molstar 2.3.2 → 2.3.7

package/CHANGELOG.md

@@ -1,160 +1,191 @@
-# Change Log
-All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/) for its most widely used - and defacto - public interfaces.
-
-Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
-
-
-## [Unreleased]
-
-## [v2.3.2] - 2021-10-01
-
-- Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.
-
-
-## [v2.3.1] - 2021-09-28
-
-- Add Charmm saccharide names
-- Treat missing occupancy column as occupany of 1
-- Fix line shader not accounting for aspect ratio
-- [Breaking] Fix point repr & shader
-    - Was unusable with ``wboit``
-    - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
-    - Set ``pointSizeAttenuation`` to false by default
-    - Set ``sizeTheme`` to ``uniform`` by default
-- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
-- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
-- Model and VolumeServer: fix argparse config
-
-## [v2.3.0] - 2021-09-06
-
-- Take include/exclude flags into account when displaying aromatic bonds
-- Improve marking performance
-    - Avoid unnecessary draw calls/ui updates when marking
-    - Check if loci is superset of visual
-    - Check if loci overlaps with unit visual
-    - Ensure ``Interval`` is used for ranges instead of ``SortedArray``
-    - Add uniform marker type
-    - Special case for reversing previous mark
-- Add optional marking pass
-    - Outlines visible and hidden parts of highlighted/selected groups
-    - Add highlightStrength/selectStrength renderer params
-
-## [v2.2.3] - 2021-08-25
-
-- Add ``invertCantorPairing`` helper function
-- Add ``Mesh`` processing helper ``.smoothEdges``
-- Smooth border of molecular-surface with ``includeParent`` enabled
-- Hide ``includeParent`` option from gaussian-surface visuals (not particularly useful)
-- Improved ``StructureElement.Loci.size`` performance (for marking large cellpack models)
-- Fix new ``TransformData`` issues (camera/bounding helper not showing up)
-- Improve marking performance (avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``)
-
-## [v2.2.2] - 2021-08-11
-
-- Fix ``TransformData`` issues [#133](https://github.com/molstar/molstar/issues/133)
-- Fix ``mol-script`` query compiler const expression recognition.
-
-## [v2.2.1] - 2021-08-02
-
-- Add surrounding atoms (5 Angstrom) structure selection query
-- [Breaking] Add maxDistance prop to ``IndexPairBonds``
-- Fix coordinateSystem not handled in ``Structure.asParent``
-- Add ``dynamicBonds`` to ``Structure`` props (force re-calc on model change)
-    - Expose as optional param in root structure transform helper
-- Add overpaint support to geometry exporters
-- ``InputObserver`` improvements
-  - normalize wheel speed across browsers/platforms
-  - support Safari gestures (used by ``TrackballControls``)
-  - ``PinchInput.fractionDelta`` and use it in ``TrackballControls``
-
-## [v2.2.0] - 2021-07-31
-
-- Add ``tubularHelices`` parameter to Cartoon representation
-- Add ``SdfFormat`` and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
-- Fix mononucleotides detected as polymer components (#229)
-- Set default outline scale back to 1
-- Improved DCD reader cell angle handling (interpret near 0 angles as 90 deg)
-- Handle more residue/atom names commonly used in force-fields
-- Add USDZ support to ``geo-export`` extension.
-- Fix ``includeParent`` support for multi-instance bond visuals.
-- Add ``operator`` Loci granularity, selecting everything with the same operator name.
-- Prefer ``_label_seq_id`` fields in secondary structure assignment.
-- Support new EMDB API (https://www.ebi.ac.uk/emdb/api/entry/map/[EMBD-ID]) for EM volume contour levels.
-- ``Canvas3D`` tweaks:
-    - Update ``forceDraw`` logic.
-    - Ensure the scene is re-rendered when viewport size changes.
-    - Support ``noDraw`` mode in ``PluginAnimationLoop``.
