3.0.0

changelog
improve/fix InteractionsIntraUnitVisual marking
2026-06-04 21:34:23 +08:00 · 2022-01-23 18:12:48 -08:00 · 2022-01-23 18:08:01 -08:00 · 2022-01-23 17:55:51 -08:00 · 2022-01-23 15:13:24 -08:00 · 2022-01-23 13:54:57 -08:00
35 changed files with 909 additions and 448 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,21 @@ Note that since we don't clearly distinguish between a public and private interf

 ## [Unreleased]

+## [v3.0.0] - 2022-01-23
+
+- Assembly handling tweaks:
+    - Do not include suffix for "identity assembly operators"
+    - Do not include assembly-related categories to export if the structure was composed from an assembly
+    - Special case for ``structAsymMap`` if Mol* asym id operator mapping is present
+- Support for opening ZIP files with multiple entries
+- Add Model Export extension
+- Bugfix: Automatically treat empty string as "non-present" value in BinaryCIF writer.
+- Fix coarse model support in entity-id color theme
+- Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
+- Add custom colors to "element-symbol", "molecule-type", "residue-name", and "secondary-structure" themes
+- Support/bugfixes for ``atom_site.pdbx_sifts_xref`` categories
+- Improve/fix marking of ``InteractionsIntraUnitVisual`` (mark when all contact-feature members are given)
+
 ## [v3.0.0-dev.10] - 2022-01-17

 - Fix ``getOperatorsForIndex``
@@ -19,7 +34,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add "camera rock" state animation
 - Add support for custom colors to "molecule-type" theme
 - [Breaking] Add style parameter to "illustrative" color theme
-    - Defaults to "entity-id" style instad of "chain-id"
+    - Defaults to "entity-id" style instead of "chain-id"
 - Add "illustrative" representation preset

