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64 Commits

Author SHA1 Message Date
Alexander Rose
6c99c575bc Handle CCD bonds with Deuterium atoms 2026-03-26 16:23:32 -07:00
David Sehnal
3e70251f38 Viewer QoL (#1734) 
* Viewer QoL

* docs
 2025-12-28 19:26:33 +01:00
David Sehnal
c21ba08fc7 Viewer improvements (#1725) 
* separate exxtensions file

* subscribe method on the Viewer object

* export lib

* Add viewer.structureInteraction

* MVS tryGetPrimitivesFromLoci util

* param select indicator

* tweaks

* mapped control icon

* docs and tweaks

* viewer color themes

* tweak

* typo

* pr feedback
 2025-12-21 11:35:49 +01:00
ddelalamo-takeda
27af73f97f Add TM-align structure alignment algorithm (#1723) 
* Delete docs/docs/plugin/superposition.md

* Add TM-align structure alignment algorithm

Implement TM-align for structure-based protein alignment, providing an
alternative to sequence-based superposition methods. TM-align finds optimal
structural alignments regardless of sequence similarity using TM-score.

New features:
- Core TM-align algorithm (src/mol-math/linear-algebra/3d/tm-align.ts)
  - TM-score calculation with length-independent normalization
  - Dynamic programming for optimal alignment
  - Gapless threading and fragment-based initialization
  - Multiple refinement passes for accuracy (~97.7% of US-align reference)

- High-level wrapper (src/mol-model/structure/structure/util/tm-align.ts)
  - tmAlign() function accepting StructureElement.Loci inputs
  - Returns transformation matrix, TM-scores, RMSD, and alignment

- BasicWrapper API (src/examples/basic-wrapper/)
  - tmAlign(pdbId1, chain1, pdbId2, chain2, color1?, color2?)
  - sequenceAlign() - sequence-based superposition
  - loadStructures() - load without alignment
  - Example HTML pages demonstrating usage

- UI integration (src/mol-plugin-ui/structure/superposition.tsx)
  - TM-align option in superposition panel

References:
Zhang Y, Skolnick J. Nucl Acids Res 33, 2302-9 (2005)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Delete src/examples/basic-wrapper/index.html

* changing reference test case

* Restoring src/examples/basic-wrapper/index.html

* Addressing comments in pull request

* Authorship added

---------

Co-authored-by: Diego del Alamo <diego.delalamo@gmail.com>
Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
 2025-12-19 13:18:11 +01:00
falko-apheris
2734d5754a Update example to use mol* v5 (#1673) 
Rename initViewer to initViewerAsync in documentation
 2025-10-16 19:14:12 +02:00
David Sehnal
4d7bd53231 Additional markdown commands (#1630) 2025-08-26 06:58:40 +02:00
David Sehnal
c11cf665c9 Additional markdown extensions (#1629) 
* additional markdown extensions

* fixes
 2025-08-25 20:12:10 +02:00
David Sehnal
b3e1e2900b Fix Markdown Commands query focus (#1626) 2025-08-24 13:18:36 +02:00
David Sehnal
fcbf39c935 Markdown & MVS: Audio support (#1621) 
* audio playback markdown commands

* trigger markdown commands from MVS primitives

* docs

* fix usage of mutative
 2025-08-22 16:00:30 +02:00
David Sehnal
dd11cacae4 Markdown Commands and MVS improvements (#1597) 
* add query command to markdown extensions

* fix typo

* better postprocessing param support in MVS

* molstar_mesh/label/line_params
 2025-08-02 18:19:01 +02:00
midlik
089148198f MVS operator_name (#1561) 
* Change symmetry operator naming

* MVS operator_name selector for inline component, color, label, tooltip

* MVS operator_name selector in annotations (component/color/label/tooltip_from_uri/source)

* Revert changes to operatorName, add canonicalOperatorName instead, rename MVS selector field operator_name -> instance_id

* Update CHANGELOG

* Remove polyfill.io in mkdocs

* MVS: MultilayerColorThemeName decide granularity smartly

* MVS: MultilayerColorThemeName refactor
 2025-07-11 20:45:22 +02:00
David Sehnal
146e95cb23 Snapshot Markdown Improvements (#1555) 
* basic markdown commands

* markdown renderers

* support markdown tables

* fix style

* indicate external links in markdown

* simplify the api

* load image from MVSX

* lint

* docs

* typo

* custom color palette support

* move manager to mol-plugin-state

* customize args parser

* better custom args parser support
 2025-07-04 10:29:03 +02:00
David Sehnal
13b1e5d59c Async Viewer Init (#1394) 
* async viewer init

* changelog

* tweak changelog

* make context init functions async
 2025-07-01 09:52:45 +02:00
dsehnal
56df6f82a7 docs tweak 2025-06-29 21:16:34 +02:00
David Sehnal
d409c4f5ea Fix SASS @import depraction warnings (#1534) 
* refactor SASS to not use @import

