 'FixedPoint': return fixedPoint(data, encoding);
@@ -53,7 +54,7 @@ function getIntArray(type: Encoding.IntDataType, size: number) {
        case Encoding.IntDataType.Uint8: return new Uint8Array(size);
        case Encoding.IntDataType.Uint16: return new Uint16Array(size);
        case Encoding.IntDataType.Uint32: return new Uint32Array(size);
-        default: throw new Error('Unsupported integer data type.');
+        default: assertUnreachable(type);
    }
 }

@@ -61,7 +62,7 @@ function getFloatArray(type: Encoding.FloatDataType, size: number) {
    switch (type) {
        case Encoding.FloatDataType.Float32: return new Float32Array(size);
        case Encoding.FloatDataType.Float64: return new Float64Array(size);
-        default: throw new Error('Unsupported floating data type.');
+        default: assertUnreachable(type);
    }
 }

--- a/src/mol-io/common/io-buffer.ts
+++ b/src/mol-io/common/io-buffer.ts
@@ -0,0 +1,453 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted and converted to TypeScript from https://github.com/image-js/iobuffer
+ * MIT License, Copyright (c) 2015 Michaël Zasso
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { TypedArray } from '../../mol-util/type-helpers';
+
+const defaultByteLength = 1024 * 8;
+const charArray: string[] = [];
+
+export interface IOBufferParameters {
+    offset?: number // Ignore the first n bytes of the ArrayBuffer
+}
+
+/**
+ * Class for writing and reading binary data
+ */
+export class IOBuffer {
+    private _lastWrittenByte: number;
+    private _mark = 0;
+    private _marks: number[] = [];
+    private _data: DataView;
+
+    offset = 0; // The current offset of the buffer's pointer
+    littleEndian = true;
+    buffer: ArrayBuffer; // Reference to the internal ArrayBuffer object
+    length: number; // Byte length of the internal ArrayBuffer
+    byteLength: number; // Byte length of the internal ArrayBuffer
+    byteOffset: number; // Byte offset of the internal ArrayBuffer
+
+    /**
+     * If it's a number, it will initialize the buffer with the number as
+     * the buffer's length. If it's undefined, it will initialize the buffer
+     * with a default length of 8 Kb. If its an ArrayBuffer, a TypedArray,
+     * it will create a view over the underlying ArrayBuffer.
+     */
+    constructor(data: number | ArrayBuffer | TypedArray, params: IOBufferParameters = {}) {
+        let dataIsGiven = false;
+        if (data === undefined) {
+            data = defaultByteLength;
+        }
+        if (typeof data === 'number') {
+            data = new ArrayBuffer(data);
+        } else {
+            dataIsGiven = true;
+        }
+
+        const offset = params.offset ? params.offset >>> 0 : 0;
+        const byteLength = data.byteLength - offset;
+        let dvOffset = offset;
+        if (!(data instanceof ArrayBuffer)) {
+            if (data.byteLength !== data.buffer.byteLength) {
+                dvOffset = data.byteOffset + offset;
+            }
+            data = data.buffer;
+        }
+        if (dataIsGiven) {
+            this._lastWrittenByte = byteLength;
+        } else {
+            this._lastWrittenByte = 0;
+        }
+
+        this.buffer = data;
+        this.length = byteLength;
+        this.byteLength = byteLength;
+        this.byteOffset = dvOffset;
+
+        this._data = new DataView(this.buffer, dvOffset, byteLength);
+    }
+
+    /**
+     * Checks if the memory allocated to the buffer is sufficient to store more bytes after the offset
+     * @param byteLength The needed memory in bytes
+     */
+    available(byteLength: number = 1) {
+        return (this.offset + byteLength) <= this.length;
+    }
+
+    /**
+     * Check if little-endian mode is used for reading and writing multi-byte values
+     * Returns true if little-endian mode is used, false otherwise
+     */
+    isLittleEndian() {
+        return this.littleEndian;
+    }
+
+    /**
+     * Set little-endian mode for reading and writing multi-byte values
+     */
+    setLittleEndian() {
+        this.littleEndian = true;
+        return this;
+    }
+
+    /**
+     * Check if big-endian mode is used for reading and writing multi-byte values
+     * Returns true if big-endian mode is used, false otherwise
+     */
+    isBigEndian() {
+        return !this.littleEndian;
+    }
+
+    /**
+     * Switches to big-endian mode for reading and writing multi-byte values
+     */
+    setBigEndian() {
+        this.littleEndian = false;
+        return this;
+    }
+
+    /**
+     * Move the pointer n bytes forward
+     */
+    skip(n: number) {
+        if (n === undefined) n = 1;
+        this.offset += n;
+        return this;
+    }
+
+    /**
+     * Move the pointer to the given offset
+     */
+    seek(offset: number) {
+        this.offset = offset;
+        return this;
+    }
+
+    /**
+     * Store the current pointer offset.
+     */
+    mark() {
+        this._mark = this.offset;
+        return this;
+    }
+
+    /**
+     * Move the pointer back to the last pointer offset set by mark
+     */
+    reset() {
+        this.offset = this._mark;
+        return this;
+    }
+
+    /**
+     * Push the current pointer offset to the mark stack
+     */
+    pushMark() {
+        this._marks.push(this.offset);
+        return this;
+    }
+
+    /**
+     * Pop the last pointer offset from the mark stack, and set the current pointer offset to the popped value
+     */
+    popMark() {
+        const offset = this._marks.pop();
+        if (offset === undefined) throw new Error('Mark stack empty');
+        this.seek(offset);
+        return this;
+    }
+
+    /**
+     * Move the pointer offset back to 0
+     */
+    rewind() {
+        this.offset = 0;
+        return this;
+    }
+
+    /**
+     * Make sure the buffer has sufficient memory to write a given byteLength at the current pointer offset
+     * If the buffer's memory is insufficient, this method will create a new buffer (a copy) with a length
+     * that is twice (byteLength + current offset)
+     */
+    ensureAvailable(byteLength: number) {
+        if (byteLength === undefined) byteLength = 1;
+        if (!this.available(byteLength)) {
+            const lengthNeeded = this.offset + byteLength;
+            const newLength = lengthNeeded * 2;
+            const newArray = new Uint8Array(newLength);
+            newArray.set(new Uint8Array(this.buffer));
+            this.buffer = newArray.buffer;
+            this.length = this.byteLength = newLength;
+            this._data = new DataView(this.buffer);
+        }
+        return this;
+    }
+
+    /**
+     * Read a byte and return false if the byte's value is 0, or true otherwise
+     * Moves pointer forward
+     */
+    readBoolean() {
+        return this.readUint8() !== 0;
+    }
+
+    /**
+     * Read a signed 8-bit integer and move pointer forward
+     */
+    readInt8() {
+        return this._data.getInt8(this.offset++);
+    }
+
+    /**
+     * Read an unsigned 8-bit integer and move pointer forward
+     */
+    readUint8() {
+        return this._data.getUint8(this.offset++);
+    }
+
+    /**
+     * Alias for {@link IOBuffer#readUint8}
+     */
+    readByte() {
+        return this.readUint8();
+    }
+
+    /**
+     * Read n bytes and move pointer forward.
+     */
+    readBytes(n: number) {
+        if (n === undefined) n = 1;
+        const bytes = new Uint8Array(n);
+        for (let i = 0; i < n; i++) {
+            bytes[i] = this.readByte();
+        }
+        return bytes;
+    }
+
+    /**
+     * Read a 16-bit signed integer and move pointer forward
+     */
+    readInt16() {
+        const value = this._data.getInt16(this.offset, this.littleEndian);
+        this.offset += 2;
+        return value;
+    }
+
+    /**
+     * Read a 16-bit unsigned integer and move pointer forward
+     */
+    readUint16() {
+        const value = this._data.getUint16(this.offset, this.littleEndian);
+        this.offset += 2;
+        return value;
+    }
+
+    /**
+     * Read a 32-bit signed integer and move pointer forward
+     */
+    readInt32() {
+        const value = this._data.getInt32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    }
+
+    /**
+     * Read a 32-bit unsigned integer and move pointer forward
+     */
+    readUint32() {
+        const value = this._data.getUint32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    }
+
+    /**
+     * Read a 32-bit floating number and move pointer forward
+     */
+    readFloat32() {
+        const value = this._data.getFloat32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    }
+
+    /**
+     * Read a 64-bit floating number and move pointer forward
+     */
+    readFloat64() {
+        const value = this._data.getFloat64(this.offset, this.littleEndian);
+        this.offset += 8;
+        return value;
+    }
+
+    /**
+     * Read 1-byte ascii character and move pointer forward
+     */
+    readChar() {
+        return String.fromCharCode(this.readInt8());
+    }
+
+    /**
+     * Read n 1-byte ascii characters and move pointer forward
+     */
+    readChars(n = 1) {
+        charArray.length = n;
+        for (let i = 0; i < n; i++) {
+            charArray[i] = this.readChar();
+        }
+        return charArray.join('');
+    }
+
+    /**
+     * Write 0xff if the passed value is truthy, 0x00 otherwise
+     */
+    writeBoolean(value = false) {
+        this.writeUint8(value ? 0xff : 0x00);
+        return this;
+    }
+
+    /**
+     * Write value as an 8-bit signed integer
+     */
+    writeInt8(value: number) {
+        this.ensureAvailable(1);
+        this._data.setInt8(this.offset++, value);
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write value as a 8-bit unsigned integer
+     */
+    writeUint8(value: number) {
+        this.ensureAvailable(1);
+        this._data.setUint8(this.offset++, value);
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * An alias for IOBuffer#writeUint8
+     */
+    writeByte(value: number) {
+        return this.writeUint8(value);
+    }
+
+    /**
+     * Write bytes
+     */
+    writeBytes(bytes: number[] | Uint8Array) {
+        this.ensureAvailable(bytes.length);
+        for (let i = 0; i < bytes.length; i++) {
+            this._data.setUint8(this.offset++, bytes[i]);
+        }
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write value as an 16-bit signed integer
+     */
+    writeInt16(value: number) {
+        this.ensureAvailable(2);
+        this._data.setInt16(this.offset, value, this.littleEndian);
+        this.offset += 2;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write value as a 16-bit unsigned integer
+     */
+    writeUint16(value: number) {
+        this.ensureAvailable(2);
+        this._data.setUint16(this.offset, value, this.littleEndian);
+        this.offset += 2;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 32-bit signed integer at the current pointer offset
+     */
+    writeInt32(value: number) {
+        this.ensureAvailable(4);
+        this._data.setInt32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 32-bit unsigned integer at the current pointer offset
+     */
+    writeUint32(value: number) {
+        this.ensureAvailable(4);
+        this._data.setUint32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 32-bit floating number at the current pointer offset
+     */
+    writeFloat32(value: number) {
+        this.ensureAvailable(4);
+        this._data.setFloat32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 64-bit floating number at the current pointer offset
+     */
+    writeFloat64(value: number) {
+        this.ensureAvailable(8);
+        this._data.setFloat64(this.offset, value, this.littleEndian);
+        this.offset += 8;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write the charCode of the passed string's first character to the current pointer offset
+     */
+    writeChar(str: string) {
+        return this.writeUint8(str.charCodeAt(0));
+    }
+
+    /**
+     * Write the charCodes of the passed string's characters to the current pointer offset
+     */
+    writeChars(str: string) {
+        for (let i = 0; i < str.length; i++) {
+            this.writeUint8(str.charCodeAt(i));
+        }
+        return this;
+    }
+
+    /**
+     * Export a Uint8Array view of the internal buffer.
+     * The view starts at the byte offset and its length
+     * is calculated to stop at the last written byte or the original length.
+     */
+    toArray() {
+        return new Uint8Array(this.buffer, this.byteOffset, this._lastWrittenByte);
+    }
+
+    /**
+     * Update the last written byte offset
+     */
+    private _updateLastWrittenByte() {
+        if (this.offset > this._lastWrittenByte) {
+            this._lastWrittenByte = this.offset;
+        }
+    }
+}
--- a/src/mol-io/common/netcdf/reader.ts
+++ b/src/mol-io/common/netcdf/reader.ts
@@ -0,0 +1,527 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from https://github.com/cheminfo-js/netcdfjs
+ * MIT License, Copyright (c) 2016 cheminfo
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+
+import { IOBuffer } from '../io-buffer';
+
+export interface NetCDFRecordDimension {
+    length: number,
+    id?: number,
+    name?: string,
+    recordStep?: number
+}
+
+export interface NetCDFVariable {
+    name: string
+    dimensions: any[]
+    attributes: any[]
+    type: string
+    size: number
+    offset: number
+    record: boolean
+}
+
+export interface NetCDFHeader {
+    recordDimension: NetCDFRecordDimension,
+    version: number,
+    dimensions: { name: string, size: number }[],
+    globalAttributes: { name: string, type: string, value: string | number }[],
+    variables: NetCDFVariable[]
+}
+
+export interface NetCDFDimension {
+    name: string,
+    size: number
+}
+
+/**
+ * Throws a non-valid NetCDF exception if the statement it's true
+ */
+function notNetcdf(statement: boolean, reason: string) {
+    if (statement) {
+        throw new TypeError('Not a valid NetCDF v3.x file: ' + reason);
+    }
+}
+
+/**
+ * Moves 1, 2, or 3 bytes to next 4-byte boundary
+ */
+function padding(buffer: IOBuffer) {
+    if ((buffer.offset % 4) !== 0) {
+        buffer.skip(4 - (buffer.offset % 4));
+    }
+}
+
+/**
+ * Reads the name
+ */
+function readName(buffer: IOBuffer) {
+    // Read name
+    const nameLength = buffer.readUint32();
+    const name = buffer.readChars(nameLength);
+
+    // validate name
+    // TODO
+
+    // Apply padding
+    padding(buffer);
+    return name;
+}
+
+const types = {
+    BYTE: 1,
+    CHAR: 2,
+    SHORT: 3,
+    INT: 4,
+    FLOAT: 5,
+    DOUBLE: 6
+};
+
+/**
+ * Parse a number into their respective type
+ */
+function num2str(type: number) {
+    switch (Number(type)) {
+        case types.BYTE:
+            return 'byte';
+        case types.CHAR:
+            return 'char';
+        case types.SHORT:
+            return 'short';
+        case types.INT:
+            return 'int';
+        case types.FLOAT:
+            return 'float';
+        case types.DOUBLE:
+            return 'double';
+        default:
+            return 'undefined';
+    }
+}
+
+/**
+ * Parse a number type identifier to his size in bytes
+ */
+function num2bytes(type: number) {
+    switch (Number(type)) {
+        case types.BYTE:
+            return 1;
+        case types.CHAR:
+            return 1;
+        case types.SHORT:
+            return 2;
+        case types.INT:
+            return 4;
+        case types.FLOAT:
+            return 4;
+        case types.DOUBLE:
+            return 8;
+        default:
+            return -1;
+    }
+}
+
+/**
+ * Reverse search of num2str
+ */
+function str2num(type: string) {
+    switch (String(type)) {
+        case 'byte':
+            return types.BYTE;
+        case 'char':
+            return types.CHAR;
+        case 'short':
+            return types.SHORT;
+        case 'int':
+            return types.INT;
+        case 'float':
+            return types.FLOAT;
+        case 'double':
+            return types.DOUBLE;
+        default:
+            return -1;
+    }
+}
+
+/**
+ * Auxiliary function to read numeric data
+ */
+function readNumber(size: number, bufferReader: Function) {
+    if (size !== 1) {
+        const numbers = new Array(size);
+        for (let i = 0; i < size; i++) {
+            numbers[i] = bufferReader();
+        }
+        return numbers;
+    } else {
+        return bufferReader();
+    }
+}
+
+/**
+ * Given a type and a size reads the next element
+ */
+function readType(buffer: IOBuffer, type: number, size: number) {
+    switch (type) {
+        case types.BYTE:
+            return buffer.readBytes(size);
+        case types.CHAR:
+            return trimNull(buffer.readChars(size));
+        case types.SHORT:
+            return readNumber(size, buffer.readInt16.bind(buffer));
+        case types.INT:
+            return readNumber(size, buffer.readInt32.bind(buffer));
+        case types.FLOAT:
+            return readNumber(size, buffer.readFloat32.bind(buffer));
+        case types.DOUBLE:
+            return readNumber(size, buffer.readFloat64.bind(buffer));
+        default:
+            notNetcdf(true, 'non valid type ' + type);
+            return undefined;
+    }