 ## [v3.0.0-dev.9] - 2022-01-09
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,19 +1,19 @@
 {
  "name": "molstar",
-  "version": "3.0.0-dev.10",
+  "version": "3.0.0",
  "lockfileVersion": 2,
  "requires": true,
  "packages": {
    "": {
      "name": "molstar",
-      "version": "3.0.0-dev.10",
+      "version": "3.0.0",
      "license": "MIT",
      "dependencies": {
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        "@types/benchmark": "^2.1.1",
        "@types/compression": "1.7.2",
        "@types/express": "^4.17.13",
-        "@types/node": "^16.11.19",
+        "@types/node": "^16.11.21",
        "@types/node-fetch": "^2.5.12",
        "@types/react": "^17.0.38",
        "@types/react-dom": "^17.0.11",
@@ -26,9 +26,9 @@
        "h264-mp4-encoder": "^1.0.12",
        "immer": "^9.0.12",
        "immutable": "^4.0.0",
-        "node-fetch": "^2.6.2",
+        "node-fetch": "^2.6.7",
        "rxjs": "^7.5.2",
-        "swagger-ui-dist": "^4.1.3",
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@@ -45,7 +45,7 @@
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@@ -1608,9 +1608,9 @@
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+      "version": "5.10.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-5.10.0.tgz",
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-        "@typescript-eslint/types": "5.9.1",
-        "@typescript-eslint/visitor-keys": "5.9.1",
+        "@typescript-eslint/types": "5.10.0",
+        "@typescript-eslint/visitor-keys": "5.10.0",
        "debug": "^4.3.2",
        "globby": "^11.0.4",
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@@ -16354,13 +16425,27 @@
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+    "@typescript-eslint/utils": {
+      "version": "5.10.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-5.10.0.tgz",
+      "integrity": "sha512-IGYwlt1CVcFoE2ueW4/ioEwybR60RAdGeiJX/iDAw0t5w0wK3S7QncDwpmsM70nKgGTuVchEWB8lwZwHqPAWRg==",
      "dev": true,
      "requires": {
-        "@typescript-eslint/types": "5.9.1",
+        "@types/json-schema": "^7.0.9",
+        "@typescript-eslint/scope-manager": "5.10.0",
+        "@typescript-eslint/types": "5.10.0",
+        "@typescript-eslint/typescript-estree": "5.10.0",
+        "eslint-scope": "^5.1.1",
+        "eslint-utils": "^3.0.0"
+      }
+    },
+    "@typescript-eslint/visitor-keys": {
+      "version": "5.10.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-5.10.0.tgz",
+      "integrity": "sha512-GMxj0K1uyrFLPKASLmZzCuSddmjZVbVj3Ouy5QVuIGKZopxvOr24JsS7gruz6C3GExE01mublZ3mIBOaon9zuQ==",
+      "dev": true,
+      "requires": {
+        "@typescript-eslint/types": "5.10.0",
        "eslint-visitor-keys": "^3.0.0"
      }
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@@ -17900,20 +17985,12 @@
      "dev": true
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-      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.4.tgz",
-      "integrity": "sha512-1eAtFWdIubi6T4XPy6ei9iUFoKpUkIF971QLN8lIvvvwueI65+Nw5haMNKUwfJxabqlIIDODJKGrQ66gxC0PbQ==",
+      "version": "3.1.5",
+      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.5.tgz",
+      "integrity": "sha512-lvb1SBsI0Z7GDwmuid+mU3kWVBwTVUbe7S0H52yaaAdQOXq2YktTCZdlAcNKFzE6QtRz0snpw9bNiPeOIkkQvw==",
      "dev": true,
      "requires": {
-        "node-fetch": "2.6.1"
-      },
-      "dependencies": {
-        "node-fetch": {
-          "version": "2.6.1",
-          "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.1.tgz",
-          "integrity": "sha512-V4aYg89jEoVRxRb2fJdAg8FHvI7cEyYdVAh94HH0UIK8oJxUfkjlDQN9RbMx+bEjP7+ggMiFRprSti032Oipxw==",
-          "dev": true
-        }
+        "node-fetch": "2.6.7"
      }
    },
    "cross-spawn": {
@@ -19119,6 +19196,30 @@
        "mime-types": "^2.1.12"
      }
    },
+    "form-data-encoder": {
+      "version": "1.7.1",
+      "resolved": "https://registry.npmjs.org/form-data-encoder/-/form-data-encoder-1.7.1.tgz",
+      "integrity": "sha512-EFRDrsMm/kyqbTQocNvRXMLjc7Es2Vk+IQFx/YW7hkUH1eBl4J1fqiP34l74Yt0pFLCNpc06fkbVk00008mzjg==",
+      "dev": true
+    },
+    "formdata-node": {
+      "version": "4.3.2",
+      "resolved": "https://registry.npmjs.org/formdata-node/-/formdata-node-4.3.2.tgz",
+      "integrity": "sha512-k7lYJyzDOSL6h917favP8j1L0/wNyylzU+x+1w4p5haGVHNlP58dbpdJhiCUsDbWsa9HwEtLp89obQgXl2e0qg==",
+      "dev": true,
+      "requires": {
+        "node-domexception": "1.0.0",
+        "web-streams-polyfill": "4.0.0-beta.1"
+      },
+      "dependencies": {
+        "web-streams-polyfill": {
+          "version": "4.0.0-beta.1",
+          "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-4.0.0-beta.1.tgz",
+          "integrity": "sha512-3ux37gEX670UUphBF9AMCq8XM6iQ8Ac6A+DSRRjDoRBm1ufCkaCDdNVbaqq60PsEkdNlLKrGtv/YBP4EJXqNtQ==",
+          "dev": true
+        }
+      }
+    },
    "forwarded": {
      "version": "0.2.0",
      "resolved": "https://registry.npmjs.org/forwarded/-/forwarded-0.2.0.tgz",
@@ -21671,9 +21772,9 @@
      "dev": true
    },
    "mini-css-extract-plugin": {
-      "version": "2.4.7",
-      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.4.7.tgz",
-      "integrity": "sha512-euWmddf0sk9Nv1O0gfeeUAvAkoSlWncNLF77C0TP2+WoPvy8mAHKOzMajcCz2dzvyt3CNgxb1obIEVFIRxaipg==",
+      "version": "2.5.2",
+      "resolved": "https://registry.npmjs.org/mini-css-extract-plugin/-/mini-css-extract-plugin-2.5.2.tgz",
+      "integrity": "sha512-Lwgq9qLNyBK6yNLgzssXnq4r2+mB9Mz3cJWlM8kseysHIvTicFhDNimFgY94jjqlwhNzLPsq8wv4X+vOHtMdYA==",
      "dev": true,
      "requires": {
        "schema-utils": "^4.0.0"
@@ -21851,9 +21952,9 @@
      "optional": true
    },
    "nanoid": {
-      "version": "3.1.30",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.30.tgz",
-      "integrity": "sha512-zJpuPDwOv8D2zq2WRoMe1HsfZthVewpel9CAvTfc/2mBD1uUT/agc5f7GHGWXlYkFvi1mVxe4IjvP2HNrop7nQ==",
+      "version": "3.2.0",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.2.0.tgz",
+      "integrity": "sha512-fmsZYa9lpn69Ad5eDn7FMcnnSR+8R34W9qJEijxYhTbfOWzr22n1QxCMzXLK+ODyW2973V3Fux959iQoUxzUIA==",
      "dev": true
    },
    "napi-build-utils": {
@@ -21898,10 +21999,16 @@
        "semver": "^7.3.5"
      }
    },
+    "node-domexception": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/node-domexception/-/node-domexception-1.0.0.tgz",
+      "integrity": "sha512-/jKZoMpw0F8GRwl4/eLROPA3cfcXtLApP0QzLmUT/HuPCZWyB7IY9ZrMeKw2O/nFIqPQB3PVM9aYm0F312AXDQ==",
+      "dev": true
+    },
    "node-fetch": {
-      "version": "2.6.6",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.6.tgz",
-      "integrity": "sha512-Z8/6vRlTUChSdIgMa51jxQ4lrw/Jy5SOW10ObaA47/RElsAN2c5Pn8bTgFGWn/ibwzXTE8qwr1Yzx28vsecXEA==",
+      "version": "2.6.7",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
+      "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==",
      "requires": {
        "whatwg-url": "^5.0.0"
      },
@@ -23079,9 +23186,9 @@
      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
    },
    "sass": {
-      "version": "1.48.0",
-      "resolved": "https://registry.npmjs.org/sass/-/sass-1.48.0.tgz",
-      "integrity": "sha512-hQi5g4DcfjcipotoHZ80l7GNJHGqQS5LwMBjVYB/TaT0vcSSpbgM8Ad7cgfsB2M0MinbkEQQPO9+sjjSiwxqmw==",
+      "version": "1.49.0",
+      "resolved": "https://registry.npmjs.org/sass/-/sass-1.49.0.tgz",
+      "integrity": "sha512-TVwVdNDj6p6b4QymJtNtRS2YtLJ/CqZriGg0eIAbAKMlN8Xy6kbv33FsEZSF7FufFFM705SQviHjjThfaQ4VNw==",
      "dev": true,
      "requires": {
        "chokidar": ">=3.0.0 <4.0.0",
@@ -23646,9 +23753,9 @@
      }
    },
    "swagger-ui-dist": {
-      "version": "4.1.3",
-      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.1.3.tgz",
-      "integrity": "sha512-WvfPSfAAMlE/sKS6YkW47nX/hA7StmhYnAHc6wWCXNL0oclwLj6UXv0hQCkLnDgvebi0MEV40SJJpVjKUgH1IQ=="
+      "version": "4.2.1",
+      "resolved": "https://registry.npmjs.org/swagger-ui-dist/-/swagger-ui-dist-4.2.1.tgz",
+      "integrity": "sha512-ZzUeNKIIMXmKI53iLscAVCpQ7jblYxI2XX5EBaoBr6UBEfxT3L0vlnE+fzPBbHc9g0sgdOMLZGhC5OW++9pqlw=="
    },
    "swap-case": {
      "version": "2.0.2",
@@ -24057,9 +24164,9 @@
      }
    },
    "typescript": {
-      "version": "4.5.4",
-      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.4.tgz",
-      "integrity": "sha512-VgYs2A2QIRuGphtzFV7aQJduJ2gyfTljngLzjpfW9FoYZF6xuw1W0vW9ghCKLfcWrCFxK81CSGRAvS1pn4fIUg==",
+      "version": "4.5.5",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-4.5.5.tgz",
+      "integrity": "sha512-TCTIul70LyWe6IJWT8QSYeA54WQe8EjQFU4wY52Fasj5UKx88LNYKCgBEHcOMOrFF1rKGbD8v/xcNWVUq9SymA==",
      "dev": true
    },
    "ua-parser-js": {
@@ -24308,6 +24415,12 @@
        "defaults": "^1.0.3"
      }
    },
+    "web-streams-polyfill": {
+      "version": "3.2.0",
+      "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.2.0.tgz",
+      "integrity": "sha512-EqPmREeOzttaLRm5HS7io98goBgZ7IVz79aDvqjD0kYXLtFZTc0T/U6wHTPKyIjb+MdN7DFIIX6hgdBEpWmfPA==",
+      "dev": true
+    },
    "webidl-conversions": {
      "version": "6.1.0",
      "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-6.1.0.tgz",
@@ -24315,9 +24428,9 @@
      "dev": true
    },
    "webpack": {
-      "version": "5.66.0",
-      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.66.0.tgz",
-      "integrity": "sha512-NJNtGT7IKpGzdW7Iwpn/09OXz9inIkeIQ/ibY6B+MdV1x6+uReqz/5z1L89ezWnpPDWpXF0TY5PCYKQdWVn8Vg==",
+      "version": "5.67.0",
+      "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.67.0.tgz",
+      "integrity": "sha512-LjFbfMh89xBDpUMgA1W9Ur6Rn/gnr2Cq1jjHFPo4v6a79/ypznSYbAyPgGhwsxBtMIaEmDD1oJoA7BEYw/Fbrw==",
      "dev": true,
      "requires": {
        "@types/eslint-scope": "^3.7.0",
@@ -24343,7 +24456,7 @@
        "tapable": "^2.1.1",
        "terser-webpack-plugin": "^5.1.3",
        "watchpack": "^2.3.1",
-        "webpack-sources": "^3.2.2"
+        "webpack-sources": "^3.2.3"
      },
      "dependencies": {
        "acorn-import-assertions": {
@@ -24397,9 +24510,9 @@
      }
    },
    "webpack-sources": {
-      "version": "3.2.2",
-      "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.2.tgz",
-      "integrity": "sha512-cp5qdmHnu5T8wRg2G3vZZHoJPN14aqQ89SyQ11NpGH5zEMDCclt49rzo+MaRazk7/UeILhAI+/sEtcM+7Fr0nw==",
+      "version": "3.2.3",
+      "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.2.3.tgz",
+      "integrity": "sha512-/DyMEOrDgLKKIG0fmvtz+4dUX/3Ghozwgm6iPp8KRhvn+eQf9+Q7GWxVNMk3+uCPWfdXYC4ExGBckIXdFEfH1w==",
      "dev": true
    },
    "whatwg-encoding": {
@@ -24512,9 +24625,9 @@
      }
    },
    "ws": {
-      "version": "8.2.3",
-      "resolved": "https://registry.npmjs.org/ws/-/ws-8.2.3.tgz",
-      "integrity": "sha512-wBuoj1BDpC6ZQ1B7DWQBYVLphPWkm8i9Y0/3YdHjHKHiohOJ1ws+3OccDWtH+PoC9DZD5WOTrJvNbWvjS6JWaA==",
+      "version": "8.4.2",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.4.2.tgz",
+      "integrity": "sha512-Kbk4Nxyq7/ZWqr/tarI9yIt/+iNNFOjBXEWgTb4ydaNHBNGgvf2QHbS9fdfsndfjFlFwEd4Al+mw83YkaD10ZA==",
      "dev": true,
      "requires": {}
    },
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
  "name": "molstar",
-  "version": "3.0.0-dev.10",
+  "version": "3.0.0",
  "description": "A comprehensive macromolecular library.",
  "homepage": "https://github.com/molstar/molstar#readme",
  "repository": {
@@ -92,7 +92,7 @@
  "license": "MIT",
  "devDependencies": {
    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.3.1",
+    "@graphql-codegen/cli": "^2.4.0",
    "@graphql-codegen/time": "^3.1.1",
    "@graphql-codegen/typescript": "^2.4.2",
    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
@@ -101,8 +101,8 @@
    "@types/cors": "^2.8.12",
    "@types/gl": "^4.1.0",
    "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.9.1",
-    "@typescript-eslint/parser": "^5.9.1",
+    "@typescript-eslint/eslint-plugin": "^5.10.0",
+    "@typescript-eslint/parser": "^5.10.0",
    "benchmark": "^2.1.4",
    "concurrently": "^7.0.0",
    "cpx2": "^4.1.2",
@@ -115,17 +115,17 @@
    "graphql": "^16.2.0",
    "http-server": "^14.1.0",
    "jest": "^27.4.7",
-    "mini-css-extract-plugin": "~2.4.7",
+    "mini-css-extract-plugin": "^2.5.2",
    "path-browserify": "^1.0.1",
    "raw-loader": "^4.0.2",
-    "sass": "^1.48.0",
+    "sass": "^1.49.0",
    "sass-loader": "^12.4.0",
    "simple-git": "^2.48.0",
    "stream-browserify": "^3.0.0",
    "style-loader": "^3.3.1",
    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.4",
-    "webpack": "^5.66.0",
+    "typescript": "^4.5.5",
+    "webpack": "^5.67.0",
    "webpack-cli": "^4.9.1"
  },
  "dependencies": {
@@ -133,7 +133,7 @@
    "@types/benchmark": "^2.1.1",
    "@types/compression": "1.7.2",
    "@types/express": "^4.17.13",
-    "@types/node": "^16.11.19",
+    "@types/node": "^16.11.21",
    "@types/node-fetch": "^2.5.12",
    "@types/react": "^17.0.38",
    "@types/react-dom": "^17.0.11",
@@ -146,9 +146,9 @@
    "h264-mp4-encoder": "^1.0.12",
    "immer": "^9.0.12",
    "immutable": "^4.0.0",
-    "node-fetch": "^2.6.2",
+    "node-fetch": "^2.6.7",
    "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.1.3",
+    "swagger-ui-dist": "^4.2.1",
    "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
@@ -13,6 +13,7 @@ import { GeometryExport } from '../../extensions/geo-export';
 import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
@@ -57,6 +58,7 @@ const Extensions = {
    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
    'g3d': PluginSpec.Behavior(G3DFormat),
+    'model-export': PluginSpec.Behavior(ModelExport),
    'mp4-export': PluginSpec.Behavior(Mp4Export),
    'geo-export': PluginSpec.Behavior(GeometryExport),
    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
@@ -99,7 +101,14 @@ export class Viewer {
    }

