David Koes
c26e390544
version bump
2026-05-22 11:33:04 -04:00
David Koes
392faa7c65
Merge pull request #852 from dxdc/aromatic-bonds-feature
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Aromatic ring rendering, per-bond style overrides, and SDF embedded styling
2026-02-28 12:10:33 -05:00
Daniel Caspi
98c3b746e9
fix: prevent crash when frames lack 3DMOL_STYLE blocks
2026-02-27 01:23:29 -06:00
Daniel Caspi
2d0796f810
feat: add aromaticStyle option with torus rendering for aromatic rings
2026-02-26 23:00:22 -06:00
Daniel Caspi
fe6c8d2472
test: add tests for ring dashed bonds, SDF style parsing, and V3000
2026-02-26 22:22:29 -06:00
Daniel Caspi
ab2b879cd6
feat: per-bond style overrides and DRY draw helpers
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Add support for per-bond style configuration via bondStyles, enabling
fine-grained control over individual bond appearance from SDF 3DMOL_STYLE
or programmatic use.
Per-bond overrides (via bondStyles[].dashedBondConfig):
- solidColor / dashedColor: override colors for solid and dashed halves
- dashLength / gapLength: override dash geometry per bond
- dashedBondFlip: force which side gets the dashed line
2026-02-26 22:22:29 -06:00
Daniel Caspi
148e42461f
feat: ring-aware dashed bond placement
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Use ring detection to place the dashed portion of aromatic bonds toward
the ring interior, matching standard chemical drawing conventions.
For bonds in rings, a BFS finds the smallest ring containing the bond
and computes its centroid to determine which side gets the dashed line.
Non-ring bonds fall back to the existing neighbor centroid heuristic.
This replaces the previous approach that used only neighbor positions,
which could place dashes on the wrong side for fused ring systems or
asymmetric substituent patterns.
2026-02-26 16:17:08 -06:00
Daniel Caspi
2586225517
fix: align frame indices with modelDatas and apply embedded styles
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When addMolData skips empty frames, the modelDatas array (populated by
3DMOL_STYLE parsing in the SDF parser) would get out of sync with
this.frames because empty-frame compaction only affected frames but not
modelDatas.
Fix by building frames and modelDatas in a single pass so their indices
stay aligned. After loading, apply any embedded 3DMOL_STYLE model-level
styles (e.g. stick radius) to the corresponding frames via setStyle.
2026-02-26 16:17:08 -06:00
Daniel Caspi
309d3dbf72
feat: add 3DMOL_STYLE SDF property parsing and parser modernization
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Add support for embedding per-bond and model-level styling in SDF files
via a `3DMOL_STYLE` data property block. This enables fine-grained bond
appearance control (colors, dashed bond config, flip) directly from
chemical structure files.
2026-02-26 16:17:08 -06:00
David Koes
8bb2f598a0
Merge pull request #850 from utkarshasinha/fix-hidden-hover-callback
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fix: skip hover callbacks for hidden objects
2026-02-12 21:10:41 -05:00
utkarshasinha
a99358b345
fix: skip hover callbacks for hidden objects
2026-02-12 20:48:56 +05:30
David Koes
b9f8c3f24b
Merge pull request #848 from dxdc/patch-4
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Refactor bond drawing colors for consistency
2026-02-02 21:57:24 -05:00
Daniel Caspi
229914b482
Refactor bond drawing colors for consistency
2026-02-02 15:37:07 -06:00
David Koes
0ca1bd2ceb
Merge pull request #847 from dxdc/dashed-bonds-fix-2
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Fix dashed bond side flipping during animation
2026-01-31 13:31:03 -05:00
Daniel Caspi
2242f1bb48