+}
+
+/**
+ * Removes null terminate value
+ */
+function trimNull(value: string) {
+    if (value.charCodeAt(value.length - 1) === 0) {
+        return value.substring(0, value.length - 1);
+    }
+    return value;
+}
+
+// const STREAMING = 4294967295;
+
+/**
+ * Read data for the given non-record variable
+ */
+function nonRecord(buffer: IOBuffer, variable: { type: string, size: number }) {
+    // variable type
+    const type = str2num(variable.type);
+
+    // size of the data
+    const size = variable.size / num2bytes(type);
+
+    // iterates over the data
+    const data = new Array(size);
+    for (let i = 0; i < size; i++) {
+        data[i] = readType(buffer, type, 1);
+    }
+
+    return data;
+}
+
+/**
+ * Read data for the given record variable
+ */
+function record(buffer: IOBuffer, variable: { type: string, size: number }, recordDimension: NetCDFRecordDimension) {
+    // variable type
+    const type = str2num(variable.type);
+    const width = variable.size ? variable.size / num2bytes(type) : 1;
+
+    // size of the data
+    // TODO streaming data
+    const size = recordDimension.length;
+
+    // iterates over the data
+    const data = new Array(size);
+    const step = recordDimension.recordStep;
+
+    for (let i = 0; i < size; i++) {
+        const currentOffset = buffer.offset;
+        data[i] = readType(buffer, type, width);
+        buffer.seek(currentOffset + step!);
+    }
+
+    return data;
+}
+
+// Grammar constants
+const ZERO = 0;
+const NC_DIMENSION = 10;
+const NC_VARIABLE = 11;
+const NC_ATTRIBUTE = 12;
+
+/**
+ * Read the header of the file
+ * Returns object with the fields:
+ *  - `recordDimension`: Number with the length of record dimension
+ *  - `dimensions`: List of dimensions
+ *  - `globalAttributes`: List of global attributes
+ *  - `variables`: List of variables
+ */
+function header(buffer: IOBuffer, version: number) {
+    // Length of record dimension
+    // sum of the varSize's of all the record variables.
+    const header: Partial<NetCDFHeader> = { recordDimension: { length: buffer.readUint32() } };
+
+    // Version
+    header.version = version;
+
+    // List of dimensions
+    const dimList = dimensionsList(buffer) as { dimensions: NetCDFDimension[], recordId: number, recordName: string };
+    header.recordDimension!.id = dimList.recordId;
+    header.recordDimension!.name = dimList.recordName;
+    header.dimensions = dimList.dimensions;
+
+    // List of global attributes
+    header.globalAttributes = attributesList(buffer);
+
+    // List of variables
+    const variables = variablesList(buffer, dimList.recordId, version) as { variables: any[], recordStep: number };
+    header.variables = variables.variables;
+    header.recordDimension!.recordStep = variables.recordStep;
+
+    return header;
+}
+
+/**
+ * List of dimensions
+ */
+function dimensionsList(buffer: IOBuffer) {
+    let dimensions: NetCDFDimension[], recordId, recordName;
+    const dimList = buffer.readUint32();
+    if (dimList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of dimensions');
+        return [];
+    } else {
+        notNetcdf((dimList !== NC_DIMENSION), 'wrong tag for list of dimensions');
+
+        // Length of dimensions
+        const dimensionSize = buffer.readUint32();
+        dimensions = new Array(dimensionSize);
+        for (let dim = 0; dim < dimensionSize; dim++) {
+            // Read name
+            const name = readName(buffer);
+
+            // Read dimension size
+            const size = buffer.readUint32();
+            if (size === 0) {
+                recordId = dim;
+                recordName = name;
+            }
+
+            dimensions[dim] = {
+                name: name,
+                size: size
+            };
+        }
+        return {
+            dimensions: dimensions,
+            recordId: recordId,
+            recordName: recordName
+        };
+    }
+}
+
+/**
+ * List of attributes
+ */
+function attributesList(buffer: IOBuffer) {
+    let attributes: { name: string, type: ReturnType<typeof num2str>, value: any }[];
+    const gAttList = buffer.readUint32();
+    if (gAttList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of attributes');
+        return [];
+    } else {
+        notNetcdf((gAttList !== NC_ATTRIBUTE), 'wrong tag for list of attributes');
+
+        // Length of attributes
+        const attributeSize = buffer.readUint32();
+        attributes = new Array(attributeSize);
+        for (let gAtt = 0; gAtt < attributeSize; gAtt++) {
+            // Read name
+            const name = readName(buffer);
+
+            // Read type
+            const type = buffer.readUint32();
+            notNetcdf(((type < 1) || (type > 6)), 'non valid type ' + type);
+
+            // Read attribute
+            const size = buffer.readUint32();
+            const value = readType(buffer, type, size);
+
+            // Apply padding
+            padding(buffer);
+
+            attributes[gAtt] = {
+                name: name,
+                type: num2str(type),
+                value: value
+            };
+        }
+    }
+    return attributes;
+}
+
+/**
+ * List of variables
+ */
+function variablesList(buffer: IOBuffer, recordId: number, version: number) {
+    const varList = buffer.readUint32();
+    let recordStep = 0;
+    let variables;
+    if (varList === ZERO) {
+        notNetcdf(
+            (buffer.readUint32() !== ZERO),
+            'wrong empty tag for list of variables'
+        );
+        return [];
+    } else {
+        notNetcdf((varList !== NC_VARIABLE), 'wrong tag for list of variables');
+
+        // Length of variables
+        const variableSize = buffer.readUint32();
+        variables = new Array(variableSize);
+        for (let v = 0; v < variableSize; v++) {
+            // Read name
+            const name = readName(buffer);
+
+            // Read dimensionality of the variable
+            const dimensionality = buffer.readUint32();
+
+            // Index into the list of dimensions
+            const dimensionsIds = new Array(dimensionality);
+            for (let dim = 0; dim < dimensionality; dim++) {
+                dimensionsIds[dim] = buffer.readUint32();
+            }
+
+            // Read variables size
+            const attributes = attributesList(buffer);
+
+            // Read type
+            const type = buffer.readUint32();
+            notNetcdf(((type < 1) && (type > 6)), 'non valid type ' + type);
+
+            // Read variable size
+            // The 32-bit varSize field is not large enough to contain the
+            // size of variables that require more than 2^32 - 4 bytes,
+            // so 2^32 - 1 is used in the varSize field for such variables.
+            const varSize = buffer.readUint32();
+
+            // Read offset
+            let offset = buffer.readUint32();
+            if (version === 2) {
+                notNetcdf((offset > 0), 'offsets larger than 4GB not supported');
+                offset = buffer.readUint32();
+            }
+
+            // Count amount of record variables
+            if (dimensionsIds[0] === recordId) {
+                recordStep += varSize;
+            }
+
+            variables[v] = {
+                name: name,
+                dimensions: dimensionsIds,
+                attributes: attributes,
+                type: num2str(type),
+                size: varSize,
+                offset: offset,
+                record: (dimensionsIds[0] === recordId)
+            };
+        }
+    }
+
+    return {
+        variables: variables,
+        recordStep: recordStep
+    };
+}
+
+/**
+ * Reads a NetCDF v3.x file
+ * https://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html
+ */
+export class NetcdfReader {
+    header: Partial<NetCDFHeader>;
+    buffer: IOBuffer;
+
+    constructor(data: ArrayBuffer) {
+        const buffer = new IOBuffer(data);
+        buffer.setBigEndian();
+
+        // Validate that it's a NetCDF file
+        notNetcdf((buffer.readChars(3) !== 'CDF'), 'should start with CDF');
+
+        // Check the NetCDF format
+        const version = buffer.readByte();
+        notNetcdf((version > 2), 'unknown version');
+
+        // Read the header
+        this.header = header(buffer, version);
+        this.buffer = buffer;
+    }
+
+    /**
+     * Version for the NetCDF format
+     */
+    get version() {
+        if (this.header.version === 1) {
+            return 'classic format';
+        } else {
+            return '64-bit offset format';
+        }
+    }
+
+    get recordDimension() {
+        return this.header.recordDimension;
+    }
+
+    get dimensions() {
+        return this.header.dimensions;
+    }
+
+    get globalAttributes() {
+        return this.header.globalAttributes;
+    }
+
+    get variables() {
+        return this.header.variables;
+    }
+
+    /**
+     * Checks if a variable is available
+     * @param {string|object} variableName - Name of the variable to check
+     * @return {Boolean} - Variable existence
+     */
+    hasDataVariable(variableName: string) {
+        return this.header.variables && this.header.variables.findIndex(val => val.name === variableName) !== -1;
+    }
+
+    /**
+     * Retrieves the data for a given variable
+     * @param {string|object} variableName - Name of the variable to search or variable object
+     * @return {Array} - List with the variable values
+     */
+    getDataVariable(variableName: string | NetCDFVariable) {
+        let variable: NetCDFVariable | undefined;
+        if (typeof variableName === 'string') {
+            // search the variable
+            variable = this.header.variables?.find((val) => val.name === variableName);
+        } else {
+            variable = variableName;
+        }
+
+        // throws if variable not found
+        if (variable === undefined) throw new Error('variable not found');
+
+        // go to the offset position
+        this.buffer.seek(variable.offset);
+
+        if (variable.record) {
+            // record variable case
+            return record(this.buffer, variable, this.header.recordDimension!);
+        } else {
+            // non-record variable case
+            return nonRecord(this.buffer, variable);
+        }
+    }
+}
--- a/src/mol-io/reader/nctraj/parser.ts
+++ b/src/mol-io/reader/nctraj/parser.ts
@@ -0,0 +1,89 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../../mol-task';
+import { Mutable } from '../../../mol-util/type-helpers';
+import { NetcdfReader } from '../../common/netcdf/reader';
+import { ReaderResult as Result } from '../result';
+
+export interface NctrajFile {
+    coordinates: number[][],
+    velocities?: number[][],
+    forces?: number[][],
+    cell_lengths?: number[][],
+    cell_angles?: number[][],
+    time?: number[],
+    timeOffset: number,
+    deltaTime: number
+}
+
+async function parseInternal(data: Uint8Array) {
+    // http://ambermd.org/netcdf/nctraj.xhtml
+
+    const nc = new NetcdfReader(data);
+
+    const f: Mutable<NctrajFile> = {
+        coordinates: [],
+        time: [],
+        timeOffset: 0,
+        deltaTime: 1
+    };
+
+    for (const c of nc.getDataVariable('coordinates')) f.coordinates.push(c);
+
+    if (nc.hasDataVariable('velocities')) {
+        const velocities: number[][] = [];
+        for (const v of nc.getDataVariable('velocities')) velocities.push(v);
+        f.velocities = velocities;
+    }
+
+    if (nc.hasDataVariable('forces')) {
+        const forces: number[][] = [];
+        for (const f of nc.getDataVariable('forces')) forces.push(f);
+        f.forces = forces;
+    }
+
+    if (nc.hasDataVariable('cell_lengths')) {
+        const cell_lengths: number[][] = [];
+        for (const l of nc.getDataVariable('cell_lengths')) cell_lengths.push(l);
+        f.cell_lengths = cell_lengths;
+    }
+
+    if (nc.hasDataVariable('cell_angles')) {
+        const cell_angles: number[][] = [];
+        for (const a of nc.getDataVariable('cell_angles')) cell_angles.push(a);
+        f.cell_angles = cell_angles;
+    }
+
+    if (nc.hasDataVariable('time')) {
+        const time: number[] = [];
+        for (const t of nc.getDataVariable('time')) time.push(t);
+        f.time = time;
+    }
+
+    if (f.time) {
+        if (f.time.length >= 1) {
+            f.timeOffset = f.time[0];
+        }
+        if (f.time.length >= 2) {
+            f.deltaTime = f.time[1] - f.time[0];
+        }
+    }
+
+    return f;
+}
+
+export function parseNctraj(data: Uint8Array) {
+    return Task.create<Result<NctrajFile>>('Parse NCTRAJ', async ctx => {
+        try {
+            ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
+            const file = await parseInternal(data);
+            return Result.success(file);
+        } catch (e) {
+            return Result.error('' + e);
+        }
+    });
+}
--- a/src/mol-io/reader/prmtop/parser.ts
+++ b/src/mol-io/reader/prmtop/parser.ts
@@ -0,0 +1,176 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task, RuntimeContext } from '../../../mol-task';
+import { Tokenizer, TokenBuilder, Tokens } from '../common/text/tokenizer';
+import { ReaderResult as Result } from '../result';
+import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+import { Column } from '../../../mol-data/db';
+import { Mutable } from '../../../mol-util/type-helpers';
+
+// http://ambermd.org/prmtop.pdf
+// https://ambermd.org/FileFormats.php#topology
+
+const Pointers = {
+    'NATOM': '', 'NTYPES': '', 'NBONH': '', 'MBONA': '', 'NTHETH': '', 'MTHETA': '',
+    'NPHIH': '', 'MPHIA': '', 'NHPARM': '', 'NPARM': '', 'NNB': '', 'NRES': '',
+    'NBONA': '', 'NTHETA': '', 'NPHIA': '', 'NUMBND': '', 'NUMANG': '', 'NPTRA': '',
+    'NATYP': '', 'NPHB': '', 'IFPERT': '', 'NBPER': '', 'NGPER': '', 'NDPER': '',
+    'MBPER': '', 'MGPER': '', 'MDPER': '', 'IFBOX': '', 'NMXRS': '', 'IFCAP': '',
+    'NUMEXTRA': '', 'NCOPY': '',
+};
+type PointerName = keyof typeof Pointers;
+const PointersNames = Object.keys(Pointers) as PointerName[];
+
+export interface PrmtopFile {
+    readonly version: string
+    readonly title: ReadonlyArray<string>
+    readonly pointers: Readonly<Record<PointerName, number>>
+    readonly atomName: Column<string>
+    readonly charge: Column<number>
+    readonly mass: Column<number>
+    readonly residueLabel: Column<string>
+    readonly residuePointer: Column<number>
+    readonly bondsIncHydrogen: Column<number>
+    readonly bondsWithoutHydrogen: Column<number>
+    readonly radii: Column<number>
+}
+
+const { readLine, markLine, trim } = Tokenizer;
+
+function State(tokenizer: Tokenizer, runtimeCtx: RuntimeContext) {
+    return {
+        tokenizer,
+        runtimeCtx,
+    };
+}
+type State = ReturnType<typeof State>
+
+function handleTitle(state: State): string[] {
+    const { tokenizer } = state;
+    const title: string[] = [];
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        if (tokenizer.data[tokenizer.position] === '%') break;
+        const line = readLine(tokenizer).trim();
+        if (line) title.push(line);
+    }
+
+    return title;
+}
+
+function handlePointers(state: State): Record<PointerName, number> {
+    const { tokenizer } = state;
+
+    const pointers: Record<PointerName, number> = Object.create(null);
+    PointersNames.forEach(name => { pointers[name] = 0; });
+
+    let curIdx = 0;
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        if (tokenizer.data[tokenizer.position] === '%') break;
+        const line = readLine(tokenizer);
+
+        const n = Math.min(curIdx + 10, 32);
+        for (let i = 0; curIdx < n; ++i, ++curIdx) {
+            pointers[PointersNames[curIdx]] = parseInt(
+                line.substring(i * 8, i * 8 + 8).trim()
+            );
+        }
+    }
+
+    return pointers;
+}
+
+function handleTokens(state: State, count: number, countPerLine: number, itemSize: number): Tokens {
+    const { tokenizer } = state;
+
+    const tokens = TokenBuilder.create(tokenizer.data, count * 2);
+
+    let curIdx = 0;
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        if (tokenizer.data[tokenizer.position] === '%') break;
+
+        tokenizer.tokenStart = tokenizer.position;
+        const n = Math.min(curIdx + countPerLine, count);
+        for (let i = 0; curIdx < n; ++i, ++curIdx) {
+            const p = tokenizer.position;
+            trim(tokenizer, tokenizer.position, tokenizer.position + itemSize);
+            TokenBuilder.addUnchecked(tokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+            tokenizer.position = p + itemSize;
+        }
+
+        markLine(tokenizer);
+    }
+
+    return tokens;
+}
+
+async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<PrmtopFile>> {
+    const t = Tokenizer(data);
+    const state = State(t, ctx);
+
+    const result: Mutable<PrmtopFile> = Object.create(null);
+    let prevPosition = 0;
+
+    while (t.tokenEnd < t.length) {
+        if (t.position - prevPosition > 100000 && ctx.shouldUpdate) {
+            prevPosition = t.position;
+            await ctx.update({ current: t.position, max: t.length });
+        }
+
+        const line = readLine(state.tokenizer).trim();
+        if (line.startsWith('%VERSION')) {
+            result.version = line.substring(8).trim();