    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
+        const definedOptions = {} as any;
+        // filter for defined properies only so the default values
+        // are property applied
+        for (const p of Object.keys(options) as (keyof ViewerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
        const defaultSpec = DefaultPluginUISpec();

        const spec: PluginUISpec = {
--- a/src/apps/viewer/index.html
+++ b/src/apps/viewer/index.html
@@ -57,7 +57,7 @@
            var pickScale = getParam('pick-scale', '[^&]+').trim();
            var pickPadding = getParam('pick-padding', '[^&]+').trim();
            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;

            molstar.Viewer.create('app', {
                layoutShowControls: !hideControls,
@@ -71,7 +71,7 @@
                pixelScale: parseFloat(pixelScale) || 1,
                pickScale: parseFloat(pickScale) || 0.25,
                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: !disableWboit,
+                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
                preferWebgl1: preferWebgl1,
            }).then(viewer => {
                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -9,4 +9,4 @@ import './embedded.html';
 import './favicon.ico';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
-export * from './app';
+export * from './app';
--- a/src/extensions/model-export/export.ts
+++ b/src/extensions/model-export/export.ts
@@ -0,0 +1,87 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { utf8ByteCount, utf8Write } from '../../mol-io/common/utf8';
+import { to_mmCIF, Unit } from '../../mol-model/structure';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { getFormattedTime } from '../../mol-util/date';
+import { download } from '../../mol-util/download';
+import { zip } from '../../mol-util/zip/zip';
+
+export async function exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
+    try {
+        await plugin.runTask(_exportHierarchy(plugin, options), { useOverlay: true });
+    } catch (e) {
+        console.error(e);
+        plugin.log.error(`Model export failed. See console for details.`);
+    }
+}
+
+function _exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
+    return Task.create('Export', async ctx => {
+        await ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false });
+
+        const format = options?.format ?? 'cif';
+        const { structures } = plugin.managers.structure.hierarchy.current;
+
+        const files: [name: string, data: string | Uint8Array][] = [];
+        const entryMap = new Map<string, number>();
+
+        for (const _s of structures) {
+            const s = _s.transform?.cell.obj?.data ?? _s.cell.obj?.data;
+            if (!s) continue;
+            if (s.models.length > 1) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`);
+                continue;
+            }
+            if (s.units.some(u => !Unit.isAtomic(u))) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`);
+                continue;
+            }
+
+            const name = entryMap.has(s.model.entryId)
+                ? `${s.model.entryId}_${entryMap.get(s.model.entryId)! + 1}.${format}`
+                : `${s.model.entryId}.${format}`;
+            entryMap.set(s.model.entryId, (entryMap.get(s.model.entryId) ?? 0) + 1);
+
+            await ctx.update({ message: `Exporting ${s.model.entryId}...`, isIndeterminate: true, canAbort: false });
+            if (s.elementCount > 100000) {
+                // Give UI chance to update, only needed for larger structures.
+                await new Promise(res => setTimeout(res, 50));
+            }
+
+            try {
+                files.push([name, to_mmCIF(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+            } catch (e) {
+                if (format === 'cif' && s.elementCount > 2000000) {
+                    plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
+                }
+                throw e;
+            }
+        }
+
+        if (files.length === 1) {
+            download(new Blob([files[0][1]]), files[0][0]);
+        } else if (files.length > 1) {
+            const zipData: Record<string, Uint8Array> = {};
+            for (const [fn, data] of files) {
+                if (data instanceof Uint8Array) {
+                    zipData[fn] = data;
+                } else {
+                    const bytes = new Uint8Array(utf8ByteCount(data));
+                    utf8Write(bytes, 0, data);
+                    zipData[fn] = bytes;
+                }
+            }
+            await ctx.update({ message: `Compressing Data...`, isIndeterminate: true, canAbort: false });
+            const buffer = await zip(ctx, zipData);
+            download(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), `structures_${getFormattedTime()}.zip`);
+        }
+
+        plugin.log.info(`[Export] Done.`);
+    });
+}
--- a/src/extensions/model-export/index.ts
+++ b/src/extensions/model-export/index.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { ModelExportUI } from './ui';
+
+export const ModelExport = PluginBehavior.create<{}>({
+    name: 'extension-model-export',
+    category: 'misc',
+    display: {
+        name: 'Model Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{}> {
+        register(): void {
+            this.ctx.customStructureControls.set('model-export', ModelExportUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customStructureControls.delete('model-export');
+        }
+    },
+    params: () => ({})
+});
--- a/src/extensions/model-export/ui.tsx
+++ b/src/extensions/model-export/ui.tsx
@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { useState } from 'react';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { GetAppSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { PluginContext } from '../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { exportHierarchy } from './export';
+
+export class ModelExportUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState {
+        return {
+            header: 'Export Models',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: GetAppSvg }
+        };
+    }
+    protected renderControls(): JSX.Element | null {
+        return <ExportControls plugin={this.plugin} />;
+    }
+}
+
+const Params = {
+    format: PD.Select<'cif' | 'bcif'>('cif', [['cif', 'mmCIF'], ['bcif', 'Binary mmCIF']])
+};
+const DefaultParams = PD.getDefaultValues(Params);
+
+function ExportControls({ plugin }: { plugin: PluginContext }) {
+    const [params, setParams] = useState(DefaultParams);
+    const [exporting, setExporting] = useState(false);
+    useBehavior(plugin.managers.structure.hierarchy.behaviors.selection); // triggers UI update
+    const isBusy = useBehavior(plugin.behaviors.state.isBusy);
+    const hierarchy = plugin.managers.structure.hierarchy.current;
+
+    let label: string = 'Nothing to Export';
+    if (hierarchy.structures.length === 1) {
+        label = 'Export';
+    } if (hierarchy.structures.length > 1) {
+        label = 'Export (as ZIP)';
+    }
+
+    const onExport = async () => {
+        setExporting(true);
+        try {
+            await exportHierarchy(plugin, { format: params.format });
+        } finally {
+            setExporting(false);
+        }
+    };
+
+    return <>
+        <ParameterControls params={Params} values={params} onChangeValues={setParams} isDisabled={isBusy || exporting} />
+        <Button
+            onClick={onExport}
+            style={{ marginTop: 1 }}
+            disabled={isBusy || hierarchy.structures.length === 0 || exporting}
+            commit={hierarchy.structures.length ? 'on' : 'off'}
+        >
+            {label}
+        </Button>
+    </>;
+}
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -191,8 +191,14 @@ function getFieldData(field: Field<any, any>, arrayCtor: ArrayCtor<string | numb
                    array[offset] = '';
                allPresent = false;
            } else {
-                mask[offset] = Column.ValueKind.Present;
-                array[offset] = getter(key, d, offset);
+                const value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = Column.ValueKind.NotPresent;
+                    allPresent = false;
+                } else {
+                    mask[offset] = Column.ValueKind.Present;
+                }
+                array[offset] = value;
            }
            offset++;
        }
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -52,24 +52,30 @@ namespace SymmetryOperator {
    export const RotationTranslationEpsilon = 0.005;

    export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number }
-    export function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator {
+    export function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator {
        let { assembly, ncsId, hkl, spgrOp } = info || { };
        const _hkl = hkl ? Vec3.clone(hkl) : Vec3();
        spgrOp = defaults(spgrOp, -1);
        ncsId = ncsId || -1;
-        const suffix = getSuffix(info);
-        if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
+        const isIdentity = Mat4.isIdentity(matrix);
+        const suffix = getSuffix(info, isIdentity);
+        if (isIdentity) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
        if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) {
            console.warn(`Symmetry operator (${name}) should be a composition of rotation and translation.`);
        }
        return { name, assembly, matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId, suffix };
    }