-
-## [v2.1.0] - 2021-07-05
-
-- Add parameter for to display aromatic bonds as dashes next to solid cylinder/line.
-- Add backbone representation
-- Fix outline in orthographic mode and set default scale to 2.
-
-## [v2.0.7] - 2021-06-23
-
-- Add ability to specify ``volumeIndex`` in ``Viewer.loadVolumeFromUrl`` to better support Volume Server inputs.
-- Support in-place reordering for trajectory ``Frame.x/y/z`` arrays for better memory efficiency.
-- Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).
-
-## [v2.0.6] - 2021-06-01
-
-- Add glTF (GLB) and STL support to ``geo-export`` extension.
-- Protein crosslink improvements
-    - Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
-    - Added NOS-bridges query & improved disulfide-bridges query
-- Fix #178: ``IndexPairBonds`` for non-single residue structures (bug due to atom reordering).
-- Add volumetric color smoothing for MolecularSurface and GaussianSurface representations (#173)
-- Fix nested 3d grid lookup that caused results being overwritten in non-covalent interactions computation.
-- Basic implementation of ``BestDatabaseSequenceMapping`` (parse from CIF, color theme, superposition).
-- Add atom id ranges support to Selection UI.
-
-## [v2.0.5] - 2021-04-26
-
-- Ability to pass ``Canvas3DContext`` to ``PluginContext.fromCanvas``.
-- Relative frame support for ``Canvas3D`` viewport.
-- Fix bug in screenshot copy UI.
-- Add ability to select residues from a list of identifiers to the Selection UI.
-- Fix SSAO bugs when used with ``Canvas3D`` viewport.
-- Support for  full pausing (no draw) rendering: ``Canvas3D.pause(true)``.
-- Add ``MeshBuilder.addMesh``.
-- Add ``Torus`` primitive.
-- Lazy volume loading support.
-- [Breaking] ``Viewer.loadVolumeFromUrl`` signature change.
-    - ``loadVolumeFromUrl(url, format, isBinary, isovalues, entryId)`` => ``loadVolumeFromUrl({ url, format, isBinary }, isovalues, { entryId, isLazy })``
-- Add ``TextureMesh`` support to ``geo-export`` extension.
-
-## [v2.0.4] - 2021-04-20
-
-- [WIP] Mesh export extension
-- ``Structure.eachAtomicHierarchyElement`` (#161)
-- Fixed reading multi-line values in SDF format
-- Fixed Measurements UI labels (#166)
-
-## [v2.0.3] - 2021-04-09
-### Added
-- Support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
-
-### Changed
-- [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
-- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
-
-## [v2.0.2] - 2021-03-29
-### Added
-- ``Canvas3D.getRenderObjects``.
-- [WIP] Animate state interpolating, including model trajectories
-
-### Changed
-- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
-
-### Fixed
-- VolumeFromDensityServerCif transform label
-
-
-## [v2.0.1] - 2021-03-23
-### Fixed
-- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
-
-
-## [v2.0.0] - 2021-03-23
-Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.
+# Change Log
+All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/) for its most widely used - and defacto - public interfaces.
+
+Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
+
+
+## [Unreleased]
+
+- Added ``ViewerOptions.collapseRightPanel``
+- Added ``Viewer.loadTrajectory`` to support loading "composed" trajectories (e.g. from gro + xtc)
+- Fix: handle parent in Structure.remapModel
+- Add ``rounded`` and ``square`` helix profile options to Cartoon representation (in addition to the default ``elliptical``)
+
+## [v2.3.6] - 2021-11-8
+
+- Add additional measurement controls: orientation (box, axes, ellipsoid) & plane (best fit)
+- Improve aromatic bond visuals (add ``aromaticScale``, ``aromaticSpacing``, ``aromaticDashCount`` params)
+- [Breaking] Change ``adjustCylinderLength`` default to ``false`` (set to true for focus representation)
+- Fix marker highlight color overriding select color
+- CellPack extension update
+    - add binary model support
+    - add compartment (including membrane) geometry support
+    - add latest mycoplasma model example
+- Prefer WebGL1 in Safari 15.1.