+        } else if (line.startsWith('%FLAG')) {
+            const flag = line.substring(5).trim();
+            const formatLine = readLine(state.tokenizer).trim();
+            if (!formatLine.startsWith('%FORMAT')) throw new Error('expected %FORMAT');
+
+            if (flag === 'TITLE') {
+                result.title = handleTitle(state);
+            } else if (flag === 'POINTERS') {
+                result.pointers = handlePointers(state);
+            } else if (flag === 'ATOM_NAME') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 20, 4);
+                result.atomName = TokenColumn(tokens)(Column.Schema.str);
+            } else if (flag === 'CHARGE') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 5, 16);
+                result.charge = TokenColumn(tokens)(Column.Schema.float);
+            } else if (flag === 'MASS') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 5, 16);
+                result.mass = TokenColumn(tokens)(Column.Schema.float);
+            } else if (flag === 'RESIDUE_LABEL') {
+                const tokens = handleTokens(state, result.pointers['NRES'], 20, 4);
+                result.residueLabel = TokenColumn(tokens)(Column.Schema.str);
+            } else if (flag === 'RESIDUE_POINTER') {
+                const tokens = handleTokens(state, result.pointers['NRES'], 10, 8);
+                result.residuePointer = TokenColumn(tokens)(Column.Schema.int);
+            } else if (flag === 'BONDS_INC_HYDROGEN') {
+                const tokens = handleTokens(state, result.pointers['NBONH'] * 3, 10, 8);
+                result.bondsIncHydrogen = TokenColumn(tokens)(Column.Schema.int);
+            } else if (flag === 'BONDS_WITHOUT_HYDROGEN') {
+                const tokens = handleTokens(state, result.pointers['NBONA'] * 3, 10, 8);
+                result.bondsWithoutHydrogen = TokenColumn(tokens)(Column.Schema.int);
+            } else if (flag === 'RADII') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 5, 16);
+                result.radii = TokenColumn(tokens)(Column.Schema.float);
+            } else {
+                while (t.tokenEnd < t.length) {
+                    if (t.data[t.position] === '%') break;
+                    markLine(t);
+                }
+            }
+        }
+    }
+
+    return Result.success(result);
+}
+
+export function parsePrmtop(data: string) {
+    return Task.create<Result<PrmtopFile>>('Parse PRMTOP', async ctx => {
+        return await parseInternal(data, ctx);
+    });
+}
--- a/src/mol-io/reader/top/parser.ts
+++ b/src/mol-io/reader/top/parser.ts
@@ -0,0 +1,303 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task, RuntimeContext } from '../../../mol-task';
+import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
+import { ReaderResult as Result } from '../result';
+import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+import { Column, Table } from '../../../mol-data/db';
+import { Mutable } from '../../../mol-util/type-helpers';
+
+// https://manual.gromacs.org/2021-current/reference-manual/file-formats.html#top
+
+const AtomsSchema = {
+    nr: Column.Schema.Int(),
+    type: Column.Schema.Str(),
+    resnr: Column.Schema.Int(),
+    residu: Column.Schema.Str(),
+    atom: Column.Schema.Str(),
+    cgnr: Column.Schema.Int(),
+    charge: Column.Schema.Float(),
+    mass: Column.Schema.Float(),
+};
+
+const BondsSchema = {
+    ai: Column.Schema.Int(),
+    aj: Column.Schema.Int(),
+};
+
+const MoleculesSchema = {
+    compound: Column.Schema.Str(),
+    molCount: Column.Schema.Int(),
+};
+
+type Compound = {
+    atoms: Table<typeof AtomsSchema>
+    bonds?: Table<typeof BondsSchema>
+}
+
+export interface TopFile {
+    readonly system: string
+    readonly molecules: Table<typeof MoleculesSchema>
+    readonly compounds: Record<string, Compound>
+}
+
+const { readLine, markLine, skipWhitespace, markStart, eatValue, eatLine } = Tokenizer;
+
+function State(tokenizer: Tokenizer, runtimeCtx: RuntimeContext) {
+    return {
+        tokenizer,
+        runtimeCtx,
+    };
+}
+type State = ReturnType<typeof State>
+
+const reField = /\[ (.+) \]/;
+const reWhitespace = /\s+/;
+
+function handleMoleculetype(state: State) {
+    const { tokenizer } = state;
+
+    let molName: string | undefined = undefined;
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        if (molName !== undefined) throw new Error('more than one molName');
+
+        const line = readLine(tokenizer);
+        molName = line.split(reWhitespace)[0];
+    }
+
+    if (molName === undefined) throw new Error('missing molName');
+
+    return molName;
+}
+
+function handleAtoms(state: State) {
+    const { tokenizer } = state;
+
+    const nr = TokenBuilder.create(tokenizer.data, 64);
+    const type = TokenBuilder.create(tokenizer.data, 64);
+    const resnr = TokenBuilder.create(tokenizer.data, 64);
+    const residu = TokenBuilder.create(tokenizer.data, 64);
+    const atom = TokenBuilder.create(tokenizer.data, 64);
+    const cgnr = TokenBuilder.create(tokenizer.data, 64);
+    const charge = TokenBuilder.create(tokenizer.data, 64);
+    const mass = TokenBuilder.create(tokenizer.data, 64);
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        for (let j = 0; j < 8; ++j) {
+            skipWhitespace(tokenizer);
+            markStart(tokenizer);
+            eatValue(tokenizer);
+
+            switch (j) {
+                case 0: TokenBuilder.add(nr, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 1: TokenBuilder.add(type, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 2: TokenBuilder.add(resnr, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 3: TokenBuilder.add(residu, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 4: TokenBuilder.add(atom, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 5: TokenBuilder.add(cgnr, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 6: TokenBuilder.add(charge, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 7: TokenBuilder.add(mass, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+            }
+        }
+        // ignore any extra columns
+        markLine(tokenizer);
+    }
+
+    return Table.ofColumns(AtomsSchema, {
+        nr: TokenColumn(nr)(Column.Schema.int),
+        type: TokenColumn(type)(Column.Schema.str),
+        resnr: TokenColumn(resnr)(Column.Schema.int),
+        residu: TokenColumn(residu)(Column.Schema.str),
+        atom: TokenColumn(atom)(Column.Schema.str),
+        cgnr: TokenColumn(cgnr)(Column.Schema.int),
+        charge: TokenColumn(charge)(Column.Schema.float),
+        mass: TokenColumn(mass)(Column.Schema.float),
+    });
+}
+
+function handleBonds(state: State) {
+    const { tokenizer } = state;
+
+    const ai = TokenBuilder.create(tokenizer.data, 64);
+    const aj = TokenBuilder.create(tokenizer.data, 64);
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        for (let j = 0; j < 2; ++j) {
+            skipWhitespace(tokenizer);
+            markStart(tokenizer);
+            eatValue(tokenizer);
+
+            switch (j) {
+                case 0: TokenBuilder.add(ai, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 1: TokenBuilder.add(aj, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+            }
+        }
+        // ignore any extra columns
+        markLine(tokenizer);
+    }
+
+    return Table.ofColumns(BondsSchema, {
+        ai: TokenColumn(ai)(Column.Schema.int),
+        aj: TokenColumn(aj)(Column.Schema.int),
+    });
+}
+
+function handleSystem(state: State) {
+    const { tokenizer } = state;
+
+    let system: string | undefined = undefined;
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        if (system !== undefined) throw new Error('more than one system');
+        system = readLine(tokenizer).trim();
+    }
+
+    if (system === undefined) throw new Error('missing system');
+
+    return system;
+}
+
+function handleMolecules(state: State) {
+    const { tokenizer } = state;
+
+    const compound = TokenBuilder.create(tokenizer.data, 64);
+    const molCount = TokenBuilder.create(tokenizer.data, 64);
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        if (tokenizer.position >= tokenizer.length) break;
+
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        for (let j = 0; j < 2; ++j) {
+            skipWhitespace(tokenizer);
+            markStart(tokenizer);
+            eatValue(tokenizer);
+
+            switch (j) {
+                case 0: TokenBuilder.add(compound, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 1: TokenBuilder.add(molCount, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+            }
+        }
+        // ignore any extra columns
+        eatLine(tokenizer);
+        markStart(tokenizer);
+    }
+
+    return Table.ofColumns(MoleculesSchema, {
+        compound: TokenColumn(compound)(Column.Schema.str),
+        molCount: TokenColumn(molCount)(Column.Schema.int),
+    });
+}
+
+async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<TopFile>> {
+    const t = Tokenizer(data);
+    const state = State(t, ctx);
+
+    const result: Mutable<TopFile> = Object.create(null);
+    let prevPosition = 0;
+
+    result.compounds = {};
+    let currentCompound: Partial<Compound> = {};
+    let currentMolName = '';
+
+    function addMol() {
+        if (currentMolName && currentCompound.atoms) {
+            result.compounds[currentMolName] = currentCompound as Compound;
+            currentCompound = {};
+            currentMolName = '';
+        }
+    }
+
+    while (t.tokenEnd < t.length) {
+        if (t.position - prevPosition > 100000 && ctx.shouldUpdate) {
+            prevPosition = t.position;
+            await ctx.update({ current: t.position, max: t.length });
+        }
+
+        const line = readLine(state.tokenizer).trim();
+
+        if (!line || line[0] === '*' || line[0] === ';') {
+            continue;
+        }
+
+        if (line.startsWith('#include')) {
+            throw new Error('#include statements not allowed');
+        }
+
+        if (line.startsWith('[')) {
+            const fieldMatch = line.match(reField);
+            if (fieldMatch === null) throw new Error('expected field name');
+
+            const fieldName = fieldMatch[1];
+            if (fieldName === 'moleculetype') {
+                addMol();
+                currentMolName = handleMoleculetype(state);
+            } else if (fieldName === 'atoms') {
+                currentCompound.atoms = handleAtoms(state);
+            } else if (fieldName === 'bonds') {
+                currentCompound.bonds = handleBonds(state);
+            } else if (fieldName === 'system') {
+                result.system = handleSystem(state);
+            } else if (fieldName === 'molecules') {
+                addMol(); // add the last compound
+                result.molecules = handleMolecules(state);
+            } else {
+                while (t.tokenEnd < t.length) {
+                    if (t.data[t.position] === '[') break;
+                    markLine(t);
+                }
+            }
+        }
+    }
+
+    return Result.success(result);
+}
+
+export function parseTop(data: string) {
+    return Task.create<Result<TopFile>>('Parse TOP', async ctx => {
+        return await parseInternal(data, ctx);
+    });
+}
--- a/src/mol-io/reader/trr/parser.ts
+++ b/src/mol-io/reader/trr/parser.ts
@@ -0,0 +1,157 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from NGL.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../../mol-task';
+import { ReaderResult as Result } from '../result';
+
+export interface TrrFile {
+    frames: { count: number, x: Float32Array, y: Float32Array, z: Float32Array }[],
+    boxes: number[][],
+    times: number[],
+    timeOffset: number,
+    deltaTime: number
+}
+
+async function parseInternal(data: Uint8Array) {
+    // https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/trrio.cpp
+
+    const dv = new DataView(data.buffer);
+
+    const f: TrrFile = {
+        frames: [],
+        boxes: [],
+        times: [],
+        timeOffset: 0,
+        deltaTime: 0
+    };
+    const coordinates = f.frames;
+    const boxes = f.boxes;
+    const times = f.times;
+
+    let offset = 0;
+
+    while (true) {
+        // const magicnum = dv.getInt32(offset)
+        // const i1 = dv.getFloat32(offset + 4)
+        offset += 8;
+
+        const versionSize = dv.getInt32(offset);
+        offset += 4;
+        offset += versionSize;
+
+        // const irSize = dv.getInt32(offset)
+        // const eSize = dv.getInt32(offset + 4)
+        const boxSize = dv.getInt32(offset + 8);
+        const virSize = dv.getInt32(offset + 12);
+        const presSize = dv.getInt32(offset + 16);
+        // const topSize = dv.getInt32(offset + 20)
+        // const symSize = dv.getInt32(offset + 24)
+        const coordSize = dv.getInt32(offset + 28);
+        const velocitySize = dv.getInt32(offset + 32);
+        const forceSize = dv.getInt32(offset + 36);
+        const natoms = dv.getInt32(offset + 40);
+        // const step = dv.getInt32(offset + 44)
+        // const nre = dv.getInt32(offset + 48)
+        offset += 52;
+
+        const floatSize = boxSize / 9;
+        const natoms3 = natoms * 3;
+
+        // let lambda
+        if (floatSize === 8) {
+            times.push(dv.getFloat64(offset));
+            // lambda = dv.getFloat64(offset + 8)
+        } else {
+            times.push(dv.getFloat32(offset));
+            // lambda = dv.getFloat32(offset + 4)
+        }
+        offset += 2 * floatSize;
+
+        if (boxSize) {
+            const box = new Float32Array(9);
+            if (floatSize === 8) {
+                for (let i = 0; i < 9; ++i) {
+                    box[i] = dv.getFloat64(offset) * 10;
+                    offset += 8;
+                }
+            } else {
+                for (let i = 0; i < 9; ++i) {
+                    box[i] = dv.getFloat32(offset) * 10;
+                    offset += 4;
+                }
+            }
+            boxes.push(box as unknown as number[]);
+        }
+
+        // ignore, unused
+        offset += virSize;
+
+        // ignore, unused
+        offset += presSize;
+
+        if (coordSize) {
+            const x = new Float32Array(natoms);
+            const y = new Float32Array(natoms);
+            const z = new Float32Array(natoms);
+            if (floatSize === 8) {
+                for (let i = 0; i < natoms; ++i) {
+                    x[i] = dv.getFloat64(offset) * 10;
+                    y[i] = dv.getFloat64(offset + 8) * 10;
+                    z[i] = dv.getFloat64(offset + 16) * 10;
+                    offset += 24;
+                }
+            } else {
+                const tmp = new Uint32Array(data.buffer, offset, natoms3);
+                for (let i = 0; i < natoms3; ++i) {
+                    const value = tmp[i];
+                    tmp[i] = (
+                        ((value & 0xFF) << 24) | ((value & 0xFF00) << 8) |
+                        ((value >> 8) & 0xFF00) | ((value >> 24) & 0xFF)
+                    );
+                }
+                const frameCoords = new Float32Array(data.buffer, offset, natoms3);
+                for (let i = 0; i < natoms; ++i) {
+                    x[i] = frameCoords[i * 3] * 10;
+                    y[i] = frameCoords[i * 3 + 1] * 10;
+                    z[i] = frameCoords[i * 3 + 2] * 10;
+                    offset += 12;
+                }
+            }
+            coordinates.push({ count: natoms, x, y, z });
+        }
+
+        // ignore, unused
+        offset += velocitySize;
+
+        // ignore, unused
+        offset += forceSize;
+
+        if (offset >= data.byteLength) break;
+    }
+
+    if (times.length >= 1) {
+        f.timeOffset = times[0];
+    }
+    if (times.length >= 2) {
+        f.deltaTime = times[1] - times[0];
+    }
+
+    return f;
+}
+
+export function parseTrr(data: Uint8Array) {
+    return Task.create<Result<TrrFile>>('Parse TRR', async ctx => {
+        try {
+            ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
+            const file = await parseInternal(data);
+            return Result.success(file);
+        } catch (e) {
+            return Result.error('' + e);
+        }
+    });
+}
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -11,6 +11,7 @@ import { Tensor } from '../../../mol-math/linear-algebra';
 import { Encoder as EncoderBase } from '../encoder';
 import { ArrayEncoder, ArrayEncoding } from '../../common/binary-cif';
 import { BinaryEncodingProvider } from './encoder/binary';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 // TODO: support for "coordinate fields", make "coordinate precision" a parameter of the encoder
 // TODO: automatically detect "precision" of floating point arrays.
@@ -324,7 +325,7 @@ function cifFieldsFromTableSchema(schema: Table.Schema) {
        } else if (t.valueType === 'tensor') {
            fields.push(...getTensorDefinitions(k, t.space));
        } else {
-            throw new Error(`Unknown valueType ${t.valueType}`);
+            assertUnreachable(t.valueType);
        }
    }
    return fields;
--- a/src/mol-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -45,15 +45,6 @@ function findHierarchyOffsets(atom_site: AtomSite) {
    return { residues, chains };
 }