-    function getSuffix(info?: CreateInfo) {
+    function isSymmetryOperator(x: any): x is SymmetryOperator {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+
+    function getSuffix(info?: CreateInfo | SymmetryOperator, isIdentity?: boolean) {
        if (!info) return '';

        if (info.assembly) {
-            return `_${info.assembly.operId}`;
+            if (isSymmetryOperator(info)) return info.suffix;
+            return isIdentity ? '' : `_${info.assembly.operId}`;
        }

        if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {
--- a/src/mol-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -7,21 +7,21 @@

 import { Column, Table } from '../../../mol-data/db';
 import { Interval, Segmentation } from '../../../mol-data/int';
-import { UUID } from '../../../mol-util/uuid';
-import { ElementIndex, ChainIndex } from '../../../mol-model/structure';
+import { toDatabase } from '../../../mol-io/reader/cif/schema';
+import { SymmetryOperator } from '../../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { ChainIndex, ElementIndex } from '../../../mol-model/structure';
+import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
 import { Model } from '../../../mol-model/structure/model/model';
 import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../../mol-model/structure/model/properties/atomic';
-import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
-import { ElementSymbol } from '../../../mol-model/structure/model/types';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
 import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
-import { AtomSite } from './schema';
+import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
+import { ElementSymbol } from '../../../mol-model/structure/model/types';
+import { UUID } from '../../../mol-util/uuid';
 import { ModelFormat } from '../../format';
-import { SymmetryOperator } from '../../../mol-math/geometry';
 import { MmcifFormat } from '../mmcif';
-import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
-import { toDatabase } from '../../../mol-io/reader/cif/schema';
-import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { AtomSite } from './schema';

 function findHierarchyOffsets(atom_site: AtomSite) {
    if (atom_site._rowCount === 0) return { residues: [], chains: [] };
--- a/src/mol-model-formats/structure/basic/coarse.ts
+++ b/src/mol-model-formats/structure/basic/coarse.ts
@@ -30,7 +30,7 @@ export interface CoarseData {

 export const EmptyCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any };

-export function getCoarse(data: CoarseData, properties: Model['properties']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
+export function getCoarse(data: CoarseData, chemicalComponentMap: Model['properties']['chemicalComponentMap']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
    const { ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;

    if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0) return EmptyCoarse;
@@ -38,12 +38,12 @@ export function getCoarse(data: CoarseData, properties: Model['properties']): {
    const sphereData = getData(ihm_sphere_obj_site);
    const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
    const sphereKeys = getCoarseKeys(sphereData, data.entities);
-    const sphereRanges = getCoarseRanges(sphereData, properties.chemicalComponentMap);
+    const sphereRanges = getCoarseRanges(sphereData, chemicalComponentMap);

    const gaussianData = getData(ihm_gaussian_obj_site);
    const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
    const gaussianKeys = getCoarseKeys(gaussianData, data.entities);
-    const gaussianRanges = getCoarseRanges(gaussianData, properties.chemicalComponentMap);
+    const gaussianRanges = getCoarseRanges(gaussianData, chemicalComponentMap);

    return {
        hierarchy: {
--- a/src/mol-model-formats/structure/basic/entities.ts
+++ b/src/mol-model-formats/structure/basic/entities.ts
@@ -11,7 +11,7 @@ import { getEntityType, getEntitySubtype } from '../../../mol-model/structure/mo
 import { ElementIndex, EntityIndex, Model } from '../../../mol-model/structure/model';
 import { BasicData, BasicSchema, Entity } from './schema';

-export function getEntities(data: BasicData, properties: Model['properties']): Entities {
+export function getEntityData(data: BasicData): Entities {
    let entityData: Entity;

    if (!data.entity.id.isDefined) {
@@ -121,28 +121,32 @@ export function getEntities(data: BasicData, properties: Model['properties']): E

    const subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype });

-    //
-
-    const prdIds: string[] = new Array(entityData._rowCount);
-    prdIds.fill('');
-
-    if (data.pdbx_molecule && data.pdbx_molecule.prd_id.isDefined) {
-        const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
-        for (let i = 0; i < _rowCount; ++i) {
-            const asymId = asym_id.value(i);
-            const entityId = properties.structAsymMap.get(asymId)?.entity_id;
-            if (entityId !== undefined) {
-                prdIds[getEntityIndex(entityId)] = prd_id.value(i);
-            }
-        }
-    }
-
-    const prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
-
    return {
        data: entityData,
        subtype: subtypeColumn,
-        prd_id: prdIdColumn,
        getEntityIndex
    };
+}
+
+export function getEntitiesWithPRD(data: BasicData, entities: Entities, structAsymMap: Model['properties']['structAsymMap']): Entities {
+    if (!data.pdbx_molecule || !data.pdbx_molecule.prd_id.isDefined) {
+        return entities;
+    }
+
+    const prdIds: string[] = new Array(entities.data._rowCount);
+    prdIds.fill('');
+    const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
+    for (let i = 0; i < _rowCount; ++i) {
+        const asymId = asym_id.value(i);
+        const entityId = structAsymMap.get(asymId)?.entity_id;
+        if (entityId !== undefined) {
+            prdIds[entities.getEntityIndex(entityId)] = prd_id.value(i);
+        }
+    }
+    const prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
+
+    return {
+        ...entities,
+        prd_id: prdIdColumn
+    };
 }
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -18,13 +18,13 @@ import { sortAtomSite } from './sort';
 import { ModelFormat } from '../../format';
 import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
 import { AtomSite, BasicData } from './schema';
-import { getProperties } from './properties';
-import { getEntities } from './entities';
+import { getChemicalComponentMap, getMissingResidues, getSaccharideComponentMap, getStructAsymMap } from './properties';
+import { getEntitiesWithPRD, getEntityData } from './entities';
 import { getModelGroupName } from './util';
 import { ArrayTrajectory } from '../../../mol-model/structure/trajectory';

 export async function createModels(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
-    const properties = getProperties(data);
+    const properties = getCommonProperties(data, format);
    const models = data.ihm_model_list._rowCount > 0
        ? await readIntegrative(ctx, data, properties, format)
        : await readStandard(ctx, data, properties, format);
@@ -36,9 +36,18 @@ export async function createModels(data: BasicData, format: ModelFormat, ctx: Ru
    return new ArrayTrajectory(models);
 }

-/** Standard atomic model */
-function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: Model['properties'], format: ModelFormat, previous?: Model): Model {
+type CommonProperties = Omit<Model['properties'], 'structAsymMap'>

+function getCommonProperties(data: BasicData, format: ModelFormat): CommonProperties {
+    return {
+        missingResidues: getMissingResidues(data),
+        chemicalComponentMap: getChemicalComponentMap(data),
+        saccharideComponentMap: getSaccharideComponentMap(data)
+    };
+}
+
+/** Standard atomic model */
+function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: CommonProperties, format: ModelFormat, previous?: Model): Model {
    const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
    const modelNum = atom_site.pdbx_PDB_model_num.value(0);
    if (previous && atomic.sameAsPrevious) {
@@ -54,6 +63,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
    const coarse = EmptyCoarse;
    const sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy);
    const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence);
+    const structAsymMap = getStructAsymMap(atomic.hierarchy);

    const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
        ? data.entry.id.value(0) : format.name;
@@ -70,7 +80,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
        sourceData: format,
        modelNum,
        parent: undefined,
-        entities,
+        entities: getEntitiesWithPRD(data, entities, structAsymMap),
        sequence,
        atomicHierarchy: atomic.hierarchy,
        atomicConformation: atomic.conformation,
@@ -78,7 +88,10 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
        atomicChainOperatorMappinng: atomic.chainOperatorMapping,
        coarseHierarchy: coarse.hierarchy,
        coarseConformation: coarse.conformation,
-        properties,
+        properties: {
+            ...properties,
+            structAsymMap
+        },
        customProperties: new CustomProperties(),
        _staticPropertyData: Object.create(null),
        _dynamicPropertyData: Object.create(null)
@@ -86,9 +99,9 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
 }

 /** Integrative model with atomic/coarse parts */
-function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Model['properties'], format: ModelFormat): Model {
+function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: CommonProperties, format: ModelFormat): Model {
    const atomic = getAtomicHierarchyAndConformation(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap, format);
-    const coarse = getCoarse(ihm, properties);
+    const coarse = getCoarse(ihm, properties.chemicalComponentMap);
    const sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
    const atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);

@@ -101,6 +114,8 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
    if (ihm.model_name) label.push(ihm.model_name);
    if (ihm.model_group_name) label.push(ihm.model_group_name);

+    const structAsymMap = getStructAsymMap(atomic.hierarchy, data);
+
    return {
        id: UUID.create22(),
        entryId: entry,
@@ -109,7 +124,7 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
        sourceData: format,
        modelNum: ihm.model_id,
        parent: undefined,
-        entities: ihm.entities,
+        entities: getEntitiesWithPRD(data, ihm.entities, structAsymMap),
        sequence,
        atomicHierarchy: atomic.hierarchy,
        atomicConformation: atomic.conformation,
@@ -117,7 +132,10 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
        atomicChainOperatorMappinng: atomic.chainOperatorMapping,
        coarseHierarchy: coarse.hierarchy,
        coarseConformation: coarse.conformation,
-        properties,
+        properties: {
+            ...properties,
+            structAsymMap
+        },
        customProperties: new CustomProperties(),
        _staticPropertyData: Object.create(null),
        _dynamicPropertyData: Object.create(null)
@@ -132,12 +150,12 @@ function findModelEnd(num: Column<number>, startIndex: number) {
    return endIndex;
 }