* changelog

* typo
 2025-06-08 09:33:39 +02:00
Sagar Pathak
b739876726 Update index.md (#1472) 
Fix command typo: changed 'npm build' to 'npm run build'
 2025-03-24 17:57:01 +01:00
David Sehnal
6e4065f779 Interactions extension (#1463) 
* move schema based element addressing from MVS to the core library

* proof of concept

* tweak

* initial visual

* tweak

* tweak structureElementLocationToSchemaItem

* show receptor residues as ball and stick

* wip data model

* custom interactions support

* add example

* wip visuals

* covalent links

* tweak

* fix bug

* cache unit features

* Add structureRef to Molecule.Structure.Selections

* optimize compute

* support multi-structure selections

* analyzeTrajectory support

* readme

* tweak

* headers

* docs

* Optimize StructureElementSchema & remove fromLoci conversion (not production ready for now, will be separate PR)

* move schema code to `StructureElement.Schema` and add fromExpression/Query/Schame functions to Loci and Bundle

* improve selection docs

* adjust covalent bond data model

* tweak fromExpression

* fix type

* remove hydrogen reference

* Fix MVS.rowsToExpression
 2025-03-17 09:25:18 +01:00
Ventura Rivera
e776138ecd fix hyperlink typo 2025-01-02 12:55:42 -08:00
David Sehnal
5cc28c9471 Add ModelWithCoordinates transform (#1378) 
* Add ModelWithCoordinates transform

* PR feedback
 2024-12-08 18:21:13 +01:00
midlik
ad1923f57b Servers object storage (#1355) 
* ModelServer: support for GS

* VolumeServer: simple support for GS

* fetch_GS abort

* file reorg

* ModelServer/VolumeServer: dynamic import @google-cloud/storage

* ModelServer/VolumeServer: update docs

* ModelServer/VolumeServer: handle HTTP and GS errors

* ModelServer/VolumeServer: update docs

* ModelServer/VolumeServer: update docs 2

* Minor tweaks
 2024-11-28 12:06:02 +01:00
Xavier M
c34aaf7c31 Add doc page to describe how to access component data (#1283) 2024-10-03 13:53:06 +02:00
dsehnal
e44e29eb9f using esbuild docs 2024-08-27 11:35:10 +02:00
Alexander Rose
2e7228f88b improve coarse-grained models handling 
- Add Zhang-Skolnick secondary-structure assignment method which handles coarse-grained models (#49)
- Calculate bonds for coarse-grained models
 2024-08-18 13:44:57 -07:00
Alexander Rose
b67f7271fc changelog & docs 2024-05-11 15:12:06 -07:00
Dušan Veľký
443fc9c60c Tunnels extension (#1105) 
* create algorithm

* create props

* create representation

* add examples

* add providers to index

* updated tunnel props

* updated tunnel transformers

* add interpolation and sampleRate

* rename tunnel example

* update examples

* add headers

* add author to contributors

* fix runVisualizeTunnel example

* add docs for tunnels extension

* create action to download tunnels

* add download tunnels to viewer

* fix description for shape provider

* update docs

* rename props to data-model

* rename transformers

* add headers

* add url to PluginConfig

* fix ChannelsDB type

* reimplement interpolation

* fix geometry condition

* remove fillFactor

* rename projectTunnel to index

* fix samplingRate

* remove fillFactor

* rename loci to highlight_label

* fix functions args

* create preset for structure tunnels

* rename ids

* change preset to show all tunnels

---------

Co-authored-by: Dušan Veľký <velky.dusko@gmail.com>
 2024-05-08 15:37:59 +02:00
David Sehnal
da9f5927d8 Merge docs from molstar/docs (#1090) 
* merge docs

* tweak actions
 2024-04-22 16:00:26 +02:00
midlik
d6b79de86d MVS docs reorganization (#1073) 2024-03-27 19:34:14 +01:00
midlik
32c3ef0801 MVS: OpenApi schema in docs (#1051) 2024-02-19 18:04:06 +01:00
midlik
46af7d03bf MVSX (#1041) 
* MVSX format provider

* MVS: Integration examples

* MVS: drag-and-drop support for MVSX

* MVS: support for URL param mvs-format=mvsx

* MVS: docs for MVSX

* MVS: mvs-render supports MVSX

* Update README
 2024-02-14 18:22:27 +01:00
midlik
f8bda3617f Mvs extension - yet another pull request (#1002) 
* MVS extension: support all X11 colors