-function substUndefinedColumn<T extends Table<any>>(table: T, a: keyof T, b: keyof T) {
-    if (!(table as any)[a].isDefined) {
-        (table as any)[a] = (table as any)[b];
-    }
-    if (!(table as any)[b].isDefined) {
-        (table as any)[b] = (table as any)[a];
-    }
-}
-
 function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
    const atoms = Table.ofColumns(AtomsSchema, {
        type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
@@ -87,12 +78,6 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
    Table.columnToArray(residues, 'label_seq_id', Int32Array);
    Table.columnToArray(residues, 'auth_seq_id', Int32Array);

-    // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
-    substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
-    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
-
    return { atoms, residues, chains, atomSourceIndex: sourceIndex };
 }

--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -186,8 +186,6 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
    return ret;
 }

-
-
 async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: CommonProperties, format: ModelFormat) {
    const entities = getEntityData(data);
    // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
--- a/src/mol-model-formats/structure/basic/schema.ts
+++ b/src/mol-model-formats/structure/basic/schema.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -7,6 +7,7 @@
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { getNormalizedAtomSite } from './util';

 // TODO split into conformation and hierarchy parts

@@ -68,7 +69,7 @@ export interface BasicData {
    pdbx_molecule: Molecule
 }

-export function createBasic(data: Partial<BasicData>): BasicData {
+export function createBasic(data: Partial<BasicData>, normalize = false): BasicData {
    const basic = Object.create(null);
    for (const name of Object.keys(BasicSchema)) {
        if (name in data) {
@@ -77,5 +78,8 @@ export function createBasic(data: Partial<BasicData>): BasicData {
            basic[name] = Table.ofUndefinedColumns(BasicSchema[name as keyof typeof BasicSchema], 0);
        }
    }
+    if (normalize) {
+        basic.atom_site = getNormalizedAtomSite(basic.atom_site);
+    }
    return basic;
 }
--- a/src/mol-model-formats/structure/basic/util.ts
+++ b/src/mol-model-formats/structure/basic/util.ts
@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

-import { BasicData } from './schema';
-import { Table } from '../../../mol-data/db';
+import { AtomSite, BasicData } from './schema';
+import { Column, Table } from '../../../mol-data/db';

 export function getModelGroupName(model_id: number, data: BasicData) {
    const { ihm_model_group, ihm_model_group_link } = data;
@@ -17,4 +17,28 @@ export function getModelGroupName(model_id: number, data: BasicData) {
        if (group) return group.name;
    }
    return '';
+}
+
+//
+
+function hasPresentValues(column: Column<any>) {
+    for (let i = 0, il = column.rowCount; i < il; i++) {
+        if (column.valueKind(i) === Column.ValueKind.Present) return true;
+    }
+    return false;
+}
+
+function substUndefinedColumn<T extends Table<any>>(table: T, a: keyof T, b: keyof T) {
+    if (!table[a].isDefined || !hasPresentValues(table[a])) table[a] = table[b];
+    if (!table[b].isDefined || !hasPresentValues(table[b])) table[b] = table[a];
+}
+
+/** Fix possibly missing auth_/label_ columns */
+export function getNormalizedAtomSite(atom_site: AtomSite) {
+    const normalized = Table.ofColumns(atom_site._schema, atom_site);
+    substUndefinedColumn(normalized, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(normalized, 'label_comp_id', 'auth_comp_id');
+    substUndefinedColumn(normalized, 'label_seq_id', 'auth_seq_id');
+    substUndefinedColumn(normalized, 'label_asym_id', 'auth_asym_id');
+    return normalized;
 }
--- a/src/mol-model-formats/structure/cif-core.ts
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -100,7 +100,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
        const element_symbol = new Array<string>(atomCount);
        for (let i = 0; i < atomCount; ++i) {
            // TODO can take as is if type_symbol not given?
-            element_symbol[i] = guessElementSymbolString(label.value(i));
+            element_symbol[i] = guessElementSymbolString(label.value(i), '');
        }
        typeSymbol = Column.ofStringArray(element_symbol);
        formalCharge = Column.Undefined(atomCount, Column.Schema.int);
@@ -146,13 +146,13 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
    componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    const models = await createModels(basics, format, ctx);
+    const models = await createModels(basic, format, ctx);

    if (models.frameCount > 0) {
        const first = models.representative;
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -9,6 +9,7 @@ import { WaterNames, PolymerNames } from '../../../mol-model/structure/model/typ
 import { SetUtils } from '../../../mol-util/set';
 import { BasicSchema } from '../basic/schema';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { SaccharideCompIdMap } from '../../../mol-model/structure/structure/carbohydrates/constants';

 type Component = Table.Row<Pick<mmCIF_chemComp_schema, 'id' | 'name' | 'type'>>

@@ -30,7 +31,7 @@ const DnaAtomIdsList = [

 /** Used to reduce false positives for atom name-based type guessing */
 const NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // Mononucleotides
 ]);

 const StandardComponents = (function () {
@@ -158,6 +159,8 @@ export class ComponentBuilder {
                this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
            } else if (NonPolymerNames.has(compId.toUpperCase())) {
                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
+            } else if (SaccharideCompIdMap.has(compId.toUpperCase())) {
+                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'saccharide' });
            } else {
                const atomIds = this.getAtomIds(index);
                if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {
--- a/src/mol-model-formats/structure/cube.ts
+++ b/src/mol-model-formats/structure/cube.ts
@@ -53,13 +53,13 @@ async function getModels(cube: CubeFile, ctx: RuntimeContext) {
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    return await createModels(basics, MolFormat.create(cube), ctx);
+    return await createModels(basic, MolFormat.create(cube), ctx);
 }

 //
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -27,6 +27,7 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
    const asymIds = new Array<string>(atoms.count);
    const seqIds = new Uint32Array(atoms.count);
    const ids = new Uint32Array(atoms.count);
+    const typeSymbol = new Array<string>(atoms.count);

    const entityBuilder = new EntityBuilder();
    const componentBuilder = new ComponentBuilder(atoms.residueNumber, atoms.atomName);
@@ -66,6 +67,8 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
        asymIds[i] = currentAsymId;
        seqIds[i] = currentSeqId;
        ids[i] = i;
+
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
    }

    const auth_asym_id = Column.ofStringArray(asymIds);
@@ -87,7 +90,7 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
        label_entity_id: Column.ofStringArray(entityIds),

        occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+        type_symbol: Column.ofStringArray(typeSymbol),

        pdbx_PDB_model_num: Column.ofConst(modelNum, atoms.count, Column.Schema.int),
    }, atoms.count);
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -19,6 +19,7 @@ import { ComponentBond } from './property/bonds/chem_comp';
 import { StructConn } from './property/bonds/struct_conn';
 import { Trajectory } from '../../mol-model/structure';
 import { GlobalModelTransformInfo } from '../../mol-model/structure/model/properties/global-transform';
+import { createBasic } from './basic/schema';

 function modelSymmetryFromMmcif(model: Model) {
    if (!MmcifFormat.is(model.sourceData)) return;
@@ -100,5 +101,6 @@ namespace MmcifFormat {

 export function trajectoryFromMmCIF(frame: CifFrame): Task<Trajectory> {
    const format = MmcifFormat.fromFrame(frame);
-    return Task.create('Create mmCIF Model', ctx => createModels(format.data.db, format, ctx));
+    const basic = createBasic(format.data.db, true);
+    return Task.create('Create mmCIF Model', ctx => createModels(basic, format, ctx));
 }
--- a/src/mol-model-formats/structure/mol.ts
+++ b/src/mol-model-formats/structure/mol.ts
@@ -68,13 +68,13 @@ export async function getMolModels(mol: MolFile, format: ModelFormat<any> | unde
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    const models = await createModels(basics, format ?? MolFormat.create(mol), ctx);
+    const models = await createModels(basic, format ?? MolFormat.create(mol), ctx);

    if (models.frameCount > 0) {
        const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
--- a/src/mol-model-formats/structure/mol2.ts
+++ b/src/mol-model-formats/structure/mol2.ts
@@ -41,7 +41,7 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
        for (let i = 0; i < atoms.count; ++i) {
            type_symbol[i] = hasAtomType
                ? atoms.atom_type.value(i).split('.')[0].toUpperCase()
-                : guessElementSymbolString(atoms.atom_name.value(i));
+                : guessElementSymbolString(atoms.atom_name.value(i), atoms.subst_name.value(i));
        }

        const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -75,13 +75,13 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
            componentBuilder.add(atoms.subst_name.value(i), i);
        }

-        const basics = createBasic({
+        const basic = createBasic({
            entity: entityBuilder.getEntityTable(),
            chem_comp: componentBuilder.getChemCompTable(),
            atom_site
        });

-        const _models = await createModels(basics, Mol2Format.create(mol2), ctx);
+        const _models = await createModels(basic, Mol2Format.create(mol2), ctx);

        if (_models.frameCount > 0) {
            const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array));
--- a/src/mol-model-formats/structure/nctraj.ts
+++ b/src/mol-model-formats/structure/nctraj.ts
@@ -0,0 +1,52 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../mol-task';
+import { NctrajFile } from '../../mol-io/reader/nctraj/parser';
+import { Coordinates, Frame, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { Mutable } from '../../mol-util/type-helpers';
+
+export function coordinatesFromNctraj(file: NctrajFile): Task<Coordinates> {
+    return Task.create('Parse NCTRAJ', async ctx => {
+        await ctx.update('Converting to coordinates');
+
+        const deltaTime = Time(file.deltaTime, 'step');
+        const offsetTime = Time(file.timeOffset, deltaTime.unit);
+
+        const frames: Frame[] = [];
+        for (let i = 0, il = file.coordinates.length; i < il; ++i) {
+            const c = file.coordinates[i];
+            const elementCount = c.length / 3;
+            const x = new Float32Array(elementCount);
+            const y = new Float32Array(elementCount);
+            const z = new Float32Array(elementCount);
+            for (let j = 0, jl = c.length; j < jl; j += 3) {
+                x[j / 3] = c[j];
+                y[j / 3] = c[j + 1];
+                z[j / 3] = c[j + 2];
+            }
+            const frame: Mutable<Frame> = {
+                elementCount,
+                x, y, z,
+                xyzOrdering: { isIdentity: true },
+                time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+            };
+            // TODO: handle case where cell_lengths and cell_angles are set, i.e., angles not 90deg
+            if (file.cell_lengths) {
+                const lengths = file.cell_lengths[i];
+                const x = Vec3.scale(Vec3(), Vec3.unitX, lengths[0]);
+                const y = Vec3.scale(Vec3(), Vec3.unitY, lengths[1]);
+                const z = Vec3.scale(Vec3(), Vec3.unitZ, lengths[2]);
+                frame.cell = Cell.fromBasis(x, y, z);
+            }
+            frames.push(frame);
+        }
+
+        return Coordinates.create(frames, deltaTime, offsetTime);
+    });
+}
--- a/src/mol-model-formats/structure/pdb.ts
+++ b/src/mol-model-formats/structure/pdb.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -14,6 +14,7 @@ import { Column } from '../../mol-data/db';
 import { AtomPartialCharge } from './property/partial-charge';
 import { Trajectory } from '../../mol-model/structure';
 import { ModelFormat } from '../format';
+import { createBasic } from './basic/schema';

 export { PdbFormat };

@@ -34,7 +35,8 @@ export function trajectoryFromPDB(pdb: PdbFile): Task<Trajectory> {
        await ctx.update('Converting to mmCIF');
        const cif = await pdbToMmCif(pdb);
        const format = MmcifFormat.fromFrame(cif, undefined, PdbFormat.create(pdb));
-        const models = await createModels(format.data.db, format, ctx);
+        const basic = createBasic(format.data.db, true);
+        const models = await createModels(basic, format, ctx);
        const partial_charge = cif.categories['atom_site']?.getField('partial_charge');
        if (partial_charge) {
            // TODO works only for single, unsorted model, to work generally
--- a/src/mol-model-formats/structure/prmtop.ts
+++ b/src/mol-model-formats/structure/prmtop.ts
@@ -0,0 +1,174 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { PrmtopFile } from '../../mol-io/reader/prmtop/parser';
+import { getMoleculeType, MoleculeType } from '../../mol-model/structure/model/types';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { getChainId } from './common/util';
+import { guessElementSymbolString } from './util';
+
+function getBasic(prmtop: PrmtopFile) {
+    const { pointers, residuePointer, residueLabel, atomName } = prmtop;
+    const atomCount = pointers.NATOM;
+    const residueCount = pointers.NRES;
+
+    //
+
+    const residueIds = new Uint32Array(atomCount);
+    const residueNames: string[] = [];
+
+    const addResidue = (i: number, from: number, to: number) => {
+        const rn = residueLabel.value(i);
+        for (let j = from, jl = to; j < jl; ++j) {
+            residueIds[j] = i + 1;
+            residueNames[j] = rn;
+        }
+    };
+
+    for (let i = 0, il = residueCount - 1; i < il; ++i) {
+        addResidue(i, residuePointer.value(i) - 1, residuePointer.value(i + 1) - 1);
+
+    }
+    addResidue(residueCount - 1, residuePointer.value(residueCount - 1) - 1, atomCount);
+
+    const residueId = Column.ofIntArray(residueIds);
+    const residueName = Column.ofStringArray(residueNames);
+
+    //
+
+    const entityIds = new Array<string>(atomCount);
+    const asymIds = new Array<string>(atomCount);
+    const seqIds = new Uint32Array(atomCount);
+    const ids = new Uint32Array(atomCount);
+
+    const entityBuilder = new EntityBuilder();
+    const componentBuilder = new ComponentBuilder(residueId, atomName);
+
+    let currentEntityId = '';
+    let currentAsymIndex = 0;
+    let currentAsymId = '';
+    let currentSeqId = 0;
+    let prevMoleculeType = MoleculeType.Unknown;
+    let prevResidueNumber = -1;
+
+    for (let i = 0, il = atomCount; i < il; ++i) {
+        const residueNumber = residueId.value(i);
+        if (residueNumber !== prevResidueNumber) {
+            const compId = residueName.value(i);
+            const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
+
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = getChainId(currentAsymIndex);
+                currentAsymIndex += 1;
+                currentSeqId = 0;
+            }
+
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
+            currentSeqId += 1;
+
+            prevResidueNumber = residueNumber;
+            prevMoleculeType = moleculeType;
+        }
+
+        entityIds[i] = currentEntityId;
+        asymIds[i] = currentAsymId;
+        seqIds[i] = currentSeqId;
+        ids[i] = i;
+    }
+
+    const id = Column.ofIntArray(ids);
+    const asym_id = Column.ofStringArray(asymIds);
+
+    //
+
+    const type_symbol = new Array<string>(atomCount);
+    for (let i = 0; i < atomCount; ++i) {
+        type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
+    }
+
+    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: Column.asArrayColumn(id),
+
+        label_asym_id: asym_id,
+        label_atom_id: Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: Column.ofIntArray(seqIds),
+        label_entity_id: Column.ofStringArray(entityIds),
+
+        occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
+        type_symbol: Column.ofStringArray(type_symbol),
+
+        pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+    }, atomCount);
+
+    const basic = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site
+    });
+
+    return basic;
+}
+
+//
+
+export { PrmtopFormat };
+
+type PrmtopFormat = ModelFormat<PrmtopFile>
+
+namespace PrmtopFormat {
+    export function is(x?: ModelFormat): x is PrmtopFormat {
+        return x?.kind === 'prmtop';
+    }
+
+    export function fromPrmtop(prmtop: PrmtopFile): PrmtopFormat {
+        return { kind: 'prmtop', name: prmtop.title.join(' ') || 'PRMTOP', data: prmtop };
+    }
+}
+
+export function topologyFromPrmtop(prmtop: PrmtopFile): Task<Topology> {
+    return Task.create('Parse PRMTOP', async ctx => {
+        const format = PrmtopFormat.fromPrmtop(prmtop);
+        const basic = getBasic(prmtop);
+
+        const { pointers: { NBONH, NBONA }, bondsIncHydrogen, bondsWithoutHydrogen } = prmtop;
+        const bondCount = NBONH + NBONA;
+
+        const bonds = {
+            indexA: Column.ofLambda({
+                value: (row: number) => {
+                    return row < NBONH
+                        ? bondsIncHydrogen.value(row * 3) / 3
+                        : bondsWithoutHydrogen.value((row - NBONH) * 3) / 3;
+                },
+                rowCount: bondCount,
+                schema: Column.Schema.int,
+            }),
+            indexB: Column.ofLambda({
+                value: (row: number) => {
+                    return row < NBONH
+                        ? bondsIncHydrogen.value(row * 3 + 1) / 3
+                        : bondsWithoutHydrogen.value((row - NBONH) * 3 + 1) / 3;
+                },
+                rowCount: bondCount,
+                schema: Column.Schema.int,
+            }),
+            order: Column.ofConst(1, bondCount, Column.Schema.int)
+        };
+
+        return Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format);
+    });
+}
--- a/src/mol-model-formats/structure/property/symmetry.ts
+++ b/src/mol-model-formats/structure/property/symmetry.ts
@@ -63,10 +63,21 @@ function getSpacegroupNameOrNumber(symmetry: Table<mmCIF_Schema['symmetry']>) {

