Sagar Pathak
b739876726
Update index.md ( #1472 )
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Fix command typo: changed 'npm build' to 'npm run build'
2025-03-24 17:57:01 +01:00
David Sehnal
6e4065f779
Interactions extension ( #1463 )
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* 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 )
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* Add ModelWithCoordinates transform
* PR feedback
2024-12-08 18:21:13 +01:00
midlik
ad1923f57b
Servers object storage ( #1355 )
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* 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
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- 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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 )
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* 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
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- overrule erroneous chem comp type in some files
2021-12-18 12:13:36 -08:00
Alexander Rose
70fa85d7d4
fix assembly-symmetry off option
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- 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
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- 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
David Sehnal
94adf7259d
model and volume server configuration and docs
2020-03-17 14:46:28 +01:00
Alexander Rose
8603ef1a9b
renamed project from molstar-proto to molstar
2019-06-03 15:04:15 -07:00
David Sehnal
c03a35ae9b
state docs
2019-02-18 16:28:40 +01:00
Alexander Rose
62fda3e3e6
transformer docs tweaks
2019-02-11 10:30:28 -08:00
David Sehnal
ebaf0a2035
basic plugin state docs
2019-02-10 21:03:21 +01:00
David Sehnal
917fc2e14c
auto-generate transformer docs
2019-02-09 20:38:19 +01:00
David Sehnal
07ee6646a1
model-server docs tweak
2018-10-11 14:43:54 +02:00
David Sehnal
5c9065469b
model-server: basic documentation
2018-10-03 14:06:04 +02:00
David Sehnal
88c9248c3f
Added VolumeServer
2018-05-22 17:45:15 +02:00
David Sehnal
6d59213c9d
Tweaks
2017-11-02 20:12:53 +01:00
David Sehnal
23ebae54ae
Naming CIF things
2017-10-16 01:11:26 +02:00
David Sehnal
28b55d95e5
cif schema docs tweaks
2017-10-14 15:10:19 +02:00
David Sehnal
050edf26e1
tweaked docs
2017-10-14 10:57:43 +02:00
David Sehnal
c2a140b7a2
docs about how CIF schemas work
2017-10-14 10:40:26 +02:00