fix: stabilize dashed bond side selection across conformations
2026-01-31 00:20:52 -06:00
David Koes
04a0849b13
Merge pull request #846 from dxdc/dashed-bonds-fix
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fix: center dashed bonds
2026-01-24 20:07:43 -05:00
Daniel Caspi
8e3f3d67f2
fix: center dashed bonds
2026-01-23 16:33:35 -06:00
David Koes
0c54f7570f
fallback on bcif failure for mmtf type too
2026-01-21 20:53:25 -05:00
David Koes
341ff319a3
packagelock
2026-01-21 20:24:43 -05:00
David Koes
b65f8e62d3
version bump
2026-01-21 17:55:44 -05:00
David Koes
6784a97d00
updated versions
2026-01-21 16:57:02 -05:00
David Koes
f833fe94cb
Merge branch 'dxdc-patch-3'
2026-01-21 16:46:08 -05:00
David Koes
e1ee2640d7
update img, packge.json
2026-01-21 16:45:41 -05:00
David Koes
eb0a5523be
Merge branch 'patch-3' of https://github.com/dxdc/3Dmol.js into dxdc-patch-3
2026-01-21 16:06:15 -05:00
Daniel Caspi
9c9a07283b
Update color variables for dashed bonds
2026-01-21 15:03:03 -06:00
David Koes
29cc020664
Merge branch 'patch-3' of https://github.com/dxdc/3Dmol.js into dxdc-patch-3
2026-01-21 15:17:03 -05:00
Daniel Caspi
69f4a01f6f
Update GLModel.ts
2026-01-20 15:54:56 -06:00
Daniel Caspi
c523665d8f
Update GLModel.ts
2026-01-20 15:52:17 -06:00
Daniel Caspi
b5667441d7
make calculateDashes safe (no divide-by-zero)
2026-01-20 15:34:07 -06:00
Daniel Caspi
1cc849ebe2
Refactor bond rendering logic in GLModel.ts
2026-01-20 15:24:34 -06:00
Daniel Caspi
aff893e4ad
Refactor bond rendering for aromatic bond types
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Updated bond rendering logic to handle aromatic bonds as 1.5.
2026-01-20 15:17:36 -06:00
David Koes
1db415155e
Merge branch 'master' of github.com:3dmol/3Dmol.js
2026-01-05 15:26:16 -05:00
David Koes
d1cf3ba01f
Merge pull request #842 from dxdc/dashed-bonds-2
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Aromatic/dashed bond order rendering #455
2026-01-05 15:25:57 -05:00
Daniel Caspi
02c2e22e26
Revert "chore: enable capture-missing in glcheck"
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This reverts commit 4bb39f2153
2026-01-03 01:48:59 -06:00
David Koes
6f65d9b969
edit for newer python
2026-01-02 21:45:41 -05:00
David Koes
fa5be597f1
Merge branch 'master' of github.com:3dmol/3Dmol.js
2026-01-02 21:45:17 -05:00
Daniel Caspi
0442ec46cc
fix: double-bond behavior
2025-12-31 21:32:11 -06:00
Daniel Caspi
2d86862b7d
test: add visual tests for partial bonds
2025-12-31 15:02:59 -06:00
Daniel Caspi
4bb39f2153
chore: enable capture-missing in glcheck
2025-12-31 15:02:59 -06:00
Daniel Caspi
f0ba78b373
treat aromatic bond type (4) as 1.5 for rendering
2025-12-31 15:02:59 -06:00
Daniel Caspi
8d32b76466
feat: add aromatic bond rendering support
2025-12-31 15:02:59 -06:00
dkoes
5bc6441492
better doc ex
2025-10-05 13:35:47 -04:00
David Koes
5f28e11ebf
version bump
2025-09-27 13:27:48 -04:00
David Koes
73e5b67138
Merge branch 'master' of github.com:3dmol/3Dmol.js
2025-09-25 22:55:17 -04:00
David Koes
c433379854
Guard calls to this._gl.drawingBufferWidth with isLost check.
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Skipping these guards can cause problems in colab (apparently, Issue
2025-09-25 22:53:40 -04:00
David Koes
77c5fbdc32
version bump
2025-07-30 12:18:42 -04:00
David Koes
e9465f52c0
test for Issue #835
2025-07-30 12:03:59 -04:00
David Koes
d43797ca11
Fix Issue #835
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Hidden shapes should not be tested for click/hover interactions.
2025-07-30 11:49:42 -04:00
David Koes
de204a682d
Fix Issue #745
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Don't show viewers with no pixels.
2025-07-30 10:48:17 -04:00
David Koes
f393cdeb4f
version bump
2025-06-26 11:23:11 -04:00
