molstar 3.0.0 → 3.2.0

package/LICENSE

@@ -1,21 +1,21 @@
-The MIT License
-
-    Copyright (c) 2017 - now, Mol* contributors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+The MIT License
+
+    Copyright (c) 2017 - now, Mol* contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.

package/README.md

@@ -1,194 +1,194 @@
-[![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)
-[![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)
-[![Build Status](https://travis-ci.org/molstar/molstar.svg?branch=master)](https://travis-ci.org/molstar/molstar)
-[![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)
-
-# Mol*
-
-The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
-
-When using Mol*, please cite:
-
-David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
-
-### Protein Data Bank Integrations
-
-- The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
-
-- [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
-
-
-## Project Structure Overview
-
-The core of Mol* consists of these modules (see under `src/`):
-
-- `mol-task` Computation abstraction with progress tracking and cancellation support.
-- `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
-- `mol-math` Math related (loosely) algorithms and data structures.
-- `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
-- `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
-- `mol-model-formats` Data format parsers for `mol-model`.
-- `mol-model-props` Common "custom properties".
-- `mol-script` A scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
-- `mol-geo` Creating (molecular) geometries.
-- `mol-theme` Theming for structure, volume and shape representations.
-- `mol-repr` Molecular representations for structures, volumes and shapes.
-- `mol-gl` A wrapper around WebGL.
-- `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
-- `mol-state` State representation tree with state saving and automatic updates.
-- `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
-- `mol-plugin-state` State transformations, builders, and managers.
-- `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
-- `mol-util` Useful things that do not fit elsewhere.
-
-Moreover, the project contains the implementation of `servers`, including
-
-- `servers/model` A tool for accessing coordinate and annotation data of molecular structures.
-- `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
-- `servers/plugin-state` A basic server to store Mol* Plugin states.
-
-The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
-
-## Previous Work
-This project builds on experience from previous solutions:
-- [LiteMol Suite](https://www.litemol.org)
-- [WebChemistry](https://webchem.ncbr.muni.cz)
-- [NGL Viewer](http://nglviewer.org)
-- [MMTF](http://mmtf.rcsb.org)
-- [MolQL](http://molql.org)
-- [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)
-- And many others (list will be continuously expanded).
-
-## Building & Running
-
-### Build:
-    npm install
-    npm run build
-
-### Build automatically on file save:
-    npm run watch
-
-If working on just the viewer, ``npm run watch-viewer`` will provide shorter compile times.
-
-### Build with debug mode enabled:
-    DEBUG=molstar npm run watch
-
-Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
-
-### Cleaning and forcing a full rebuild
-    npm run clean
-
-Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
-
-    npm run rebuild
-
-Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
-
-Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
-
-### Build for production:
-    NODE_ENV=production npm run build
-
-**Run**
-
-If not installed previously:
-
-    npm install -g http-server
-
-...or a similar solution.
-
-From the root of the project:
-
-    http-server -p PORT-NUMBER
-
-and navigate to `build/viewer`
-
-
-### Code generation
-**CIF schemas**
-
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
-    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
-
-**Lipid names**
-
-    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
-
-**Ion names**
-
-    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
-
-
-**GraphQL schemas**
-
-    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
-
-### Other scripts
-**Create chem comp bond table**
-
-    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
-
-**Test model server**
-
-    export NODE_PATH="lib"; node build/src/servers/model/test.js
-
-**State Transformer Docs**
-
-    export NODE_PATH="lib"; node build/state-docs
-
-**Convert any CIF to BinaryCIF**
-
-    node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
-
-To see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.