-async function readStandard(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
+async function readStandard(ctx: RuntimeContext, data: BasicData, properties: CommonProperties, format: ModelFormat) {
    const models: Model[] = [];

    if (data.atom_site) {
        const atomCount = data.atom_site.id.rowCount;
-        const entities = getEntities(data, properties);
+        const entities = getEntityData(data);

        let modelStart = 0;
        while (modelStart < atomCount) {
@@ -170,8 +188,8 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {



-async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
-    const entities = getEntities(data, properties);
+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`
    const atom_sites_modelColumn = data.atom_site.ihm_model_id.isDefined
        ? data.atom_site.ihm_model_id : data.atom_site.pdbx_PDB_model_num;
@@ -206,7 +224,7 @@ async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties:
                model_id: id,
                model_name: model_name.value(i),
                model_group_name: getModelGroupName(id, data),
-                entities: entities,
+                entities,
                atom_site,
                atom_site_sourceIndex,
                ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)!.table : Table.window(data.ihm_sphere_obj_site, data.ihm_sphere_obj_site._schema, 0, 0),
--- a/src/mol-model-formats/structure/basic/properties.ts
+++ b/src/mol-model-formats/structure/basic/properties.ts
@@ -5,15 +5,16 @@
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

+import { Table } from '../../../mol-data/db';
 import { Model } from '../../../mol-model/structure/model/model';
+import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
 import { ChemicalComponent, MissingResidue, StructAsym } from '../../../mol-model/structure/model/properties/common';
-import { getMoleculeType, MoleculeType, getDefaultChemicalComponent } from '../../../mol-model/structure/model/types';
-import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
+import { getDefaultChemicalComponent, getMoleculeType, MoleculeType } from '../../../mol-model/structure/model/types';
+import { SaccharideCompIdMap, SaccharideComponent, SaccharideComponentMap, SaccharidesSnfgMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
 import { memoize1 } from '../../../mol-util/memoize';
 import { BasicData } from './schema';
-import { Table } from '../../../mol-data/db';

-function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
+export function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
    const map = new Map<string, MissingResidue>();
    const getKey = (model_num: number, asym_id: string, seq_id: number) => {
        return `${model_num}|${asym_id}|${seq_id}`;
@@ -36,7 +37,7 @@ function getMissingResidues(data: BasicData): Model['properties']['missingResidu
    };
 }

-function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
+export function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
    const map = new Map<string, ChemicalComponent>();

    if (data.chem_comp._rowCount > 0) {
@@ -53,7 +54,7 @@ function getChemicalComponentMap(data: BasicData): Model['properties']['chemical
    return map;
 }

-function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
+export function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
    const map = new Map<string, SaccharideComponent>();

    if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -108,22 +109,18 @@ const getUniqueComponentNames = memoize1((data: BasicData) => {
 });


-function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap'] {
+export function getStructAsymMap(atomic: AtomicHierarchy, data?: BasicData): Model['properties']['structAsymMap'] {
    const map = new Map<string, StructAsym>();

-    const { label_asym_id, auth_asym_id, label_entity_id } = data.atom_site;
-    for (let i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+    const { auth_asym_id, label_asym_id, label_entity_id } = atomic.chains;
+
+    for (let i = 0, _i = atomic.chains._rowCount; i < _i; i ++) {
        const id = label_asym_id.value(i);
-        if (!map.has(id)) {
-            map.set(id, {
-                id,
-                auth_id: auth_asym_id.value(i),
-                entity_id: label_entity_id.value(i)
-            });
-        }
+        map.set(id, { id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
    }

-    if (data.struct_asym._rowCount > 0) {
+    // to get asym mapping for coarse/ihm data
+    if (data?.struct_asym._rowCount) {
        const { id, entity_id } = data.struct_asym;
        for (let i = 0, il = id.rowCount; i < il; ++i) {
            const _id = id.value(i);
@@ -136,14 +133,6 @@ function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap']
            }
        }
    }
-    return map;
-}

-export function getProperties(data: BasicData): Model['properties'] {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
+    return map;
 }
--- a/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
+++ b/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 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>
 */
@@ -123,6 +123,8 @@ function getInteractionLoci(pickingId: PickingId, structureGroup: StructureGroup
    return EmptyLoci;
 }

+const __contactIndicesSet = new Set<number>();
+
 function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean) {
    let changed = false;
    if (Interactions.isLoci(loci)) {
@@ -156,21 +158,36 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int

        const { offset } = contacts;
        const { offsets: fOffsets, indices: fIndices } = features.elementsIndex;
+        const { members, offsets } = features;

-        // TODO: when isMarking, all elements of contact features need to be in the loci
        for (const e of loci.elements) {
            const unitIdx = group.unitIndexMap.get(e.unit.id);
-            if (unitIdx !== undefined) continue;
-            if (isMarking && OrderedSet.size(e.indices) === 1) continue;
+            if (unitIdx === undefined) continue;

+            __contactIndicesSet.clear();
            OrderedSet.forEach(e.indices, v => {
                for (let i = fOffsets[v], il = fOffsets[v + 1]; i < il; ++i) {
                    const fI = fIndices[i];
                    for (let j = offset[fI], jl = offset[fI + 1]; j < jl; ++j) {
-                        if (apply(Interval.ofSingleton(unitIdx * groupCount + j))) changed = true;
+                        __contactIndicesSet.add(j);
                    }
                }
            });
+
+            __contactIndicesSet.forEach(i => {
+                if (isMarking) {
+                    const fA = contacts.a[i];
+                    for (let j = offsets[fA], jl = offsets[fA + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members[j])) return;
+                    }
+                    const fB = contacts.b[i];
+                    for (let j = offsets[fB], jl = offsets[fB + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members[j])) return;
+                    }
+                }
+
+                if (apply(Interval.ofSingleton(unitIdx * groupCount + i))) changed = true;
+            });
        }
    }
    return changed;
--- a/src/mol-model-props/sequence/best-database-mapping.ts
+++ b/src/mol-model-props/sequence/best-database-mapping.ts
@@ -29,7 +29,7 @@ namespace BestDatabaseSequenceMapping {
        type: 'static',
        defaultParams: {},
        getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('db_name') >= 0,
+        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('pdbx_sifts_xref_db_name') >= 0,
        obtain: async (ctx, data) => {
            return { value: fromCif(data) };
        }
@@ -40,7 +40,7 @@ namespace BestDatabaseSequenceMapping {
        const data = Provider.get(model).value;
        if (!data) return '';
        const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
        return data.accession[rI];
    }

@@ -49,7 +49,7 @@ namespace BestDatabaseSequenceMapping {
        const data = Provider.get(model).value;
        if (!data) return;
        const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
        const dbName = data.dbName[rI];
        if (!dbName) return;
        return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
@@ -59,10 +59,10 @@ namespace BestDatabaseSequenceMapping {
        if (!MmcifFormat.is(model.sourceData)) return;

        const { atom_site } = model.sourceData.data.frame.categories;
-        const db_name = atom_site.getField('db_name');
-        const db_acc = atom_site.getField('db_acc');
-        const db_num = atom_site.getField('db_num');
-        const db_res = atom_site.getField('db_res');
+        const db_name = atom_site.getField('pdbx_sifts_xref_db_name');
+        const db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
+        const db_num = atom_site.getField('pdbx_sifts_xref_db_num');
+        const db_res = atom_site.getField('pdbx_sifts_xref_db_res');

        if (!db_name || !db_acc || !db_num || !db_res) return;

@@ -77,17 +77,17 @@ namespace BestDatabaseSequenceMapping {
            const row = atomSourceIndex.value(residueOffsets[i]);

            if (db_name.valueKind(row) !== Column.ValueKind.Present) {
-                dbName[row] = '';
-                accession[row] = '';
-                num[row] = 0;
-                residue[row] = '';
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = 0;
+                residue[i] = '';
                continue;
            }

-            dbName[row] = db_name.str(row);
-            accession[row] = db_acc.str(row);
-            num[row] = db_num.int(row);
-            residue[row] = db_res.str(row);
+            dbName[i] = db_name.str(row);
+            accession[i] = db_acc.str(row);
+            num[i] = db_num.int(row);
+            residue[i] = db_res.str(row);
        }

        return { dbName, accession, num, residue };
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -52,6 +52,10 @@ function isWithoutSymmetry(structure: Structure) {
    return structure.units.every(u => u.conformation.operator.isIdentity);
 }