 function getSpacegroup(symmetry: Table<mmCIF_Schema['symmetry']>, cell: Table<mmCIF_Schema['cell']>): Spacegroup {
    if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
+
+    const a = cell.length_a.value(0);
+    const b = cell.length_b.value(0);
+    const c = cell.length_c.value(0);
+    if (a === 0 || b === 0 || c === 0) return Spacegroup.ZeroP1;
+
+    const alpha = cell.angle_alpha.value(0);
+    const beta = cell.angle_beta.value(0);
+    const gamma = cell.angle_gamma.value(0);
+    if (alpha === 0 || beta === 0 || gamma === 0) return Spacegroup.ZeroP1;
+
    const nameOrNumber = getSpacegroupNameOrNumber(symmetry);
    const spaceCell = SpacegroupCell.create(nameOrNumber,
-        Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
-        Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+        Vec3.create(a, b, c),
+        Vec3.scale(Vec3(), Vec3.create(alpha, beta, gamma), Math.PI / 180));

    return Spacegroup.create(spaceCell);
 }
--- a/src/mol-model-formats/structure/psf.ts
+++ b/src/mol-model-formats/structure/psf.ts
@@ -21,6 +21,7 @@ function getBasic(atoms: PsfFile['atoms']) {
    const asymIds = new Array<string>(atoms.count);
    const seqIds = new Uint32Array(atoms.count);
    const ids = new Uint32Array(atoms.count);
+    const typeSymbol = new Array<string>(atoms.count);

    const entityBuilder = new EntityBuilder();
    const componentBuilder = new ComponentBuilder(atoms.residueId, atoms.atomName);
@@ -68,6 +69,8 @@ function getBasic(atoms: PsfFile['atoms']) {
        asymIds[i] = currentAsymId;
        seqIds[i] = currentSeqId;
        ids[i] = i;
+
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
    }

    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -84,7 +87,7 @@ function getBasic(atoms: PsfFile['atoms']) {
        label_entity_id: Column.ofStringArray(entityIds),

        occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+        type_symbol: Column.ofStringArray(typeSymbol),

        pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
    }, atoms.count);
--- a/src/mol-model-formats/structure/top.ts
+++ b/src/mol-model-formats/structure/top.ts
@@ -0,0 +1,226 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { TopFile } from '../../mol-io/reader/top/parser';
+import { getMoleculeType, MoleculeType } from '../../mol-model/structure/model/types';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { getChainId } from './common/util';
+import { guessElementSymbolString } from './util';
+
+function getBasic(top: TopFile) {
+    const { molecules, compounds } = top;
+
+    const singleResidue: Record<string, boolean> = {};
+    let atomCount = 0;
+
+    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
+        const mol = molecules.compound.value(i);
+        const count = molecules.molCount.value(i);
+        const { atoms } = compounds[mol];
+
+        Column.asArrayColumn(atoms.atom);
+        Column.asArrayColumn(atoms.resnr);
+        Column.asArrayColumn(atoms.residu);
+
+        atomCount += count * atoms._rowCount;
+
+        let prevResnr = atoms.resnr.value(0);
+        singleResidue[mol] = true;
+        for (let j = 1, jl = atoms._rowCount; j < jl; ++j) {
+            const resnr = atoms.resnr.value(j);
+            if (resnr !== prevResnr) {
+                singleResidue[mol] = false;
+                break;
+            }
+            prevResnr = resnr;
+        }
+    }
+
+    //
+
+    const atomNames = new Array<string>(atomCount);
+    const residueIds = new Uint32Array(atomCount);
+    const residueNames = new Array<string>(atomCount);
+
+    let k = 0;
+    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
+        const mol = molecules.compound.value(i);
+        const count = molecules.molCount.value(i);
+        const { atoms } = compounds[mol];
+        const isSingleResidue = singleResidue[mol];
+        for (let j = 0; j < count; ++j) {
+            for (let l = 0, ll = atoms._rowCount; l < ll; ++l) {
+                atomNames[k] = atoms.atom.value(l);
+                residueIds[k] = atoms.resnr.value(l);
+                residueNames[k] = atoms.residu.value(l);
+
+                if (isSingleResidue) residueIds[k] += j;
+
+                k += 1;
+            }
+        }
+    }
+
+    const atomName = Column.ofStringArray(atomNames);
+    const residueId = Column.ofIntArray(residueIds);
+    const residueName = Column.ofStringArray(residueNames);
+
+    //
+
+    const entityIds = new Array<string>(atomCount);
+    const asymIds = new Array<string>(atomCount);
+    const seqIds = new Uint32Array(atomCount);
+    const ids = new Uint32Array(atomCount);
+
+    const entityBuilder = new EntityBuilder();
+    const componentBuilder = new ComponentBuilder(residueId, atomName);
+
+    let currentEntityId = '';
+    let currentAsymIndex = 0;
+    let currentAsymId = '';
+    let currentSeqId = 0;
+    let prevMoleculeType = MoleculeType.Unknown;
+    let prevResidueNumber = -1;
+
+    for (let i = 0, il = atomCount; i < il; ++i) {
+        const residueNumber = residueId.value(i);
+        if (residueNumber !== prevResidueNumber) {
+            const compId = residueName.value(i);
+            const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
+
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = getChainId(currentAsymIndex);
+                currentAsymIndex += 1;
+                currentSeqId = 0;
+            }
+
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
+            currentSeqId += 1;
+
+            prevResidueNumber = residueNumber;
+            prevMoleculeType = moleculeType;
+        }
+
+        entityIds[i] = currentEntityId;
+        asymIds[i] = currentAsymId;
+        seqIds[i] = currentSeqId;
+        ids[i] = i;
+    }
+
+    const id = Column.ofIntArray(ids);
+    const asym_id = Column.ofStringArray(asymIds);
+
+    //
+
+    const type_symbol = new Array<string>(atomCount);
+    for (let i = 0; i < atomCount; ++i) {
+        type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
+    }
+
+    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: Column.asArrayColumn(id),
+
+        label_asym_id: asym_id,
+        label_atom_id: Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: Column.ofIntArray(seqIds),
+        label_entity_id: Column.ofStringArray(entityIds),
+
+        occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
+        type_symbol: Column.ofStringArray(type_symbol),
+
+        pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+    }, atomCount);
+
+    const basic = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site
+    });
+
+    return basic;
+}
+
+function getBonds(top: TopFile) {
+    const { molecules, compounds } = top;
+
+    const indexA: number[] = [];
+    const indexB: number[] = [];
+
+    let atomOffset = 0;
+
+    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
+        const mol = molecules.compound.value(i);
+        const count = molecules.molCount.value(i);
+        const { atoms, bonds } = compounds[mol];
+
+
+
+        if (bonds) {
+            for (let j = 0; j < count; ++j) {
+
+                for (let l = 0, ll = bonds._rowCount; l < ll; ++l) {
+                    indexA.push(bonds.ai.value(l) - 1 + atomOffset);
+                    indexB.push(bonds.aj.value(l) - 1 + atomOffset);
+                }
+
+                atomOffset += atoms._rowCount;
+            }
+        } else if (mol === 'TIP3') {
+            for (let j = 0; j < count; ++j) {
+                indexA.push(0 + atomOffset);
+                indexB.push(1 + atomOffset);
+                indexA.push(0 + atomOffset);
+                indexB.push(2 + atomOffset);
+                atomOffset += atoms._rowCount;
+            }
+        } else {
+            atomOffset += count * atoms._rowCount;
+        }
+    }
+
+    return {
+        indexA: Column.ofIntArray(indexA),
+        indexB: Column.ofIntArray(indexB),
+        order: Column.ofConst(1, indexA.length, Column.Schema.int)
+    };
+}
+
+//
+
+export { TopFormat };
+
+type TopFormat = ModelFormat<TopFile>
+
+namespace TopFormat {
+    export function is(x?: ModelFormat): x is TopFormat {
+        return x?.kind === 'top';
+    }
+
+    export function fromTop(top: TopFile): TopFormat {
+        return { kind: 'top', name: top.system || 'TOP', data: top };
+    }
+}
+
+export function topologyFromTop(top: TopFile): Task<Topology> {
+    return Task.create('Parse TOP', async ctx => {
+        const format = TopFormat.fromTop(top);
+        const basic = getBasic(top);
+        const bonds = getBonds(top);
+
+        return Topology.create(top.system || 'TOP', basic, bonds, format);
+    });
+}
--- a/src/mol-model-formats/structure/trr.ts
+++ b/src/mol-model-formats/structure/trr.ts
@@ -0,0 +1,39 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../mol-task';
+import { TrrFile } from '../../mol-io/reader/trr/parser';
+import { Coordinates, Frame, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+import { Vec3 } from '../../mol-math/linear-algebra';
+
+export function coordinatesFromTrr(file: TrrFile): Task<Coordinates> {
+    return Task.create('Parse TRR', async ctx => {
+        await ctx.update('Converting to coordinates');
+
+        const deltaTime = Time(file.deltaTime, 'step');
+        const offsetTime = Time(file.timeOffset, deltaTime.unit);
+
+        const frames: Frame[] = [];
+        for (let i = 0, il = file.frames.length; i < il; ++i) {
+            const box = file.boxes[i];
+            const x = Vec3.fromArray(Vec3(), box, 0);
+            const y = Vec3.fromArray(Vec3(), box, 3);
+            const z = Vec3.fromArray(Vec3(), box, 6);
+            frames.push({
+                elementCount: file.frames[i].count,
+                cell: Cell.fromBasis(x, y, z),
+                x: file.frames[i].x,
+                y: file.frames[i].y,
+                z: file.frames[i].z,
+                xyzOrdering: { isIdentity: true },
+                time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+            });
+        }
+
+        return Coordinates.create(frames, deltaTime, offsetTime);
+    });
+}
--- a/src/mol-model-formats/structure/util.ts
+++ b/src/mol-model-formats/structure/util.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -46,31 +46,30 @@ export function guessElementSymbolTokens(tokens: Tokens, str: string, start: num
    TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }

+const TwoCharElementNames = new Set(['NA', 'CL', 'FE', 'SI', 'BR', 'AS']);
+const OneCharElementNames = new Set(['C', 'H', 'N', 'O', 'P', 'S']);
+
 const reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
-export function guessElementSymbolString(str: string) {
+export function guessElementSymbolString(atomId: string, compId: string) {
    // trim spaces and numbers, convert to upper case
-    str = str.replace(reTrimSpacesAndNumbers, '').toUpperCase();
-    const l = str.length;
+    atomId = atomId.replace(reTrimSpacesAndNumbers, '').toUpperCase();
+    const l = atomId.length;

-    if (l === 0) return str; // empty
-    if (l === 1) return str; // one char
+    if (l === 0) return atomId; // empty
+    if (l === 1) return atomId; // one char
+    if (TwoCharElementNames.has(atomId)) return atomId; // two chars

-    if (l === 2) { // two chars
-        if (str === 'NA' || str === 'CL' || str === 'FE' || str === 'SI' ||
-            str === 'BR' || str === 'AS'
-        ) return str;
+    // check for Charmm ion names where component and atom id are the same
+    if (l === 3 && compId === atomId) {
+        if (atomId === 'SOD') return 'NA';
+        if (atomId === 'POT') return 'K';
+        if (atomId === 'CES') return 'CS';
+        if (atomId === 'CAL') return 'CA';
+        if (atomId === 'CLA') return 'CL';
    }

-    if (l === 3) { // three chars
-        if (str === 'SOD') return 'NA';
-        if (str === 'POT') return 'K';
-        if (str === 'CES') return 'CS';
-        if (str === 'CAL') return 'CA';
-        if (str === 'CLA') return 'CL';
-    }
-
-    const c = str[0];
-    if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S') return c;
+    if (OneCharElementNames.has(atomId[0])) return atomId[0];

    return ''; // no reasonable guess, return empty string
-}
+}
+
--- a/src/mol-model-formats/structure/xyz.ts
+++ b/src/mol-model-formats/structure/xyz.ts
@@ -78,13 +78,13 @@ function getModels(mol: XyzFile, ctx: RuntimeContext) {
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    return createModels(basics, XyzFormat.create(mol), ctx);
+    return createModels(basic, XyzFormat.create(mol), ctx);
 }

 //
--- a/src/mol-model/sequence/sequence.ts
+++ b/src/mol-model/sequence/sequence.ts
@@ -7,6 +7,7 @@

 import { AminoAlphabet, NuclecicAlphabet, getProteinOneLetterCode, getRnaOneLetterCode, getDnaOneLetterCode } from './constants';
 import { Column } from '../../mol-data/db';
+import { assertUnreachable } from '../../mol-util/type-helpers';

 // TODO add mapping support to other sequence spaces, e.g. uniprot

@@ -66,7 +67,7 @@ namespace Sequence {
            case Kind.DNA: code = getDnaOneLetterCode; break;
            case Kind.RNA: code = getRnaOneLetterCode; break;
            case Kind.Generic: code = () => 'X'; break;
-            default: throw new Error(`unknown kind '${kind}'`);
+            default: assertUnreachable(kind);
        }
        if (map && map.size > 0) {
            return (name: string) => {
--- a/src/mol-model/structure/model/types/saccharides.ts
+++ b/src/mol-model/structure/model/types/saccharides.ts
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -1,11 +1,12 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @author David Sehnal <david.sehnal@gmail.com>
 */

 import { Color, ColorMap } from '../../../../mol-util/color';
+import { SaccharideNames } from '../../model/types/saccharides';

 // follows community standard from https://www.ncbi.nlm.nih.gov/glycans/snfg.html

@@ -302,13 +303,6 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
    Psi: ['PSV', 'SF6', 'SF9', 'TTV'],
 };

-const UnknownSaccharideNames = [
-    'NGZ', // via CCD
-    'LAT', // BETA-LACTOSE, Gal-Glc di-saccharide via GlyFinder
-
-    'PUF', 'GDA', '9WJ', // via updated CCD
-];
-
 /**
 * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
 */
@@ -354,9 +348,9 @@ export const SaccharideCompIdMap = (function () {
            }
        }
    }
-    for (let i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], UnknownSaccharideComponent);
-    }
+    SaccharideNames.forEach(name => {
+        if (!map.has(name)) map.set(name, UnknownSaccharideComponent);
+    });
    return map;
 })();

--- a/src/mol-plugin-state/actions/file.ts
+++ b/src/mol-plugin-state/actions/file.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -13,6 +13,27 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { unzip } from '../../mol-util/zip/zip';
 import { PluginStateObject } from '../objects';

+async function processFile(file: Asset.File, plugin: PluginContext, format: string, visuals: boolean) {
+    const info = getFileInfo(file.file!);
+    const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
+    const { data } = await plugin.builders.data.readFile({ file, isBinary });
+    const provider = format === 'auto'
+        ? plugin.dataFormats.auto(info, data.cell?.obj!)
+        : plugin.dataFormats.get(format);
+
+    if (!provider) {
+        plugin.log.warn(`OpenFiles: could not find data provider for '${info.ext}'`);
+        await plugin.state.data.build().delete(data).commit();
+        return;
+    }
+
+    // need to await so that the enclosing Task finishes after the update is done.
+    const parsed = await provider.parse(plugin, data);
+    if (visuals) {
+        await provider.visuals?.(plugin, parsed);
+    }
+};
+
 export const OpenFiles = StateAction.build({
    display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
    from: PluginStateObject.Root,
@@ -36,36 +57,19 @@ export const OpenFiles = StateAction.build({
            return;
        }