-
-Or
-
-    node lib/commonjs/cli/cif2bcif
-
-## Development
-
-### Installation
-
-If node complains about a missing acorn peer dependency, run the following commands
-
-    npm update acorn --depth 20
-    npm dedupe
-
-### Editor
-
-To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
-
-    "files.associations": {
-        "*.glsl.ts": "glsl",
-        "*.frag.ts": "glsl",
-        "*.vert.ts": "glsl",
-        "*.gql.ts": "graphql"
-    },
-
-## Publish
-
-### Prerelease
-    npm version prerelease # assumes the current version ends with '-dev.X'
-    npm publish --tag next
-
-### Release
-    npm version 0.X.0 # provide valid semver string
-    npm publish
-
-## Deploy
-    npm run test
-    npm run build
-    node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
-
-## Contributing
-Just open an issue or make a pull request. All contributions are welcome.
-
-## Funding
-Funding sources include but are not limited to:
-* [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
-* [PDBe, EMBL-EBI](https://pdbe.org)
-* [CEITEC](https://www.ceitec.eu/)
-* [EntosAI](https://www.entos.ai)
+[![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](./LICENSE)
+[![npm version](https://badge.fury.io/js/molstar.svg)](https://www.npmjs.com/package/molstar)
+[![Build Status](https://travis-ci.org/molstar/molstar.svg?branch=master)](https://travis-ci.org/molstar/molstar)
+[![Gitter](https://badges.gitter.im/molstar/Lobby.svg)](https://gitter.im/molstar/Lobby)
+
+# Mol*
+
+The goal of **Mol\*** (*/'mol-star/*) is to provide a technology stack that serves as a basis for the next-generation data delivery and analysis tools for (not only) macromolecular structure data. Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of [LiteMol](https://litemol.org) (developed by PDBe) and [NGL](https://nglviewer.org) (developed by RCSB PDB) viewers.
+
+When using Mol*, please cite:
+
+David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: [Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314), *Nucleic Acids Research*, 2021; https://doi.org/10.1093/nar/gkab314.
+
+### Protein Data Bank Integrations
+
+- The [pdbe-molstar](https://github.com/molstar/pdbe-molstar) library is the Mol* implementation used by EMBL-EBI data resources such as [PDBe](https://pdbe.org/), [PDBe-KB](https://pdbe-kb.org/) and [AlphaFold DB](https://alphafold.ebi.ac.uk/). This implementation can be used as a JS plugin and a Web component and supports property/attribute-based easy customisation. It provides helper methods to facilitate programmatic interactions between the web application and the 3D viewer. It also provides a superposition view for overlaying all the observed ligand molecules on representative protein conformations.
+
+- [rcsb-molstar](https://github.com/molstar/rcsb-molstar) is the Mol* plugin used by [RCSB PDB](https://www.rcsb.org). The project provides additional presets for the visualization of structure alignments and structure motifs such as ligand binding sites. Furthermore, [rcsb-molstar](https://github.com/molstar/rcsb-molstar) allows to interactively add or hide of (parts of) chains, as seen in the [3D Protein Feature View](https://www.rcsb.org/3d-sequence/4hhb).
+
+
+## Project Structure Overview
+
+The core of Mol* consists of these modules (see under `src/`):
+
+- `mol-task` Computation abstraction with progress tracking and cancellation support.
+- `mol-data` Collections (integer-based sets, interface to columns/tables, etc.)
+- `mol-math` Math related (loosely) algorithms and data structures.
+- `mol-io` Parsing library. Each format is parsed into an interface that corresponds to the data stored by it. Support for common coordinate, experimental/map, and annotation data formats.
+- `mol-model` Data structures and algorithms (such as querying) for representing molecular data (including coordinate, experimental/map, and annotation data).
+- `mol-model-formats` Data format parsers for `mol-model`.
+- `mol-model-props` Common "custom properties".
+- `mol-script` A scripting language for creating representations/scenes and querying (includes the [MolQL query language](https://molql.github.io)).
+- `mol-geo` Creating (molecular) geometries.
+- `mol-theme` Theming for structure, volume and shape representations.
+- `mol-repr` Molecular representations for structures, volumes and shapes.
+- `mol-gl` A wrapper around WebGL.