+function isWithoutOperator(structure: Structure) {
+    return isWithoutSymmetry(structure) && structure.units.every(u => !u.conformation.operator.assembly && !u.conformation.operator.suffix);
+}
+
 const Categories = [
    // Basics
    copy_mmCif_category('entry'),
@@ -63,9 +67,9 @@ const Categories = [
    copy_mmCif_category('symmetry', isWithoutSymmetry),

    // Assemblies
-    copy_mmCif_category('pdbx_struct_assembly', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_oper_list', isWithoutSymmetry),
+    copy_mmCif_category('pdbx_struct_assembly', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_oper_list', isWithoutOperator),

    // Secondary structure
    _struct_conf,
@@ -250,10 +254,10 @@ function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExp
 }


-function to_mmCIF(name: string, structure: Structure, asBinary = false) {
+function to_mmCIF(name: string, structure: Structure, asBinary = false, params?: encode_mmCIF_categories_Params) {
    const enc = CifWriter.createEncoder({ binary: asBinary });
    enc.startDataBlock(name);
-    encode_mmCIF_categories(enc, structure);
+    encode_mmCIF_categories(enc, structure, params);
    return enc.getData();
 }

--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -22,7 +22,7 @@ export const EntitySubtype = Column.Schema.Aliased<EntitySubtype>(Column.Schema.
 export interface Entities {
    data: mmCIF_Database['entity'],
    subtype: Column<EntitySubtype>,
-    prd_id: Column<string>,
+    prd_id?: Column<string>,
    getEntityIndex(id: string): EntityIndex
 }

--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -126,6 +126,7 @@ const coarse = {
    z: atom.z,

    asym_id: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element)),
+    entity_id: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entity_id.value(l.element)),
    seq_id_begin: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element)),
    seq_id_end: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element)),

@@ -162,7 +163,7 @@ const entity = {
    pdbx_ec: p(l => l.unit.model.entities.data.pdbx_ec.value(eK(l))),

    subtype: p(l => l.unit.model.entities.subtype.value(eK(l))),
-    prd_id: p(l => l.unit.model.entities.prd_id.value(eK(l))),
+    prd_id: p(l => l.unit.model.entities.prd_id?.value(eK(l)) ?? ''),
 };

 const _emptyList: any[] = [];
--- a/src/mol-model/structure/structure/util/superposition-db-mapping.ts
+++ b/src/mol-model/structure/structure/util/superposition-db-mapping.ts
@@ -5,6 +5,7 @@
 */

 import { Segmentation } from '../../../../mol-data/int';
+import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
 import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
 import { ElementIndex } from '../../model/indexing';
@@ -33,6 +34,7 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]
    for (const p of pairs) {
        const [a, b] = getPositionTables(index, p.i, p.j, p.count);
        const transform = MinimizeRmsd.compute({ a, b });
+        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
        ret.push({ transform, pivot: p.i, other: p.j });
    }

@@ -51,6 +53,8 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:

        const l = Math.min(a[2] - a[1], b[2] - b[1]);

+        // TODO: allow to use just backbone atoms?
+        // TODO: check if residue types match?
        for (let i = 0; i < l; i++) {
            let eI = (a[1] + i) as ElementIndex;
            xs.x[o] = a[0].conformation.x(eI);
@@ -122,7 +126,6 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
        if (unit.kind !== Unit.Kind.Atomic) continue;

        const { elements, model } = unit;
-        const { offsets: residueOffset } = model.atomicHierarchy.residueAtomSegments;

        const map = BestDatabaseSequenceMapping.Provider.get(model).value;
        if (!map) return;
@@ -137,23 +140,27 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
            residuesIt.setSegment(chainSegment);
            while (residuesIt.hasNext) {
                const residueSegment = residuesIt.move();
-                const eI = elements[residueSegment.start];
-                const rI = residueOffset[eI];
+                const rI = residueSegment.index;

                if (!dbName[rI]) continue;

+                const start = elements[residueSegment.start];
+                const end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+
                const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;

                if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, eI, elements[residueSegment.end]] } });
+                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
                } else {
                    const entry = index.get(key)!;

                    if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, eI, elements[residueSegment.end]];
+                        entry.pivots[sI] = [unit, start, end];
                    }
                }
            }
        }
    }
+
+    console.log(index);
 }
--- a/src/mol-plugin-state/actions/file.ts
+++ b/src/mol-plugin-state/actions/file.ts
@@ -7,8 +7,10 @@
 import { PluginContext } from '../../mol-plugin/context';
 import { StateAction } from '../../mol-state';
 import { Task } from '../../mol-task';
+import { Asset } from '../../mol-util/assets';
 import { getFileInfo } from '../../mol-util/file-info';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { unzip } from '../../mol-util/zip/zip';
 import { PluginStateObject } from '../objects';

 export const OpenFiles = StateAction.build({
@@ -33,24 +35,37 @@ export const OpenFiles = StateAction.build({
            plugin.log.error('No file(s) selected');
            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 {
-                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}'`);
-                    continue;
-                }
-
-                // 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);
+                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);
+                    }
+                } else {
+                    await processFile(file);
                }
            } catch (e) {
                console.error(e);
--- a/src/mol-plugin-ui/structure/superposition.tsx
+++ b/src/mol-plugin-ui/structure/superposition.tsx
@@ -185,9 +185,9 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
            rmsd += xform.transform.rmsd;
        }

-        rmsd /= transforms.length - 1;
+        rmsd /= Math.max(transforms.length - 1, 1);

-        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)}.`);
+        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
        await new Promise(res => requestAnimationFrame(res));
        PluginCommands.Camera.Reset(this.plugin);
    };
--- a/src/mol-repr/structure/visual/carbohydrate-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-link-cylinder.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -101,6 +101,8 @@ function getLinkLoci(pickingId: PickingId, structure: Structure, id: number) {
    return EmptyLoci;
 }

+const __linkIndicesSet = new Set<number>();
+
 function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
    let changed = false;
    if (!StructureElement.Loci.is(loci)) return false;
@@ -110,11 +112,14 @@ function eachCarbohydrateLink(loci: Loci, structure: Structure, apply: (interval
    for (const { unit, indices } of loci.elements) {
        if (!Unit.isAtomic(unit)) continue;

+        __linkIndicesSet.clear();
        OrderedSet.forEach(indices, v => {
-            // TODO avoid duplicate calls to apply
            const linkIndices = getLinkIndices(unit, unit.elements[v]);
            for (let i = 0, il = linkIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                }
            }
        });
    }
--- a/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-symbol-mesh.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -29,8 +29,8 @@ import { getAltResidueLociFromId } from './util/common';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';

 const t = Mat4.identity();
-const sVec = Vec3.zero();
-const pd = Vec3.zero();
+const sVec = Vec3();
+const pd = Vec3();

 const SideFactor = 2 * 0.806; // 0.806 == Math.cos(Math.PI / 4)

@@ -212,6 +212,8 @@ function getCarbohydrateLoci(pickingId: PickingId, structure: Structure, id: num
    return EmptyLoci;
 }

+const __elementIndicesSet = new Set<number>();
+
 /** For each carbohydrate (usually a monosaccharide) when all its residue's elements are in a loci. */
 function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
    const { getElementIndices } = structure.carbohydrates;
@@ -222,11 +224,14 @@ function eachCarbohydrate(loci: Loci, structure: Structure, apply: (interval: In
    for (const { unit, indices } of loci.elements) {
        if (!Unit.isAtomic(unit)) continue;

+        __elementIndicesSet.clear();
        OrderedSet.forEach(indices, v => {
-            // TODO avoid duplicate calls to apply
            const elementIndices = getElementIndices(unit, unit.elements[v]);
            for (let i = 0, il = elementIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(elementIndices[i] * 2))) changed = true;
+                if (!__elementIndicesSet.has(elementIndices[i])) {
+                    __elementIndicesSet.add(elementIndices[i]);
+                    if (apply(Interval.ofSingleton(elementIndices[i] * 2))) changed = true;
+                }
            }
        });
    }
--- a/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.ts
+++ b/src/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -123,6 +123,8 @@ function getTerminalLinkLoci(pickingId: PickingId, structure: Structure, id: num
    return EmptyLoci;
 }

+const __linkIndicesSet = new Set<number>();
+
 function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
    let changed = false;
    if (!StructureElement.Loci.is(loci)) return false;
@@ -132,11 +134,14 @@ function eachTerminalLink(loci: Loci, structure: Structure, apply: (interval: In
    for (const { unit, indices } of loci.elements) {
        if (!Unit.isAtomic(unit)) continue;

