dsehnal
ea07cd89de
better canvas background handling
2025-12-21 16:15:56 +01:00
dsehnal
a7330f40d7
MVS getCurrentMVSSnapshot util
2025-12-21 15:38:57 +01:00
David Sehnal
c21ba08fc7
Viewer improvements ( #1725 )
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* 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
Alexander Rose
3133dc1543
Fix flipSided for meshes
2025-12-20 13:55:06 -08:00
ddelalamo-takeda
27af73f97f
Add TM-align structure alignment algorithm ( #1723 )
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* 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
Lukas Polak
e9a442ca6e
Add Residue Charge color scheme ( #1722 )
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* Add charged residue color scheme
* Changelog + file header
* Address PR comments
* Remove residue-name.ts contribution info
* PR suggestion
* Changelog reference PR
2025-12-19 13:15:51 +01:00
Alexander Rose
e86e282bb4
Fix missing gl.flush for async picking
2025-12-16 21:24:23 -08:00
Alexander Rose
213506dff0
Fix program not compiled for sync picking
2025-12-16 21:23:22 -08:00
Alexander Rose
bc7aa7c9aa
Fix webgl1 shader syntax
2025-12-16 21:21:58 -08:00
Alexander Rose
b234bf8890
Fix molecular-surface when probe diameter smaller then resolution
2025-12-14 10:30:21 -08:00
Alexander Rose
36b4dcf7a8
Fix molecular-surface "auto" quality params not hidden
2025-12-13 22:07:11 -08:00
Alexander Rose
ecaf19c5fb
changelog
2025-12-07 10:59:26 -08:00
Alexander Rose
a0f7349ef6
reduce automatic quality on standalone HMD devices
2025-12-06 10:50:00 -08:00
Alexander Rose
3dee03d9b6
cleanup & changelog
2025-12-06 10:26:59 -08:00
giagitom
c1ba5248b0
postprocessing improvements
2025-12-04 16:06:30 +01:00
Alexander Rose
1ecb960b82
changelog
2025-11-16 10:17:14 -08:00
Alexander Rose
387d59f97b
Merge branch 'master' of https://github.com/molstar/molstar
2025-11-16 10:13:12 -08:00
Alexander Rose
5eaa73d56d
changelog
2025-11-16 10:11:07 -08:00
Alexander Rose
b9428fd3cd
Merge pull request #1708 from molstar/volume-improvements
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Volume improvements
2025-11-16 10:10:11 -08:00
David Sehnal
d11aa6ea77
improve guessCifVariant ( #1709 )
2025-11-16 17:53:16 +01:00
Alexander Rose
98049ed02d
Merge branch 'master' of https://github.com/molstar/molstar into volume-improvements
2025-11-15 16:25:44 -08:00
Alexander Rose
e96157c890
changelog
2025-11-15 16:19:40 -08:00
Alexander Rose
ad2b5e687d
Volume improvements
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- Add `Volume.periodicity`
- Wrap isosurfaces for periodic volumes
- Fix dimensions for slices
2025-11-15 16:09:47 -08:00
Alexander Rose
bccc68f6df
Merge branch 'master' of https://github.com/molstar/molstar into pr/midlik/1701
2025-11-15 09:06:55 -08:00
Alexander Rose
2b4741c8ee
Use PluginCommands to set canvas3d props in camera behavior
2025-11-15 08:52:25 -08:00
Alexander Rose
7960ee06d4
Fix default trackball animated spin speed
2025-11-15 08:50:24 -08:00
Alexander Rose
f73f5af131
Fix direct-volume not drawn in illumination mode
2025-11-15 08:48:22 -08:00
midlik
154063638d
MVS: Allow canvas background interpolation ( #1704 )
2025-11-13 12:02:10 +01:00
midlik
a720b98365
MVS transformed primitives ( #1705 )
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* MVS: Fix primitives in root not being transformed with reference structure
* MultilayerColorTheme only preferSmoothing when a nested theme prefers
* MVSAnnotationColorTheme do not prefer smoothing
* Update file header
2025-11-11 16:47:35 +01:00
Adam Midlik
d4a2937e0b
Merge branch 'master' into bounding-spheres
2025-11-11 15:39:20 +00:00
midlik
b0ca7ffbb7
Fix all-selector color not applying on substructure ( #1700 )
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* Fix all-selector color not applying on substructure
* Fix CHANGELOG
* Size uniform computed from the first included location
2025-11-11 10:32:01 +01:00
David Sehnal
c42b738abe
MVS: Fix appendSnapshots when loading MVSX ( #1702 )
2025-11-11 10:31:06 +01:00
Alexander Rose
8d96131962
changelog
2025-11-09 17:49:27 -08:00
Alexander Rose
95bbcd8b24
Merge branch 'master' of https://github.com/molstar/molstar into pr/midlik/1697
2025-11-09 17:49:06 -08:00
Alexander Rose
a21f5c2c23
Add viewport button to toggle illumination mode
2025-11-09 16:45:26 -08:00
Adam Midlik
94b7b1281c
Merge branch 'master' into bounding-spheres
2025-11-07 10:19:00 +00:00
Adam Midlik
16dba586df
Relax camera limits to allow focusing any selection with >1 atom
2025-11-07 10:13:39 +00:00
midlik
72b761f959
Fix ugly camera clipping in snapshot transitions ( #1699 )
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* Fix ugly camera clipping in snapshot transitions
* Update CHANGELOG.md
---------
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com >
2025-11-06 16:04:20 +01:00
Adam Midlik
943d81cbf9
Fix bounding sphere computation for 3D text
2025-11-06 09:28:09 +00:00
dsehnal
dccfd35c7a
changelog
2025-11-05 14:39:06 +01:00
Dominik Andrew Tichy
9e81a4f7a6
fix: validation and default params for primitives_from_uri ( #1690 )
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* fix: primitives default param values
* chore: changelog
---------
Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com >
2025-11-05 14:37:00 +01:00
David Sehnal
c248ae11bf
fix wheel scrolling edge case ( #1696 )
2025-11-05 13:27:14 +01:00
David Sehnal
1cb617524d
MVS: Fix coarse structure selection ( #1694 )
2025-11-04 23:07:47 +01:00
David Sehnal
e2e348240b
MVS: topology format support ( #1691 )
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* MVS: topology format support
* bugfix
* mvs: additional coordinate formats
* fix
2025-11-04 22:16:49 +01:00
Alexander Rose
b54908492c
Add Canvas3D.setAttribs
2025-11-03 23:52:26 -08:00
dsehnal
33172862bd
mvs stories loading message
2025-11-02 14:07:52 +01:00
dsehnal
66f5a81a5d
changelog
2025-10-31 17:25:24 +01:00
David Sehnal
9e90e11bfc
MVS Improvements ( #1684 )
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* MVS primitives clipping
* camera near distance
2025-10-31 16:43:59 +01:00
midlik
ab372a89d6
MVS: fix persisting tooltips and other fixes ( #1688 )
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* MVS: Fix tooltips persisting across snapshots
* MVS: Fix CIF annotations with no selector columns being ignored
* Vec3.orthogonalize handle special cases (fixes trackpad lock in MVS)
* Update CHANGELOG
2025-10-31 14:35:56 +01:00
David Sehnal
c6506d515f
Fix CIF Parser edge case ( #1687 )
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* Fix CIF Parser edge case
* header
2025-10-28 15:02:35 +01:00