* MVS extension: nicer validation messages for literal types

* MVS extension: no need to call HexColor in builder

* MVS extension: Support relative URIs

* MVS extension: docs

* MVS extension: docs - fix markdown

* MVS extension: docs

* MVS extension: docs for selectors

* MVS extension: docs for selectors

* Support for label rendering in HeadlessPluginContext

* MVS extension: CLI utils

* MVS extension: nicer component node labels

* MVS extension: labels applied in one node

* MVS extension: labels applied in one node - fixed label colors

* MVS extensions: removed unused params from "Custom Label"

---------

Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>
 2023-12-21 11:58:10 +01:00
midlik
c592a3b93d MVS extension - additional work (#991) 
* MVS extension: deterministic transform refs, updated metadata structure

* Perf-test for `sortIfNeeded`

* MVS extension: README

* MVS extension: show loading errors in the Mol* console

* MVS extension: auto-fix rotation matrix imprecisions

* MVS extension: data format provider

* MVS extension: Updated README

* MVS extension: rename deletePrevious -> replaceExisting, default to false in "Load MVS Data" to allow loading multiple files

* Perf-test for sortIfNeeded uses Benchmark.js
 2023-11-29 17:21:02 +01:00
midlik
b7b52f5c7d MVS extension (#976) 
* Moved MVS extension from mol-view-spec repo

* Viewer supports URL params mvs-url, mvs-data, mvs-format

* Tests

* MVS sanity checks

* MVS extension: drag-and-drop support

* mvs-render try1

* Example CLI utility mvs-render

* Example CLI utility mvs-validate

* MVS extension: renaming

* MVS extension: fixed FOV in mvs-render

* Moved stuff to mol-util/array.ts

* Moved stuff to mol-util/object.ts

* MVS extension: renamed `additions` to `components`

* MVS extension: trying plugin.managers.camera.focusSphere

* MVS extension: refactor focus

* MVS extension: fixed label color once again

* MVS extension: camera position adjustment (compensate FOV differences)

* Fixed formula for camera focus in orthographic mode

* Moved Choice to mol-util/param-choice.ts

* Moved stuff to mol-util/json.ts

* Object.hasOwn polyfill

* MVS extension: small refactor

* Fixed bug in hashString
 2023-11-24 14:38:08 +01:00
valasatava
649e779100 Add HYP to the list of amino acids (#815) 
* add modified amino acid "hydroxyproline" (HYP) present in collagen molecules to the list of amino acids

* update changelog
 2023-05-09 16:27:42 +02:00
midlik
315401c166 struct-conn extension (#802) 
* struct-conn extension toy example

* Minor changes (David's feedback)

* Showing struct_conn visuals

* Removed Interactions visual

* Caching struct_conns

* Removed testing buttons in index.html, updated CHANGELOG

* Addressed most of PR feedback

* Fixed structure node selection, docs

* Addressed feedback round 2
 2023-05-03 18:01:51 +02:00
Alexander Rose
a7ef0fb85f add interesting pdb entry 2022-05-05 22:41:16 -07:00
Alexander Rose
0df3bcd65d document supported file formats 2022-04-19 17:43:33 -07:00
Alexander Rose
90ad32d936 add ring example PDB IDs 2022-02-21 13:48:43 -08:00
Alexander Rose
ce1e3960a2 avoid standard polymers misqualified as ligands 
- overrule erroneous chem comp type in some files
 2021-12-18 12:13:36 -08:00
Alexander Rose
70fa85d7d4 fix assembly-symmetry off option 
- would not remove cage/axes visuals
 2021-05-28 23:04:08 -07:00
Alexander Rose
a2b4ed7c1c queries: add nos-bridge, improve disulfide-bridge 2021-05-09 13:56:40 -07:00
Alexander Rose
0bb376706d fix ellipsoid repr and support includeParent 
- switch off adjustCylinderLength
- handle structure with child
 2021-03-20 23:58:48 -07:00
Alexander Rose
2e561a8de7 added interesting pdb entry 2021-02-27 18:25:34 -08:00
Alexander Rose
7015309db6 added more interesting pdb entries 2021-01-16 11:37:48 -08:00
David Sehnal
89eae0807e docs fix 2020-07-06 15:13:13 +02:00
Alexander Rose
aa2899bfbd fix sequence label for non-standard residues, #70 2020-06-21 18:54:10 -07:00
Alexander Rose
3a737099ad add micro het todos and example pdb id 2020-06-01 17:49:47 -07:00
David Sehnal
422f4567f1 full commonjs build for servers and cli tools 2020-05-27 20:37:12 +02:00
Alexander Rose
2797b451fb add interesting pdb entries info 2020-05-22 17:10:03 -07:00
David Sehnal
e78cf18a38 separate build for servers 
- because of problems with ES6 modules (might revert later)
+ css tweaks
 2020-04-15 01:40:52 +02:00
David Sehnal
8f211a0785 servers readme tweak 2020-03-17 15:50:05 +01:00