+        __linkIndicesSet.clear();
        OrderedSet.forEach(indices, v => {
-            // TODO avoid duplicate calls to apply
            const linkIndices = getTerminalLinkIndices(unit, unit.elements[v]);
            for (let i = 0, il = linkIndices.length; i < il; ++i) {
-                if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                if (!__linkIndicesSet.has(linkIndices[i])) {
+                    __linkIndicesSet.add(linkIndices[i]);
+                    if (apply(Interval.ofSingleton(linkIndices[i]))) changed = true;
+                }
            }
        });
    }
--- a/src/mol-repr/visual.ts
+++ b/src/mol-repr/visual.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -88,6 +88,7 @@ namespace Visual {
        const currentStatus = markerStatus.ref.value as MarkerInfo['status'];

        if (!isEveryLoci(loci)) {
+            // assume that all interval are non-overlapping
            let intervalSize = 0;
            lociApply(loci, interval => {
                intervalSize += Interval.size(interval);
--- a/src/mol-theme/color/element-symbol.ts
+++ b/src/mol-theme/color/element-symbol.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -13,6 +13,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
 import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator-name';

@@ -34,7 +35,11 @@ export const ElementSymbolColorThemeParams = {
        'element-symbol': PD.Group({})
    }, { description: 'Use chain-id coloring for carbon atoms.' }),
    saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ElementSymbolColors))
+    })
 };
 export type ElementSymbolColorThemeParams = typeof ElementSymbolColorThemeParams
 export function getElementSymbolColorThemeParams(ctx: ThemeDataContext) {
@@ -47,7 +52,7 @@ export function elementSymbolColor(colorMap: ElementSymbolColors, element: Eleme
 }

 export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<ElementSymbolColorThemeParams>): ColorTheme<ElementSymbolColorThemeParams> {
-    const colorMap = getAdjustedColorMap(ElementSymbolColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ElementSymbolColors : props.colors.params, props.saturation, props.lightness);

    const carbonColor = props.carbonColor.name === 'chain-id'
        ? ChainIdColorTheme(ctx, props.carbonColor.params).color
@@ -86,8 +91,8 @@ export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<
        color,
        props,
        description: Description,
-        legend: TableLegend(Object.keys(ElementSymbolColors).map(name => {
-            return [name, (ElementSymbolColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
        }))
    };
 }
--- a/src/mol-theme/color/entity-id.ts
+++ b/src/mol-theme/color/entity-id.ts
@@ -1,10 +1,10 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

-import { StructureProperties, StructureElement, Bond, Structure } from '../../mol-model/structure';
+import { StructureProperties, StructureElement, Bond, Structure, Unit } from '../../mol-model/structure';
 import { Color } from '../../mol-util/color';
 import { Location } from '../../mol-model/location';
 import { ColorTheme, LocationColor } from '../color';
@@ -38,10 +38,30 @@ function getEntityIdSerialMap(structure: Structure) {
            const k = key(label_entity_id.value(j), i);
            if (!map.has(k)) map.set(k, map.size);
        }
+        const { entity_id: spheres_entity_id } = structure.models[i].coarseHierarchy.spheres;
+        for (let j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
+            const k = key(spheres_entity_id.value(j), i);
+            if (!map.has(k)) map.set(k, map.size);
+        }
+        const { entity_id: gaussians_entity_id } = structure.models[i].coarseHierarchy.gaussians;
+        for (let j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
+            const k = key(gaussians_entity_id.value(j), i);
+            if (!map.has(k)) map.set(k, map.size);
+        }
    }
    return map;
 }

+function getEntityId(location: StructureElement.Location): string {
+    switch (location.unit.kind) {
+        case Unit.Kind.Atomic:
+            return StructureProperties.chain.label_entity_id(location);
+        case Unit.Kind.Spheres:
+        case Unit.Kind.Gaussians:
+            return StructureProperties.coarse.entity_id(location);
+    }
+}
+
 export function EntityIdColorTheme(ctx: ThemeDataContext, props: PD.Values<EntityIdColorThemeParams>): ColorTheme<EntityIdColorThemeParams> {
    let color: LocationColor;
    let legend: ScaleLegend | TableLegend | undefined;
@@ -59,16 +79,16 @@ export function EntityIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Entit
        color = (location: Location): Color => {
            let serial: number | undefined = undefined;
            if (StructureElement.Location.is(location)) {
-                const atomId = StructureProperties.chain.label_entity_id(location);
+                const entityId = getEntityId(location);
                const modelIndex = location.structure.models.indexOf(location.unit.model);
-                const k = key(atomId, modelIndex);
+                const k = key(entityId, modelIndex);
                serial = entityIdSerialMap.get(k);
            } else if (Bond.isLocation(location)) {
                l.unit = location.aUnit;
                l.element = location.aUnit.elements[location.aIndex];
-                const atomId = StructureProperties.chain.label_entity_id(l);
+                const entityId = getEntityId(l);
                const modelIndex = l.structure.models.indexOf(l.unit.model);
-                const k = key(atomId, modelIndex);
+                const k = key(entityId, modelIndex);
                serial = entityIdSerialMap.get(k);
            }
            return serial === undefined ? DefaultColor : palette.color(serial);
--- a/src/mol-theme/color/molecule-type.ts
+++ b/src/mol-theme/color/molecule-type.ts
@@ -4,7 +4,7 @@
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

-import { Color } from '../../mol-util/color';
+import { Color, ColorMap } from '../../mol-util/color';
 import { StructureElement, Unit, Bond, ElementIndex } from '../../mol-model/structure';
 import { Location } from '../../mol-model/location';
 import { ColorTheme } from '../color';
@@ -13,6 +13,19 @@ import { getElementMoleculeType } from '../../mol-model/structure/util';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
+import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
+
+export const MoleculeTypeColors = ColorMap({
+    water: 0x386cb0,
+    ion: 0xf0027f,
+    protein: 0xbeaed4,
+    RNA: 0xfdc086,
+    DNA: 0xbf5b17,
+    PNA: 0x42A49A,
+    saccharide: 0x7fc97f,
+});
+export type MoleculeTypeColors = typeof MoleculeTypeColors

 const DefaultMoleculeTypeColor = Color(0xffff99);
 const Description = 'Assigns a color based on the molecule type of a residue.';
@@ -20,15 +33,9 @@ const Description = 'Assigns a color based on the molecule type of a residue.';
 export const MoleculeTypeColorThemeParams = {
    saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    colors: PD.Group({
-        water: PD.Color(Color(0x386cb0)),
-        ion: PD.Color(Color(0xf0027f)),
-        protein: PD.Color(Color(0xbeaed4)),
-        rna: PD.Color(Color(0xfdc086)),
-        dna: PD.Color(Color(0xbf5b17)),
-        pna: PD.Color(Color(0x42A49A)),
-        saccharide: PD.Color(Color(0x7fc97f)),
-        lipid: PD.Color(Color(0xcccccc)),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(MoleculeTypeColors))
    })
 };
 export type MoleculeTypeColorThemeParams = typeof MoleculeTypeColorThemeParams
@@ -36,32 +43,28 @@ export function getMoleculeTypeColorThemeParams(ctx: ThemeDataContext) {
    return MoleculeTypeColorThemeParams; // TODO return copy
 }

-type MoleculeTypeColorThemeProps = PD.Values<MoleculeTypeColorThemeParams>;
-export function moleculeTypeColor(props: MoleculeTypeColorThemeProps, unit: Unit, element: ElementIndex): Color {
-    let c = DefaultMoleculeTypeColor;
+export function moleculeTypeColor(colorMap: MoleculeTypeColors, unit: Unit, element: ElementIndex): Color {
    const moleculeType = getElementMoleculeType(unit, element);
    switch (moleculeType) {
-        case MoleculeType.Water: c = props.colors.water; break;
-        case MoleculeType.Ion: c = props.colors.ion; break;
-        case MoleculeType.Protein: c = props.colors.protein; break;
-        case MoleculeType.RNA: c = props.colors.rna; break;
-        case MoleculeType.DNA: c = props.colors.dna; break;
-        case MoleculeType.PNA: c = props.colors.pna; break;
-        case MoleculeType.Saccharide: c = props.colors.saccharide; break;
-        case MoleculeType.Lipid: c = props.colors.lipid; break;
+        case MoleculeType.Water: return colorMap.water;
+        case MoleculeType.Ion: return colorMap.ion;
+        case MoleculeType.Protein: return colorMap.protein;
+        case MoleculeType.RNA: return colorMap.RNA;
+        case MoleculeType.DNA: return colorMap.DNA;
+        case MoleculeType.PNA: return colorMap.PNA;
+        case MoleculeType.Saccharide: return colorMap.saccharide;
    }
-    c = Color.saturate(c, props.saturation);
-    c = Color.darken(c, -props.lightness);
-    return c;
+    return DefaultMoleculeTypeColor;
 }

 export function MoleculeTypeColorTheme(ctx: ThemeDataContext, props: PD.Values<MoleculeTypeColorThemeParams>): ColorTheme<MoleculeTypeColorThemeParams> {
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? MoleculeTypeColors : props.colors.params, props.saturation, props.lightness);

    function color(location: Location): Color {
        if (StructureElement.Location.is(location)) {
-            return moleculeTypeColor(props, location.unit, location.element);
+            return moleculeTypeColor(colorMap, location.unit, location.element);
        } else if (Bond.isLocation(location)) {
-            return moleculeTypeColor(props, location.aUnit, location.aUnit.elements[location.aIndex]);
+            return moleculeTypeColor(colorMap, location.aUnit, location.aUnit.elements[location.aIndex]);
        }
        return DefaultMoleculeTypeColor;
    }
@@ -72,8 +75,8 @@ export function MoleculeTypeColorTheme(ctx: ThemeDataContext, props: PD.Values<M
        color,
        props,
        description: Description,
-        legend: TableLegend(Object.keys(props.colors).map(name => {
-            return [name, (props.colors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
        }).concat([['Other/unknown', DefaultMoleculeTypeColor]]))
    };
 }
--- a/src/mol-theme/color/residue-name.ts
+++ b/src/mol-theme/color/residue-name.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 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>
 */
@@ -12,6 +12,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';