-        const processFile = async (file: Asset.File) => {
-            const info = getFileInfo(file.file!);
-            const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
-            const { data } = await plugin.builders.data.readFile({ file, isBinary });
-            const provider = params.format.name === 'auto'
-                ? plugin.dataFormats.auto(info, data.cell?.obj!)
-                : plugin.dataFormats.get(params.format.params);
-
-            if (!provider) {
-                plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
-                return;
-            }
-
-            // need to await so that the enclosing Task finishes after the update is done.
-            const parsed = await provider.parse(plugin, data);
-            if (params.visuals) {
-                await provider.visuals?.(plugin, parsed);
-            }
-        };
-
        for (const file of params.files) {
            try {
                if (file.file && file.name.toLowerCase().endsWith('.zip')) {
                    const zippedFiles = await unzip(taskCtx, await file.file.arrayBuffer());
                    for (const [fn, filedata] of Object.entries(zippedFiles)) {
-                        const asset = Asset.File(new File([filedata as Uint8Array], fn));
-                        await processFile(asset);
+                        if (!(filedata instanceof Uint8Array) || filedata.length === 0) continue;
+
+                        const asset = Asset.File(new File([filedata], fn));
+                        await processFile(asset, plugin, 'auto', params.visuals);
                    }
                } else {
-                    await processFile(file);
+                    const format = params.format.name === 'auto' ? 'auto' : params.format.params;
+                    await processFile(file, plugin, format, params.visuals);
                }
            } catch (e) {
                console.error(e);
@@ -79,7 +83,7 @@ export const DownloadFile = StateAction.build({
    display: { name: 'Download File', description: 'Load one or more file from an URL' },
    from: PluginStateObject.Root,
    params: (a, ctx: PluginContext) => {
-        const { options } = ctx.dataFormats;
+        const options = [...ctx.dataFormats.options, ['zip', 'Zip'] as const];
        return {
            url: PD.Url(''),
            format: PD.Select(options[0][0], options),
@@ -92,16 +96,30 @@ export const DownloadFile = StateAction.build({

    await state.transaction(async () => {
        try {
-            const provider = plugin.dataFormats.get(params.format);
-            if (!provider) {
-                plugin.log.warn(`DownloadFile: could not find data provider for '${params.format}'`);
-                return;
-            }
+            if (params.format === 'zip') {
+                // TODO: add ReadZipFile transformer so this can be saved as a simple state snaphot,
+                //       would need support for extracting individual files from zip
+                const data = await plugin.builders.data.download({ url: params.url, isBinary: true });
+                const zippedFiles = await unzip(taskCtx, (data.obj?.data as Uint8Array).buffer);
+                for (const [fn, filedata] of Object.entries(zippedFiles)) {
+                    if (!(filedata instanceof Uint8Array) || filedata.length === 0) continue;

-            const data = await plugin.builders.data.download({ url: params.url, isBinary: params.isBinary });
-            const parsed = await provider.parse(plugin, data);
-            if (params.visuals) {
-                await provider.visuals?.(plugin, parsed);
+                    const asset = Asset.File(new File([filedata], fn));
+
+                    await processFile(asset, plugin, 'auto', params.visuals);
+                }
+            } else {
+                const provider = plugin.dataFormats.get(params.format);
+                if (!provider) {
+                    plugin.log.warn(`DownloadFile: could not find data provider for '${params.format}'`);
+                    return;
+                }
+
+                const data = await plugin.builders.data.download({ url: params.url, isBinary: params.isBinary });
+                const parsed = await provider.parse(plugin, data);
+                if (params.visuals) {
+                    await provider.visuals?.(plugin, parsed);
+                }
            }
        } catch (e) {
            console.error(e);
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,16 +10,18 @@ import { StateAction, StateSelection, StateTransformer } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../builder/structure/representation-preset';
-import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats } from '../formats/trajectory';
+import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats, TrajectoryFormatCategory } from '../formats/trajectory';
 import { RootStructureDefinition } from '../helpers/root-structure';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
 import { Download } from '../transforms/data';
-import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
+import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, TrajectoryFromModelAndCoordinates } from '../transforms/model';
 import { Asset } from '../../mol-util/assets';
 import { PluginConfig } from '../../mol-plugin/config';
 import { getFileInfo } from '../../mol-util/file-info';
 import { assertUnreachable } from '../../mol-util/type-helpers';
+import { TopologyFormatCategory } from '../formats/topology';
+import { CoordinatesFormatCategory } from '../formats/coordinates';

 const DownloadModelRepresentationOptions = (plugin: PluginContext) => {
    const representationDefault = plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
@@ -155,7 +157,7 @@ const DownloadStructure = StateAction.build({
            asTrajectory = !!src.params.options.asTrajectory;
            format = 'mol';
            break;
-        default: throw new Error(`${(src as any).name} not supported.`);
+        default: assertUnreachable(src);
    }

    const representationPreset: any = params.source.params.options.representation || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
@@ -311,4 +313,127 @@ export const AddTrajectory = StateAction.build({
        const structure = await ctx.builders.structure.createStructure(model.selector);
        await ctx.builders.structure.representation.applyPreset(structure, 'auto');
    }).runInContext(taskCtx);
+}));
+
+export const LoadTrajectory = StateAction.build({
+    display: { name: 'Load Trajectory', description: 'Load trajectory of model/topology and coordinates from URL or file.' },
+    from: PluginStateObject.Root,
+    params(a, ctx: PluginContext) {
+        const { options } = ctx.dataFormats;
+        const modelOptions = options.filter(o => o[2] === TrajectoryFormatCategory || o[2] === TopologyFormatCategory);
+        const coordinatesOptions = options.filter(o => o[2] === CoordinatesFormatCategory);
+
+        const modelExts: string[] = [];
+        const coordinatesExts: string[] = [];
+        for (const { provider } of ctx.dataFormats.list) {
+            if (provider.category === TrajectoryFormatCategory || provider.category === TopologyFormatCategory) {
+                if (provider.binaryExtensions) modelExts.push(...provider.binaryExtensions);
+                if (provider.stringExtensions) modelExts.push(...provider.stringExtensions);
+            } else if (provider.category === CoordinatesFormatCategory) {
+                if (provider.binaryExtensions) coordinatesExts.push(...provider.binaryExtensions);
+                if (provider.stringExtensions) coordinatesExts.push(...provider.stringExtensions);
+            }
+        }
+
+        return {
+            source: PD.MappedStatic('file', {
+                url: PD.Group({
+                    model: PD.Group({
+                        url: PD.Url(''),
+                        format: PD.Select(modelOptions[0][0], modelOptions),
+                        isBinary: PD.Boolean(false),
+                    }, { isExpanded: true }),
+                    coordinates: PD.Group({
+                        url: PD.Url(''),
+                        format: PD.Select(coordinatesOptions[0][0], coordinatesOptions),
+                    }, { isExpanded: true })
+                }, { isFlat: true }),
+                file: PD.Group({
+                    model: PD.File({ accept: modelExts.map(e => `.${e}`).join(','), label: 'Model' }),
+                    coordinates: PD.File({ accept: coordinatesExts.map(e => `.${e}`).join(','), label: 'Coordinates' }),
+                }, { isFlat: true }),
+            }, { options: [['url', 'URL'], ['file', 'File']] })
+        };
+    }
+})(({ params, state }, ctx: PluginContext) => Task.create('Load Trajectory', taskCtx => {
+    return state.transaction(async () => {
+        const s = params.source;
+
+        if (s.name === 'file' && (s.params.model === null || s.params.coordinates === null)) {
+            ctx.log.error('No file(s) selected');
+            return;
+        }
+
+        if (s.name === 'url' && (!s.params.model || !s.params.coordinates)) {
+            ctx.log.error('No URL(s) given');
+            return;
+        }
+
+        const processUrl = async (url: string | Asset.Url, format: string, isBinary: boolean) => {
+            const data = await ctx.builders.data.download({ url, isBinary });
+            const provider = ctx.dataFormats.get(format);
+
+            if (!provider) {
+                ctx.log.warn(`LoadTrajectory: could not find data provider for '${format}'`);
+                return;
+            }
+
+            return provider.parse(ctx, data);
+        };
+
+        const processFile = async (file: Asset.File | null) => {
+            if (!file) throw new Error('No file selected');
+
+            const info = getFileInfo(file.file!);
+            const isBinary = ctx.dataFormats.binaryExtensions.has(info.ext);
+            const { data } = await ctx.builders.data.readFile({ file, isBinary });
+            const provider = ctx.dataFormats.auto(info, data.cell?.obj!);
+
+            if (!provider) {
+                ctx.log.warn(`LoadTrajectory: could not find data provider for '${info.ext}'`);
+                await ctx.state.data.build().delete(data).commit();
+                return;
+            }
+
+            return provider.parse(ctx, data);
+        };
+
+        try {
+            const modelParsed = s.name === 'url'
+                ? await processUrl(s.params.model.url, s.params.model.format, s.params.model.isBinary)
+                : await processFile(s.params.model);
+
+            let model;
+            if ('trajectory' in modelParsed) {
+                model = await state.build().to(modelParsed.trajectory)
+                    .apply(ModelFromTrajectory, { modelIndex: 0 })
+                    .commit();
+            } else {
+                model = modelParsed.topology;
+            }
+
+            //
+
+            const coordinates = s.name === 'url'
+                ? await processUrl(s.params.coordinates.url, s.params.coordinates.format, true)
+                : await processFile(s.params.coordinates);
+
+            //
+
+            const dependsOn = [model.ref, coordinates.ref];
+            const traj = state.build().toRoot()
+                .apply(TrajectoryFromModelAndCoordinates, {
+                    modelRef: model.ref,
+                    coordinatesRef: coordinates.ref
+                }, { dependsOn })
+                .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
+
+            await state.updateTree(traj).runInContext(taskCtx);
+            const structure = await ctx.builders.structure.createStructure(traj.selector);
+            await ctx.builders.structure.representation.applyPreset(structure, 'auto');
+        } catch (e) {
+            console.error(e);
+            ctx.log.error(`Error loading trajectory`);
+        }
+    }).runInContext(taskCtx);
 }));
--- a/src/mol-plugin-state/actions/volume.ts
+++ b/src/mol-plugin-state/actions/volume.ts
@@ -15,6 +15,7 @@ import { Download } from '../transforms/data';
 import { DataFormatProvider } from '../formats/provider';
 import { Asset } from '../../mol-util/assets';
 import { StateTransforms } from '../transforms';
+import { assertUnreachable } from '../../mol-util/type-helpers';

 export type EmdbDownloadProvider = 'pdbe' | 'rcsb'

@@ -109,7 +110,7 @@ const DownloadDensity = StateAction.build({
                label: `RCSB PDB X-ray Density Server: ${src.params.provider.id}`
            };
            break;
-        default: throw new Error(`${(src as any).name} not supported.`);
+        default: assertUnreachable(src);
    }

    const data = await plugin.builders.data.download(downloadParams);
@@ -131,7 +132,7 @@ const DownloadDensity = StateAction.build({
            entryId = src.params.provider.id;
            provider = plugin.dataFormats.get('dscif');
            break;
-        default: throw new Error(`${(src as any).name} not supported.`);
+        default: assertUnreachable(src);
    }

    if (!provider) {
--- a/src/mol-plugin-state/formats/coordinates.ts
+++ b/src/mol-plugin-state/formats/coordinates.ts
@@ -0,0 +1,86 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateTransforms } from '../transforms';
+import { DataFormatProvider } from './provider';
+
+export const CoordinatesFormatCategory = 'Coordinates';
+
+export { DcdProvider };
+const DcdProvider = DataFormatProvider({
+    label: 'DCD',
+    description: 'DCD',
+    category: CoordinatesFormatCategory,
+    binaryExtensions: ['dcd'],
+    parse: (plugin, data) => {
+        const coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Model.CoordinatesFromDcd);
+
+        return coordinates.commit();
+    }
+});
+type DcdProvider = typeof DcdProvider;
+
+export { XtcProvider };
+const XtcProvider = DataFormatProvider({
+    label: 'XTC',
+    description: 'XTC',
+    category: CoordinatesFormatCategory,
+    binaryExtensions: ['xtc'],
+    parse: (plugin, data) => {
+        const coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Model.CoordinatesFromXtc);
+
+        return coordinates.commit();
+    }
+});
+type XtcProvider = typeof XtcProvider;
+
+export { TrrProvider };
+const TrrProvider = DataFormatProvider({
+    label: 'TRR',
+    description: 'TRR',
+    category: CoordinatesFormatCategory,
+    binaryExtensions: ['trr'],
+    parse: (plugin, data) => {
+        const coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Model.CoordinatesFromTrr);
+
+        return coordinates.commit();
+    }
+});
+type TrrProvider = typeof TrrProvider;
+
+export { NctrajProvider };
+const NctrajProvider = DataFormatProvider({
+    label: 'NCTRAJ',
+    description: 'NCTRAJ',
+    category: CoordinatesFormatCategory,
+    binaryExtensions: ['nc', 'nctraj'],
+    parse: (plugin, data) => {
+        const coordinates = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Model.CoordinatesFromNctraj);
+
+        return coordinates.commit();
+    }
+});
+type NctrajProvider = typeof NctrajProvider;
+
+export type CoordinatesProvider = DcdProvider | XtcProvider | TrrProvider;
+
+export const BuiltInCoordinatesFormats = [
+    ['dcd', DcdProvider] as const,
+    ['xtc', XtcProvider] as const,
+    ['trr', TrrProvider] as const,
+    ['nctraj', NctrajProvider] as const,
+] as const;
+
+export type BuiltInCoordinatesFormat = (typeof BuiltInCoordinatesFormats)[number][0]
--- a/src/mol-plugin-state/formats/registry.ts
+++ b/src/mol-plugin-state/formats/registry.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @author David Sehnal <david.sehnal@gmail.com>
@@ -11,17 +11,18 @@ import { DataFormatProvider } from './provider';
 import { BuiltInTrajectoryFormats } from './trajectory';
 import { BuiltInVolumeFormats } from './volume';
 import { BuiltInShapeFormats } from './shape';
-import { BuiltInStructureFormats } from './structure';
+import { BuiltInTopologyFormats } from './topology';
+import { BuiltInCoordinatesFormats } from './coordinates';

 export class DataFormatRegistry {
    private _list: { name: string, provider: DataFormatProvider }[] = [];
    private _map = new Map<string, DataFormatProvider>();
    private _extensions: Set<string> | undefined = undefined;
    private _binaryExtensions: Set<string> | undefined = undefined;
-    private _options: [string, string, string][] | undefined = undefined;
+    private _options: [name: string, label: string, category: string][] | undefined = undefined;