+- `mol-canvas3d` A low-level 3d view component. Uses `mol-geo` to generate geometries.
+- `mol-state` State representation tree with state saving and automatic updates.
+- `mol-plugin` Allow to define modular Mol* plugin instances utilizing `mol-state` and `mol-canvas3d`.
+- `mol-plugin-state` State transformations, builders, and managers.
+- `mol-plugin-ui` React-based user interface for the Mol* plugin. Some components of the UI are usable outside the main plugin and can be integrated into 3rd party solutions.
+- `mol-util` Useful things that do not fit elsewhere.
+
+Moreover, the project contains the implementation of `servers`, including
+
+- `servers/model` A tool for accessing coordinate and annotation data of molecular structures.
+- `servers/volume` A tool for accessing volumetric experimental data related to molecular structures.
+- `servers/plugin-state` A basic server to store Mol* Plugin states.
+
+The project also contains performance tests (`perf-tests`), `examples`, and `cli` apps (CIF to BinaryCIF converter and JSON domain annotation to CIF converter).
+
+## Previous Work
+This project builds on experience from previous solutions:
+- [LiteMol Suite](https://www.litemol.org)
+- [WebChemistry](https://webchem.ncbr.muni.cz)
+- [NGL Viewer](http://nglviewer.org)
+- [MMTF](http://mmtf.rcsb.org)
+- [MolQL](http://molql.org)
+- [PDB Component Library](https://www.ebi.ac.uk/pdbe/pdb-component-library/)
+- And many others (list will be continuously expanded).
+
+## Building & Running
+
+### Build:
+    npm install
+    npm run build
+
+### Build automatically on file save:
+    npm run watch
+
+If working on just the viewer, ``npm run watch-viewer`` will provide shorter compile times.
+
+### Build with debug mode enabled:
+    DEBUG=molstar npm run watch
+
+Debug/production mode in browsers can be turned on/off during runtime by calling ``setMolStarDebugMode(true/false, true/false)`` from the dev console.
+
+### Cleaning and forcing a full rebuild
+    npm run clean
+
+Wipes the `build` and `lib` directories and `.tsbuildinfo` files.
+
+    npm run rebuild
+
+Runs the cleanup script prior to building the project, forcing a full rebuild of the project.
+
+Use these commands to resolve occassional build failures which may arise after some dependency updates. Once done, `npm run build` should work again. Note that full rebuilds take more time to complete.
+
+### Build for production:
+    NODE_ENV=production npm run build
+
+**Run**
+
+If not installed previously:
+
+    npm install -g http-server
+
+...or a similar solution.
+
+From the root of the project:
+
+    http-server -p PORT-NUMBER
+
+and navigate to `build/viewer`
+
+
+### Code generation
+**CIF schemas**
+
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/ccd.ts -p CCD
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
+    node ./lib/commonjs/cli/cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
+
+**Lipid names**
+
+    node lib/commonjs/cli/lipid-params -o src/mol-model/structure/model/types/lipids.ts
+
+**Ion names**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts
+
+
+**GraphQL schemas**
+
+    node node_modules//@graphql-codegen/cli/bin -c src/extensions/rcsb/graphql/codegen.yml
+
+### Other scripts
+**Create chem comp bond table**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-table.js build/data/ccb.bcif -b
+
+**Test model server**
+
+    export NODE_PATH="lib"; node build/src/servers/model/test.js
+
+**State Transformer Docs**
+
+    export NODE_PATH="lib"; node build/state-docs
+
+**Convert any CIF to BinaryCIF**
+
+    node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif
+
+To see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.
+
+Or
+
+    node lib/commonjs/cli/cif2bcif
+
+## Development
+
+### Installation
+
+If node complains about a missing acorn peer dependency, run the following commands
+
+    npm update acorn --depth 20
+    npm dedupe
+
+### Editor
+
+To get syntax highlighting for shader and graphql files add the following to Visual Code's settings files and make sure relevant extensions are installed in the editor.