 // protein colors from Jmol http://jmol.sourceforge.net/jscolors/
 export const ResidueNameColors = ColorMap({
@@ -66,7 +67,11 @@ const Description = 'Assigns a color to every residue according to its name.';

 export const ResidueNameColorThemeParams = {
    saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(1, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(ResidueNameColors))
+    })
 };
 export type ResidueNameColorThemeParams = typeof ResidueNameColorThemeParams
 export function getResidueNameColorThemeParams(ctx: ThemeDataContext) {
@@ -93,7 +98,7 @@ export function residueNameColor(colorMap: ResidueNameColors, residueName: strin
 }

 export function ResidueNameColorTheme(ctx: ThemeDataContext, props: PD.Values<ResidueNameColorThemeParams>): ColorTheme<ResidueNameColorThemeParams> {
-    const colorMap = getAdjustedColorMap(ResidueNameColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ResidueNameColors : props.colors.params, props.saturation, props.lightness);

    function color(location: Location): Color {
        if (StructureElement.Location.is(location)) {
@@ -123,8 +128,8 @@ export function ResidueNameColorTheme(ctx: ThemeDataContext, props: PD.Values<Re
        color,
        props,
        description: Description,
-        legend: TableLegend(Object.keys(ResidueNameColors).map(name => {
-            return [name, (ResidueNameColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
        }).concat([['Unknown', DefaultResidueNameColor]]))
    };
 }
--- a/src/mol-theme/color/secondary-structure.ts
+++ b/src/mol-theme/color/secondary-structure.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 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>
 */
@@ -15,6 +15,7 @@ import { ThemeDataContext } from '../theme';
 import { TableLegend } from '../../mol-util/legend';
 import { SecondaryStructureProvider, SecondaryStructureValue } from '../../mol-model-props/computed/secondary-structure';
 import { getAdjustedColorMap } from '../../mol-util/color/color';
+import { getColorMapParams } from '../../mol-util/color/params';
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { hash2 } from '../../mol-data/util';

@@ -41,7 +42,11 @@ const Description = 'Assigns a color based on the type of secondary structure an

 export const SecondaryStructureColorThemeParams = {
    saturation: PD.Numeric(-1, { min: -6, max: 6, step: 0.1 }),
-    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 })
+    lightness: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
+    colors: PD.MappedStatic('default', {
+        'default': PD.EmptyGroup(),
+        'custom': PD.Group(getColorMapParams(SecondaryStructureColors))
+    })
 };
 export type SecondaryStructureColorThemeParams = typeof SecondaryStructureColorThemeParams
 export function getSecondaryStructureColorThemeParams(ctx: ThemeDataContext) {
@@ -88,7 +93,7 @@ export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Va
    const computedSecondaryStructure = ctx.structure && SecondaryStructureProvider.get(ctx.structure);
    const contextHash = computedSecondaryStructure ? hash2(computedSecondaryStructure.id, computedSecondaryStructure.version) : -1;

-    const colorMap = getAdjustedColorMap(SecondaryStructureColors, props.saturation, props.lightness);
+    const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? SecondaryStructureColors : props.colors.params, props.saturation, props.lightness);

    function color(location: Location): Color {
        if (StructureElement.Location.is(location)) {
@@ -107,8 +112,8 @@ export function SecondaryStructureColorTheme(ctx: ThemeDataContext, props: PD.Va
        props,
        contextHash,
        description: Description,
-        legend: TableLegend(Object.keys(SecondaryStructureColors).map(name => {
-            return [name, (SecondaryStructureColors as any)[name] as Color] as [string, Color];
+        legend: TableLegend(Object.keys(colorMap).map(name => {
+            return [name, (colorMap as any)[name] as Color] as [string, Color];
        }).concat([['Other', DefaultSecondaryStructureColor]]))
    };
 }
--- a/src/mol-util/color/color.ts
+++ b/src/mol-util/color/color.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
--- a/src/mol-util/color/params.ts
+++ b/src/mol-util/color/params.ts
@@ -0,0 +1,17 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { objectForEach } from '../object';
+import { ColorMap } from './color';
+
+export function getColorMapParams<T extends { [k: string]: number }>(map: ColorMap<T>) {
+    const colors: Record<string, PD.Color> = {};
+    objectForEach(map, (_, k) => {
+        colors[k] = PD.Color(map[k]);
+    });
+    return colors as { [k in keyof T]: PD.Color };
+}
Author	SHA1	Message	Date
Alexander Rose	2ad0754b90	3.0.0	2022-01-23 18:12:48 -08:00
Alexander Rose	3ecb3af57b	changelog	2022-01-23 18:08:01 -08:00
Alexander Rose	ec4f15f549	improve/fix InteractionsIntraUnitVisual marking	2022-01-23 17:55:51 -08:00
Alexander Rose	2458ea7b92	Merge pull request #349 from molstar/custom-theme-colors add custom theme colors	2022-01-23 15:13:24 -08:00
Alexander Rose	c5e6bedf11	Merge branch 'master' into custom-theme-colors	2022-01-23 13:54:57 -08:00
dsehnal	8528e5a666	Support/bugfixes for atom_site.pdbx_sifts_xref categories	2022-01-23 20:46:49 +01:00
dsehnal	6ed232b3d9	fix using default values for webgl1/wboit features in the default viewer app	2022-01-23 19:25:09 +01:00
dsehnal	f8aae8cbd1	skip Coarse models in export extension	2022-01-23 16:13:02 +01:00
Alexander Rose	00c2517045	package updates	2022-01-22 14:06:26 -08:00
Alexander Rose	99b043a929	avoid circular dependency	2022-01-22 11:10:41 -08:00
Alexander Rose	5900e27e39	add custom theme colors - element-symbol - molecule-type - residue-name - secondary-structure	2022-01-22 10:51:41 -08:00
Alexander Rose	1b79d34907	fix marking of carbohydrate visuals	2022-01-22 08:53:47 -08:00
Alexander Rose	fc52e29c92	re-add using _struct_asym cat in getStructAsymMap - needed for ihm model support	2022-01-22 08:50:29 -08:00
Alexander Rose	df23b3c0fe	fix coarse model support in entity-id color theme - add StructureProperties.coarse.entity_id	2022-01-22 08:48:07 -08:00
David Sehnal	5e25716c98	Merge pull request #334 from molstar/export-extension Model export extension & related improvements	2022-01-18 13:23:11 +01:00
dsehnal	f70a10bc56	add info about CIF export failure	2022-01-18 13:20:53 +01:00
dsehnal	0ccb045f4e	Merge branch 'master' of https://github.com/molstar/molstar into export-extension	2022-01-18 12:30:45 +01:00
dsehnal	fbb60c9493	Treat empty string as non-present value in BinaryCIF	2022-01-17 16:21:14 +01:00
dsehnal	9f953ef51c	add Model Export overlay	2022-01-17 15:47:56 +01:00
dsehnal	4871f1547c	Generate structAsymMap from normalized atomic hierarchy - Fixes issue with remapped chains - Requires to parse PRD separately	2022-01-17 14:52:53 +01:00
dsehnal	d6413529f4	PR feedback	2022-01-17 13:58:20 +01:00
dsehnal	b6847907ca	Add ModelExport to viewer/app.ts	2022-01-17 11:37:49 +01:00
dsehnal	fb54a1aed7	Merge branch 'master' of https://github.com/molstar/molstar into export-extension	2022-01-17 11:37:16 +01:00
dsehnal	c0880b647f	changelog	2022-01-03 13:51:09 +01:00
dsehnal	039dc6a76b	changelog	2022-01-03 13:49:59 +01:00
dsehnal	042a7625ad	isWithoutOperator tweak	2022-01-03 13:46:13 +01:00
dsehnal	41827c478d	open zip files with multiple entries	2022-01-03 13:42:37 +01:00
dsehnal	9a73180c3c	support transformed export & structAsymMap parsing fix	2022-01-03 13:15:51 +01:00
dsehnal	333ee85fdb	omit suffix for identity assembly operators	2022-01-03 12:52:05 +01:00
dsehnal	fa8ca45b6a	do not include assembly categories in export if an operator has been applied	2022-01-03 12:34:37 +01:00
dsehnal	c2bae1aeb7	model export extension	2022-01-03 12:26:36 +01:00