-    get types(): [string, string][] {
-        return this._list.map(e => [e.name, e.provider.label] as [string, string]);
+    get types(): [name: string, label: string][] {
+        return this._list.map(e => [e.name, e.provider.label] as [name: string, label: string]);
    }

    get extensions() {
@@ -45,7 +46,7 @@ export class DataFormatRegistry {

    get options() {
        if (this._options) return this._options;
-        const options: [string, string, string][] = [];
+        const options: [name: string, label: string, category: string][] = [];
        this._list.forEach(({ name, provider }) => options.push([name, provider.label, provider.category || '']));
        this._options = options;
        return options;
@@ -53,7 +54,8 @@ export class DataFormatRegistry {

    constructor() {
        for (const [id, p] of BuiltInVolumeFormats) this.add(id, p);
-        for (const [id, p] of BuiltInStructureFormats) this.add(id, p);
+        for (const [id, p] of BuiltInTopologyFormats) this.add(id, p);
+        for (const [id, p] of BuiltInCoordinatesFormats) this.add(id, p);
        for (const [id, p] of BuiltInShapeFormats) this.add(id, p);
        for (const [id, p] of BuiltInTrajectoryFormats) this.add(id, p);
    };
--- a/src/mol-plugin-state/formats/structure.ts
+++ b/src/mol-plugin-state/formats/structure.ts
@@ -1,64 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { StateTransforms } from '../transforms';
-import { DataFormatProvider } from './provider';
-
-export const StructureFormatCategory = 'Structure';
-
-export const PsfProvider = DataFormatProvider({
-    label: 'PSF',
-    description: 'PSF',
-    category: StructureFormatCategory,
-    stringExtensions: ['psf'],
-    parse: async (plugin, data) => {
-        const format = plugin.state.data.build()
-            .to(data)
-            .apply(StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
-        const topology = format.apply(StateTransforms.Model.TopologyFromPsf);
-
-        await format.commit();
-
-        return { format: format.selector, topology: topology.selector };
-    }
-});
-
-export const DcdProvider = DataFormatProvider({
-    label: 'DCD',
-    description: 'DCD',
-    category: StructureFormatCategory,
-    binaryExtensions: ['dcd'],
-    parse: (plugin, data) => {
-        const coordinates = plugin.state.data.build()
-            .to(data)
-            .apply(StateTransforms.Model.CoordinatesFromDcd);
-
-        return coordinates.commit();
-    }
-});
-
-export const XtcProvider = DataFormatProvider({
-    label: 'XTC',
-    description: 'XTC',
-    category: StructureFormatCategory,
-    binaryExtensions: ['xtc'],
-    parse: (plugin, data) => {
-        const coordinates = plugin.state.data.build()
-            .to(data)
-            .apply(StateTransforms.Model.CoordinatesFromXtc);
-
-        return coordinates.commit();
-    }
-});
-
-export const BuiltInStructureFormats = [
-    ['psf', PsfProvider] as const,
-    ['dcd', DcdProvider] as const,
-    ['xtc', XtcProvider] as const,
-] as const;
-
-export type BuildInStructureFormat = (typeof BuiltInStructureFormats)[number][0]
--- a/src/mol-plugin-state/formats/topology.ts
+++ b/src/mol-plugin-state/formats/topology.ts
@@ -0,0 +1,78 @@
+/**
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StateTransforms } from '../transforms';
+import { DataFormatProvider } from './provider';
+
+export const TopologyFormatCategory = 'Topology';
+
+export { PsfProvider };
+const PsfProvider = DataFormatProvider({
+    label: 'PSF',
+    description: 'PSF',
+    category: TopologyFormatCategory,
+    stringExtensions: ['psf'],
+    parse: async (plugin, data) => {
+        const format = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
+        const topology = format.apply(StateTransforms.Model.TopologyFromPsf);
+
+        await format.commit();
+
+        return { format: format.selector, topology: topology.selector };
+    }
+});
+type PsfProvider = typeof PsfProvider;
+
+export { PrmtopProvider };
+const PrmtopProvider = DataFormatProvider({
+    label: 'PRMTOP',
+    description: 'PRMTOP',
+    category: TopologyFormatCategory,
+    stringExtensions: ['prmtop', 'parm7'],
+    parse: async (plugin, data) => {
+        const format = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Data.ParsePrmtop, {}, { state: { isGhost: true } });
+        const topology = format.apply(StateTransforms.Model.TopologyFromPrmtop);
+
+        await format.commit();
+
+        return { format: format.selector, topology: topology.selector };
+    }
+});
+type PrmtopProvider = typeof PrmtopProvider;
+
+export { TopProvider };
+const TopProvider = DataFormatProvider({
+    label: 'TOP',
+    description: 'TOP',
+    category: TopologyFormatCategory,
+    stringExtensions: ['top'],
+    parse: async (plugin, data) => {
+        const format = plugin.state.data.build()
+            .to(data)
+            .apply(StateTransforms.Data.ParseTop, {}, { state: { isGhost: true } });
+        const topology = format.apply(StateTransforms.Model.TopologyFromTop);
+
+        await format.commit();
+
+        return { format: format.selector, topology: topology.selector };
+    }
+});
+type TopProvider = typeof TopProvider;
+
+export type TopologyProvider = PsfProvider;
+
+export const BuiltInTopologyFormats = [
+    ['psf', PsfProvider] as const,
+    ['prmtop', PrmtopProvider] as const,
+    ['top', TopProvider] as const,
+] as const;
+
+export type BuiltInTopologyFormat = (typeof BuiltInTopologyFormats)[number][0]
--- a/src/mol-plugin-state/helpers/structure-component.ts
+++ b/src/mol-plugin-state/helpers/structure-component.ts
@@ -13,6 +13,7 @@ import { PluginStateObject as SO } from '../objects';
 import { StructureSelectionQueries } from './structure-selection-query';
 import { StateTransformer, StateObject } from '../../mol-state';
 import { Script } from '../../mol-script/script';
+import { assertUnreachable } from '../../mol-util/type-helpers';

 export const StaticStructureComponentTypes = [
    'all',
@@ -72,7 +73,7 @@ export function createStructureComponent(a: Structure, params: StructureComponen

                case 'coarse': query = StructureSelectionQueries.coarse.query; label = 'Coarse'; break;

-                default: throw new Error(`${params.type} is a not valid complex element.`);
+                default: assertUnreachable(params.type);
            }
            const result = query(new QueryContext(a));
            component = Sel.unionStructure(result);
--- a/src/mol-plugin-state/manager/snapshots.ts
+++ b/src/mol-plugin-state/manager/snapshots.ts
@@ -238,12 +238,12 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
                }
            } else {
                const data = await this.plugin.runTask(readFromFile(file, 'zip'));
-                const assets = Object.create(null);
+                const assetData = Object.create(null);

                objectForEach(data, (v, k) => {
                    if (k === 'state.json' || k === 'assets.json') return;
                    const name = k.substring(k.indexOf('/') + 1);
-                    assets[name] = new File([v], name);
+                    assetData[name] = v;
                });
                const stateFile = new File([data['state.json']], 'state.json');
                const stateData = await this.plugin.runTask(readFromFile(stateFile, 'string'));
@@ -253,7 +253,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
                    const json = JSON.parse(await this.plugin.runTask(readFromFile(file, 'string')));

                    for (const [id, asset] of json) {
-                        this.plugin.managers.asset.set(asset, assets[id]);
+                        this.plugin.managers.asset.set(asset, new File([assetData[id]], asset.name));
                    }
                }

--- a/src/mol-plugin-state/objects.ts
+++ b/src/mol-plugin-state/objects.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -24,6 +24,8 @@ import { CubeFile } from '../mol-io/reader/cube/parser';
 import { DxFile } from '../mol-io/reader/dx/parser';
 import { Color } from '../mol-util/color/color';
 import { Asset } from '../mol-util/assets';
+import { PrmtopFile } from '../mol-io/reader/prmtop/parser';
+import { TopFile } from '../mol-io/reader/top/parser';

 export type TypeClass = 'root' | 'data' | 'prop'

@@ -72,6 +74,8 @@ export namespace PluginStateObject {
        export class Cif extends Create<CifFile>({ name: 'CIF File', typeClass: 'Data' }) { }
        export class Cube extends Create<CubeFile>({ name: 'Cube File', typeClass: 'Data' }) { }
        export class Psf extends Create<PsfFile>({ name: 'PSF File', typeClass: 'Data' }) { }
+        export class Prmtop extends Create<PrmtopFile>({ name: 'PRMTOP File', typeClass: 'Data' }) { }
+        export class Top extends Create<TopFile>({ name: 'TOP File', typeClass: 'Data' }) { }
        export class Ply extends Create<PlyFile>({ name: 'PLY File', typeClass: 'Data' }) { }
        export class Ccp4 extends Create<Ccp4File>({ name: 'CCP4/MRC/MAP File', typeClass: 'Data' }) { }
        export class Dsn6 extends Create<Dsn6File>({ name: 'DSN6/BRIX File', typeClass: 'Data' }) { }
--- a/src/mol-plugin-state/transforms/data.ts
+++ b/src/mol-plugin-state/transforms/data.ts
@@ -20,6 +20,9 @@ import { Asset } from '../../mol-util/assets';
 import { parseCube } from '../../mol-io/reader/cube/parser';
 import { parseDx } from '../../mol-io/reader/dx/parser';
 import { ColorNames } from '../../mol-util/color/names';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { parsePrmtop } from '../../mol-io/reader/prmtop/parser';
+import { parseTop } from '../../mol-io/reader/top/parser';

 export { Download };
 export { DownloadBlob };
@@ -29,6 +32,8 @@ export { ParseBlob };
 export { ParseCif };
 export { ParseCube };
 export { ParsePsf };
+export { ParsePrmtop };
+export { ParseTop };
 export { ParsePly };
 export { ParseCcp4 };
 export { ParseDsn6 };
@@ -151,7 +156,7 @@ const RawData = PluginStateTransform.BuiltIn({
            } else if (p.data instanceof Uint8Array) {
                return new SO.Data.Binary(p.data, { label: p.label ? p.label : 'Binary' });
            } else {
-                throw new Error('Supplied binary data must be a plain array, ArrayBuffer, or Uint8Array.');
+                assertUnreachable(p.data);
            }
        });
    },
@@ -316,6 +321,38 @@ const ParsePsf = PluginStateTransform.BuiltIn({
    }
 });

+type ParsePrmtop = typeof ParsePrmtop
+const ParsePrmtop = PluginStateTransform.BuiltIn({
+    name: 'parse-prmtop',
+    display: { name: 'Parse PRMTOP', description: 'Parse PRMTOP from String data' },
+    from: [SO.Data.String],
+    to: SO.Format.Prmtop
+})({
+    apply({ a }) {
+        return Task.create('Parse PRMTOP', async ctx => {
+            const parsed = await parsePrmtop(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            return new SO.Format.Prmtop(parsed.result);
+        });
+    }
+});
+
+type ParseTop = typeof ParseTop
+const ParseTop = PluginStateTransform.BuiltIn({
+    name: 'parse-top',
+    display: { name: 'Parse TOP', description: 'Parse TOP from String data' },
+    from: [SO.Data.String],
+    to: SO.Format.Top
+})({
+    apply({ a }) {
+        return Task.create('Parse TOP', async ctx => {
+            const parsed = await parseTop(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            return new SO.Format.Top(parsed.result);
+        });
+    }
+});
+
 type ParsePly = typeof ParsePly
 const ParsePly = PluginStateTransform.BuiltIn({
    name: 'parse-ply',
--- a/src/mol-plugin-state/transforms/model.ts
+++ b/src/mol-plugin-state/transforms/model.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -41,10 +41,21 @@ import { parseXyz } from '../../mol-io/reader/xyz/parser';
 import { trajectoryFromXyz } from '../../mol-model-formats/structure/xyz';
 import { parseSdf } from '../../mol-io/reader/sdf/parser';
 import { trajectoryFromSdf } from '../../mol-model-formats/structure/sdf';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { parseTrr } from '../../mol-io/reader/trr/parser';
+import { coordinatesFromTrr } from '../../mol-model-formats/structure/trr';
+import { parseNctraj } from '../../mol-io/reader/nctraj/parser';
+import { coordinatesFromNctraj } from '../../mol-model-formats/structure/nctraj';
+import { topologyFromPrmtop } from '../../mol-model-formats/structure/prmtop';
+import { topologyFromTop } from '../../mol-model-formats/structure/top';

 export { CoordinatesFromDcd };
 export { CoordinatesFromXtc };
+export { CoordinatesFromTrr };
+export { CoordinatesFromNctraj };
 export { TopologyFromPsf };
+export { TopologyFromPrmtop };
+export { TopologyFromTop };
 export { TrajectoryFromModelAndCoordinates };
 export { TrajectoryFromBlob };
 export { TrajectoryFromMmCif };
@@ -87,7 +98,7 @@ const CoordinatesFromDcd = PluginStateTransform.BuiltIn({
    }
 });

-type CoordinatesFromXtc = typeof CoordinatesFromDcd
+type CoordinatesFromXtc = typeof CoordinatesFromXtc
 const CoordinatesFromXtc = PluginStateTransform.BuiltIn({
    name: 'coordinates-from-xtc',
    display: { name: 'Parse XTC', description: 'Parse XTC binary data.' },
@@ -104,10 +115,44 @@ const CoordinatesFromXtc = PluginStateTransform.BuiltIn({
    }
 });

+type CoordinatesFromTrr = typeof CoordinatesFromTrr
+const CoordinatesFromTrr = PluginStateTransform.BuiltIn({
+    name: 'coordinates-from-trr',
+    display: { name: 'Parse TRR', description: 'Parse TRR binary data.' },
+    from: [SO.Data.Binary],
+    to: SO.Molecule.Coordinates
+})({
+    apply({ a }) {
+        return Task.create('Parse TRR', async ctx => {
+            const parsed = await parseTrr(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            const coordinates = await coordinatesFromTrr(parsed.result).runInContext(ctx);
+            return new SO.Molecule.Coordinates(coordinates, { label: a.label, description: 'Coordinates' });
+        });
+    }
+});
+
+type CoordinatesFromNctraj = typeof CoordinatesFromNctraj
+const CoordinatesFromNctraj = PluginStateTransform.BuiltIn({
+    name: 'coordinates-from-nctraj',
+    display: { name: 'Parse NCTRAJ', description: 'Parse NCTRAJ binary data.' },
+    from: [SO.Data.Binary],
+    to: SO.Molecule.Coordinates
+})({
+    apply({ a }) {
+        return Task.create('Parse NCTRAJ', async ctx => {
+            const parsed = await parseNctraj(a.data).runInContext(ctx);
+            if (parsed.isError) throw new Error(parsed.message);
+            const coordinates = await coordinatesFromNctraj(parsed.result).runInContext(ctx);
+            return new SO.Molecule.Coordinates(coordinates, { label: a.label, description: 'Coordinates' });
+        });
+    }
+});
+
 type TopologyFromPsf = typeof TopologyFromPsf
 const TopologyFromPsf = PluginStateTransform.BuiltIn({
    name: 'topology-from-psf',
-    display: { name: 'PSF Topology', description: 'Parse PSF string data.' },
+    display: { name: 'PSF Topology', description: 'Create topology from PSF.' },
    from: [SO.Format.Psf],
    to: SO.Molecule.Topology
 })({
@@ -119,6 +164,36 @@ const TopologyFromPsf = PluginStateTransform.BuiltIn({
    }
 });

+type TopologyFromPrmtop = typeof TopologyFromPrmtop
+const TopologyFromPrmtop = PluginStateTransform.BuiltIn({
+    name: 'topology-from-prmtop',
+    display: { name: 'PRMTOP Topology', description: 'Create topology from PRMTOP.' },
+    from: [SO.Format.Prmtop],
+    to: SO.Molecule.Topology
+})({
+    apply({ a }) {
+        return Task.create('Create Topology', async ctx => {
+            const topology = await topologyFromPrmtop(a.data).runInContext(ctx);
+            return new SO.Molecule.Topology(topology, { label: topology.label || a.label, description: 'Topology' });
+        });
+    }
+});
+
+type TopologyFromTop = typeof TopologyFromTop
+const TopologyFromTop = PluginStateTransform.BuiltIn({
+    name: 'topology-from-top',
+    display: { name: 'TOP Topology', description: 'Create topology from TOP.' },
+    from: [SO.Format.Top],
+    to: SO.Molecule.Topology
+})({
+    apply({ a }) {
+        return Task.create('Create Topology', async ctx => {
+            const topology = await topologyFromTop(a.data).runInContext(ctx);
+            return new SO.Molecule.Topology(topology, { label: topology.label || a.label, description: 'Topology' });
+        });
+    }
+});
+
 async function getTrajectory(ctx: RuntimeContext, obj: StateObject, coordinates: Coordinates) {
    if (obj.type === SO.Molecule.Topology.type) {
        const topology = obj.data as Topology;
@@ -846,7 +921,7 @@ const StructureComplexElement = PluginStateTransform.BuiltIn({
            case 'atomic-het': query = Queries.internal.atomicHet(); label = 'HET Groups/Ligands'; break;
            case 'spheres': query = Queries.internal.spheres(); label = 'Coarse Spheres'; break;

-            default: throw new Error(`${params.type} is a not valid complex element.`);
+            default: assertUnreachable(params.type);
        }

        const result = query(new QueryContext(a.data));
--- a/src/mol-plugin-ui/left-panel.tsx
+++ b/src/mol-plugin-ui/left-panel.tsx
@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

 import * as React from 'react';
@@ -19,6 +20,20 @@ import { StateTree } from './state/tree';
 import { HelpContent } from './viewport/help';
 import { HomeOutlinedSvg, AccountTreeOutlinedSvg, TuneSvg, HelpOutlineSvg, SaveOutlinedSvg, DeleteOutlinedSvg } from './controls/icons';