+
+    "files.associations": {
+        "*.glsl.ts": "glsl",
+        "*.frag.ts": "glsl",
+        "*.vert.ts": "glsl",
+        "*.gql.ts": "graphql"
+    },
+
+## Publish
+
+### Prerelease
+    npm version prerelease # assumes the current version ends with '-dev.X'
+    npm publish --tag next
+
+### Release
+    npm version 0.X.0 # provide valid semver string
+    npm publish
+
+## Deploy
+    npm run test
+    npm run build
+    node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
+
+## Contributing
+Just open an issue or make a pull request. All contributions are welcome.
+
+## Funding
+Funding sources include but are not limited to:
+* [RCSB PDB](https://www.rcsb.org) funding by a grant [DBI-1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE
+* [PDBe, EMBL-EBI](https://pdbe.org)
+* [CEITEC](https://www.ceitec.eu/)
+* [EntosAI](https://www.entos.ai)

package/build/viewer/embedded.html

@@ -1,44 +1,44 @@
-<!DOCTYPE html>
-<html lang="en">
-    <head>
-        <meta charset="utf-8" />
-        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
-        <link rel="icon" href="./favicon.ico" type="image/x-icon">
-        <title>Embedded Mol* Viewer</title>
-        <style>
-            #app {
-                position: absolute;
-                left: 100px;
-                top: 100px;
-                width: 800px;
-                height: 600px;
-            }
-        </style>
-        <link rel="stylesheet" type="text/css" href="molstar.css" />
-    </head>
-    <body>
-        <div id="app"></div>
-        <script type="text/javascript" src="./molstar.js"></script>
-        <script type="text/javascript">
-            molstar.Viewer.create('app', {
-                layoutIsExpanded: true,
-                layoutShowControls: false,
-                layoutShowRemoteState: false,
-                layoutShowSequence: true,
-                layoutShowLog: false,
-                layoutShowLeftPanel: true,
-
-                viewportShowExpand: true,
-                viewportShowSelectionMode: false,
-                viewportShowAnimation: false,
-
-                pdbProvider: 'rcsb',
-                emdbProvider: 'rcsb',
-            }).then(viewer => {
-                viewer.loadPdb('7bv2');
-                viewer.loadEmdb('EMD-30210', { detail: 6 });
-                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
-            });
-        </script>
-    </body>
+<!DOCTYPE html>
+<html lang="en">
+    <head>
+        <meta charset="utf-8" />
+        <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
+        <link rel="icon" href="./favicon.ico" type="image/x-icon">
+        <title>Embedded Mol* Viewer</title>
+        <style>
+            #app {
+                position: absolute;
+                left: 100px;
+                top: 100px;
+                width: 800px;
+                height: 600px;
+            }
+        </style>
+        <link rel="stylesheet" type="text/css" href="molstar.css" />
+    </head>
+    <body>
+        <div id="app"></div>
+        <script type="text/javascript" src="./molstar.js"></script>
+        <script type="text/javascript">
+            molstar.Viewer.create('app', {
+                layoutIsExpanded: true,
+                layoutShowControls: false,
+                layoutShowRemoteState: false,
+                layoutShowSequence: true,
+                layoutShowLog: false,
+                layoutShowLeftPanel: true,
+
+                viewportShowExpand: true,
+                viewportShowSelectionMode: false,
+                viewportShowAnimation: false,
+
+                pdbProvider: 'rcsb',
+                emdbProvider: 'rcsb',
+            }).then(viewer => {
+                viewer.loadPdb('7bv2');
+                viewer.loadEmdb('EMD-30210', { detail: 6 });
+                // viewer.loadAllModelsOrAssemblyFromUrl('https://cs.litemol.org/5ire/full', 'mmcif', false, { representationParams: { theme: { globalName: 'operator-name' } } })
+            });
+        </script>
+    </body>
 </html>