+export class CustomImportControls extends PluginUIComponent<{ initiallyCollapsed?: boolean }> {
+    componentDidMount() {
+        this.subscribe(this.plugin.state.behaviors.events.changed, () => this.forceUpdate());
+    }
+
+    render() {
+        const controls: JSX.Element[] = [];
+        this.plugin.customImportControls.forEach((Controls, key) => {
+            controls.push(<Controls initiallyCollapsed={this.props.initiallyCollapsed} key={key} />);
+        });
+        return controls.length > 0 ? <>{controls}</> : null;
+    }
+}
+
 export class LeftPanelControls extends PluginUIComponent<{}, { tab: LeftPanelTabName }> {
    state = { tab: this.plugin.behaviors.layout.leftPanelTabName.value };

@@ -54,6 +69,7 @@ export class LeftPanelControls extends PluginUIComponent<{}, { tab: LeftPanelTab
        'root': <>
            <SectionHeader icon={HomeOutlinedSvg} title='Home' />
            <StateObjectActions state={this.plugin.state.data} nodeRef={StateTransform.RootRef} hideHeader={true} initiallyCollapsed={true} alwaysExpandFirst={true} />
+            <CustomImportControls />
            {this.plugin.spec.components?.remoteState !== 'none' && <RemoteStateSnapshots listOnly /> }
        </>,
        'data': <>
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -176,6 +176,7 @@ export class PluginContext {
    readonly customStructureProperties = new CustomProperty.Registry<Structure>();

    readonly customStructureControls = new Map<string, { new(): any /* constructible react components with <action.customControl /> */ }>();
+    readonly customImportControls = new Map<string, { new(): any /* constructible react components with <action.customControl /> */ }>();
    readonly genericRepresentationControls = new Map<string, (selection: StructureHierarchyManager['selection']) => [StructureHierarchyRef[], string]>();

    /**
--- a/src/mol-plugin/spec.ts
+++ b/src/mol-plugin/spec.ts
@@ -64,10 +64,10 @@ namespace PluginSpec {
 export const DefaultPluginSpec = (): PluginSpec => ({
    actions: [
        PluginSpec.Action(StateActions.Structure.DownloadStructure),
-        PluginSpec.Action(StateActions.Structure.AddTrajectory),
        PluginSpec.Action(StateActions.Volume.DownloadDensity),
        PluginSpec.Action(StateActions.DataFormat.DownloadFile),
        PluginSpec.Action(StateActions.DataFormat.OpenFiles),
+        PluginSpec.Action(StateActions.Structure.LoadTrajectory),
        PluginSpec.Action(StateActions.Structure.EnableModelCustomProps),
        PluginSpec.Action(StateActions.Structure.EnableStructureCustomProps),

--- a/src/mol-script/language/parser.ts
+++ b/src/mol-script/language/parser.ts
@@ -7,6 +7,7 @@
 import { MonadicParser as P } from '../../mol-util/monadic-parser';
 import { Expression } from './expression';
 import { MolScriptBuilder as B } from './builder';
+import { assertUnreachable } from '../../mol-util/type-helpers';

 export function parseMolScript(input: string) {
    return Language.parse(input);
@@ -17,6 +18,7 @@ namespace Language {

    namespace ASTNode {
        export type Expression = Str | Symb | List | Comment
+        export type ExpressionWithoutComment = Str | Symb | List

        export interface Str {
            kind: 'string',
@@ -60,7 +62,7 @@ namespace Language {

    function getAST(input: string) { return Expressions.tryParse(input); }

-    function visitExpr(expr: ASTNode.Expression): Expression {
+    function visitExpr(expr: ASTNode.ExpressionWithoutComment): Expression {
        switch (expr.kind) {
            case 'string': return expr.value;
            case 'symbol': {
@@ -82,15 +84,14 @@ namespace Language {
                    case '[': return B.core.type.list(withoutComments(expr.nodes).map(visitExpr));
                    case '{': return B.core.type.set(withoutComments(expr.nodes).map(visitExpr));
                    case '(': {
+                        if (expr.nodes[0].kind === 'comment') throw new Error('Invalid expression');
                        const head = visitExpr(expr.nodes[0]);
                        return Expression.Apply(head, getArgs(expr.nodes));
                    }
+                    default: assertUnreachable(expr.bracket);
                }
-                return 0 as any;
-            }
-            default: {
-                throw new Error('should not happen');
            }
+            default: assertUnreachable(expr);
        }
    }

@@ -116,7 +117,8 @@ namespace Language {
                ++i;
                while (i < _i && nodes[i].kind === 'comment') { i++; }
                if (i >= _i) throw new Error(`There must be a value foolowed a named arg ':${name}'.`);
-                args[name] = visitExpr(nodes[i]);
+                if (nodes[i].kind === 'comment') throw new Error('Invalid expression');
+                args[name] = visitExpr(nodes[i] as ASTNode.ExpressionWithoutComment);
                if (isNaN(+name)) allNumeric = false;
            } else {
                args[pos++] = visitExpr(n);
@@ -158,8 +160,8 @@ namespace Language {
                break;
            }
        }
-        if (!hasComment) return nodes;
-        return nodes.filter(n => n.kind !== 'comment');
+        if (!hasComment) return nodes as ASTNode.ExpressionWithoutComment[];
+        return nodes.filter(n => n.kind !== 'comment') as ASTNode.ExpressionWithoutComment[];
    }

    function isNumber(value: string) {
--- a/src/mol-task/util/scheduler.ts
+++ b/src/mol-task/util/scheduler.ts
@@ -12,7 +12,7 @@

 declare const WorkerGlobalScope: any;
 function createImmediateActions() {
-    const global: any = (function () {
+    const thisGlobal: any = (function () {
        const _window = typeof window !== 'undefined' && window;
        const _self = typeof self !== 'undefined' && typeof WorkerGlobalScope !== 'undefined' && self instanceof WorkerGlobalScope && self;
        const _global = typeof global !== 'undefined' && global;
@@ -79,14 +79,14 @@ function createImmediateActions() {
    }

    function canUsePostMessage() {
-        if (global && global.postMessage && !global.importScripts) {
+        if (thisGlobal && thisGlobal.postMessage && !thisGlobal.importScripts) {
            let postMessageIsAsynchronous = true;
-            const oldOnMessage = global.onmessage;
-            global.onmessage = function () {
+            const oldOnMessage = thisGlobal.onmessage;
+            thisGlobal.onmessage = function () {
                postMessageIsAsynchronous = false;
            };
-            global.postMessage('', '*');
-            global.onmessage = oldOnMessage;
+            thisGlobal.postMessage('', '*');
+            thisGlobal.onmessage = oldOnMessage;
            return postMessageIsAsynchronous;
        }
    }
@@ -98,7 +98,7 @@ function createImmediateActions() {

        const messagePrefix = 'setImmediate$' + Math.random() + '$';
        const onGlobalMessage = function (event: any) {
-            if (event.source === global &&
+            if (event.source === thisGlobal &&
                typeof event.data === 'string' &&
                event.data.indexOf(messagePrefix) === 0) {
                runIfPresent(+event.data.slice(messagePrefix.length));
--- a/src/mol-theme/color/hydrophobicity.ts
+++ b/src/mol-theme/color/hydrophobicity.ts
@@ -59,8 +59,8 @@ export function HydrophobicityColorTheme(ctx: ThemeDataContext, props: PD.Values
    const scale = ColorScale.create({
        listOrName: props.list.colors,
        domain: [max, min],
-        minLabel: 'Hydrophobic',
-        maxLabel: 'Hydrophilic'
+        minLabel: 'Hydrophilic',
+        maxLabel: 'Hydrophobic'
    });

    function color(location: Location): Color {
--- a/src/mol-util/data-source.ts
+++ b/src/mol-util/data-source.ts
@@ -130,13 +130,15 @@ function getCompression(name: string) {
            DataCompressionMethod.None;
 }

+const reFilterPath = /^(__MACOSX|.DS_Store)/;
+
 async function decompress(ctx: RuntimeContext, data: Uint8Array, compression: DataCompressionMethod): Promise<Uint8Array> {
    switch (compression) {
        case DataCompressionMethod.None: return data;
        case DataCompressionMethod.Gzip: return ungzip(ctx, data);
        case DataCompressionMethod.Zip:
            const parsed = await unzip(ctx, data.buffer);
-            const names = Object.keys(parsed);
+            const names = Object.keys(parsed).filter(n => !reFilterPath.test(n));
            if (names.length !== 1) throw new Error('can only decompress zip files with a single entry');
            return parsed[names[0]] as Uint8Array;
    }
--- a/src/mol-util/file-info.ts
+++ b/src/mol-util/file-info.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -11,17 +11,12 @@ export type FileInput = File | Blob | string
 // TODO store globally with decompression plugins?
 const compressedExtList = ['gz', 'zip'];

-// TODO store globally with parser plugins?
-const binaryExtList = ['bcif', 'ccp4', 'dcd'];
-
 export interface FileInfo {
    path: string
    name: string
    ext: string
    base: string
    dir: string
-    compressed: string | boolean
-    binary: boolean
    protocol: string
    query: string
    src: FileInput
@@ -29,7 +24,6 @@ export interface FileInfo {

 export function getFileInfo(file: FileInput): FileInfo {
    let path: string;
-    let compressed: string|false;
    let protocol = '';

    if (file instanceof File) {
@@ -58,16 +52,11 @@ export function getFileInfo(file: FileInput): FileInfo {
    const dir = path.substring(0, path.lastIndexOf('/') + 1);

    if (compressedExtList.includes(ext)) {
-        compressed = ext;
        const n = path.length - ext.length - 1;
        ext = (path.substr(0, n).split('.').pop() || '').toLowerCase();
        const m = base.length - ext.length - 1;
        base = base.substr(0, m);
-    } else {
-        compressed = false;
    }

-    const binary = binaryExtList.includes(ext);
-
-    return { path, name, ext, base, dir, compressed, binary, protocol, query, src: file };
+    return { path, name, ext, base, dir, protocol, query, src: file };
 }
--- a/src/mol-util/index.ts
+++ b/src/mol-util/index.ts
@@ -202,4 +202,10 @@ export function formatProgress(p: Progress) {
    if (tp.isIndeterminate) return tp.message;
    const x = (100 * tp.current / tp.max).toFixed(2);
    return `${tp.message} ${x}%`;
+}
+
+export function formatBytes(count: number) {
+    const units = ['B', 'KB', 'MB', 'GB', 'TB', 'PB', 'EB', 'ZB', 'YB'];
+    const i = Math.floor(Math.log(count) / Math.log(1024));
+    return `${(count / Math.pow(1024, i)).toFixed(2)} ${units[i]}`;
 }
--- a/src/mol-util/zip/deflate.ts
+++ b/src/mol-util/zip/deflate.ts
@@ -8,7 +8,7 @@
 */

 import { RuntimeContext } from '../../mol-task';
-import { NumberArray } from '../type-helpers';
+import { assertUnreachable, NumberArray } from '../type-helpers';
 import { _hufTree } from './huffman';
 import { U, revCodes, makeCodes } from './util';

@@ -250,7 +250,7 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
            pos = _codeTiny(lset, U.itree, out, pos);
            pos = _codeTiny(dset, U.itree, out, pos);
        } else {
-            throw new Error(`unknown BTYPE ${BTYPE}`);
+            assertUnreachable(BTYPE);
        }

        let off = o0;
--- a/src/mol-util/zip/zip.ts
+++ b/src/mol-util/zip/zip.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 *
@@ -15,6 +15,10 @@ import { _inflate } from './inflate';
 import { _deflateRaw } from './deflate';
 import { RuntimeContext, Task } from '../../mol-task';

+export function Unzip(buf: ArrayBuffer, onlyNames = false) {
+    return Task.create('Unzip', ctx => unzip(ctx, buf, onlyNames));
+}
+
 export async function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames = false) {
    const out: { [k: string]: Uint8Array | { size: number, csize: number } } = Object.create(null);
    const data = new Uint8Array(buf);
Author	SHA1	Message	Date
Alexander Rose	23ec35d1f9	3.4.0	2022-03-13 13:12:32 -07:00
Alexander Rose	ff089c2b9f	changelog	2022-03-13 12:50:44 -07:00
Alexander Rose	1ab088718a	package updates	2022-03-13 12:49:03 -07:00
Alexander Rose	0cb2e5857a	Merge pull request #393 from molstar/zenodo-import Zenodo import	2022-03-13 12:19:04 -07:00
Alexander Rose	7c5ae5d7ee	tweak guessElementSymbolString	2022-03-13 12:16:12 -07:00
Alexander Rose	6e2665d98d	Merge branch 'master' of https://github.com/molstar/molstar into zenodo-import	2022-03-12 18:03:45 -08:00
Alexander Rose	b3b4692237	add top format support	2022-03-12 17:46:29 -08:00
Alexander Rose	55ff1d4999	add nctraj format support	2022-03-12 14:17:58 -08:00
Alexander Rose	511c839237	add prmtop format support	2022-03-12 13:48:10 -08:00
Alexander Rose	384cd6e5d9	add trr format support	2022-03-12 13:02:50 -08:00
Alexander Rose	6fd9dcc72e	split structure formats into topology & coordinates	2022-03-12 11:51:03 -08:00
Alexander Rose	12ca06fe91	fix handling of empty symmetry cell data	2022-03-12 11:44:27 -08:00
Alexander Rose	652f6c651b	fix wrong element assignment	2022-03-12 10:58:33 -08:00
Alexander Rose	7dd808a772	add custom import controls	2022-03-12 10:52:43 -08:00
Alexander Rose	945e55f8a7	add formated file size	2022-03-07 22:06:22 -08:00
Alexander Rose	866a30abe5	cleanup getFileInfo	2022-03-07 22:05:11 -08:00
Alexander Rose	f0e33e1e4e	fix legend of hydrophobicity color theme	2022-03-07 21:44:57 -08:00
Alexander Rose	8723ca38b4	improve saccharide detection	2022-03-07 21:31:33 -08:00
Alexander Rose	efffca0026	zenode import fixes	2022-03-06 21:57:42 -08:00
Alexander Rose	6c5eb3035f	remove default record id	2022-03-06 17:55:52 -08:00
Alexander Rose	0bf385f2ca	add zip file support to zenodo extension	2022-03-06 17:37:39 -08:00
Alexander Rose	9d5f51f513	improve handling of compressed files - fix loading of some compressed files within sessions - ignore some hidden MACOSX files	2022-03-06 17:32:56 -08:00
Alexander Rose	a1448131d8	add Zenodo import extension	2022-03-06 11:12:21 -08:00
Alexander Rose	664cacc7ac	add LoadTrajectory action	2022-03-06 11:11:16 -08:00
Alexander Rose	1aec37dd05	fix	2022-03-06 11:09:51 -08:00
Alexander Rose	3ff2c0840e	Merge pull request #392 from molstar/assert-unreachable make use of assertUnreachable	2022-03-06 11:06:04 -08:00
Alexander Rose	5ca3c3ac52	Update src/mol-script/language/parser.ts	2022-03-06 11:04:58 -08:00
Alexander Rose	714ee50965	Update src/mol-script/language/parser.ts Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>	2022-03-06 11:03:33 -08:00
Alexander Rose	ae1df3c5aa	Update src/mol-script/language/parser.ts Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>	2022-03-06 11:03:28 -08:00
Alexander Rose	28afb39550	make use of assertUnreachable	2022-03-05 10:18:40 -08:00
Alexander Rose	3466a8a024	Merge pull request #389 from molstar/cif-check-present fix handling of mmcif with empty label_asym_id	2022-03-05 09:20:19 -08:00
Alexander Rose	90db3321f5	changelog Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>	2022-03-05 09:20:04 -08:00
Alexander Rose	bf4e5ed7c2	normalize mmcif data	2022-03-04 22:47:14 -08:00
Alexander Rose	d3b2c20c26	normalize atom_site early	2022-03-03 18:31:54 -08:00
Alexander Rose	c3afabb4b1	spelling	2022-03-02 19:50:30 -08:00
Alexander Rose	18cc9790d1	fix handling of mmcif with empty label_asym_id	2022-03-02 19:17:31 -08:00