+
+## [v2.3.5] - 2021-10-19
+
+- Fix sequence viewer for PDB files with COMPND record and multichain entities.
+- Fix index pair bonds order assignment
+
+## [v2.3.4] - 2021-10-12
+
+- Fix pickScale not taken into account in line/point shader
+- Add pixel-scale, pick-scale & pick-padding GET params to Viewer app
+- Fix selecting bonds not adding their atoms in selection manager
+- Add ``preferAtoms`` option to SelectLoci/HighlightLoci behaviors
+- Make the implicit atoms of bond visuals pickable
+    - Add ``preferAtomPixelPadding`` to Canvas3dInteractionHelper
+- Add points & crosses visuals to Line representation
+- Add ``pickPadding`` config option (look around in case target pixel is empty)
+- Add ``multipleBonds`` param to bond visuals with options: off, symmetric, offset
+- Fix ``argparse`` config in servers.
+
+## [v2.3.3] - 2021-10-01
+
+- Fix direct volume shader
+
+## [v2.3.2] - 2021-10-01
+
+- Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.
+
+## [v2.3.1] - 2021-09-28
+
+- Add Charmm saccharide names
+- Treat missing occupancy column as occupancy of 1
+- Fix line shader not accounting for aspect ratio
+- [Breaking] Fix point repr & shader
+    - Was unusable with ``wboit``
+    - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
+    - Set ``pointSizeAttenuation`` to false by default
+    - Set ``sizeTheme`` to ``uniform`` by default
+- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
+- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
+- Model and VolumeServer: fix argparse config
+
+## [v2.3.0] - 2021-09-06
+
+- Take include/exclude flags into account when displaying aromatic bonds
+- Improve marking performance
+    - Avoid unnecessary draw calls/ui updates when marking
+    - Check if loci is superset of visual
+    - Check if loci overlaps with unit visual
+    - Ensure ``Interval`` is used for ranges instead of ``SortedArray``
+    - Add uniform marker type
+    - Special case for reversing previous mark
+- Add optional marking pass
+    - Outlines visible and hidden parts of highlighted/selected groups
+    - Add highlightStrength/selectStrength renderer params
+
+## [v2.2.3] - 2021-08-25
+
+- Add ``invertCantorPairing`` helper function
+- Add ``Mesh`` processing helper ``.smoothEdges``
+- Smooth border of molecular-surface with ``includeParent`` enabled
+- Hide ``includeParent`` option from gaussian-surface visuals (not particularly useful)
+- Improved ``StructureElement.Loci.size`` performance (for marking large cellpack models)
+- Fix new ``TransformData`` issues (camera/bounding helper not showing up)
+- Improve marking performance (avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``)
+
+## [v2.2.2] - 2021-08-11
+
+- Fix ``TransformData`` issues [#133](https://github.com/molstar/molstar/issues/133)
+- Fix ``mol-script`` query compiler const expression recognition.
+
+## [v2.2.1] - 2021-08-02
+
+- Add surrounding atoms (5 Angstrom) structure selection query
+- [Breaking] Add maxDistance prop to ``IndexPairBonds``
+- Fix coordinateSystem not handled in ``Structure.asParent``
+- Add ``dynamicBonds`` to ``Structure`` props (force re-calc on model change)
+    - Expose as optional param in root structure transform helper
+- Add overpaint support to geometry exporters
+- ``InputObserver`` improvements
+  - normalize wheel speed across browsers/platforms
+  - support Safari gestures (used by ``TrackballControls``)
+  - ``PinchInput.fractionDelta`` and use it in ``TrackballControls``
+
+## [v2.2.0] - 2021-07-31
+
+- Add ``tubularHelices`` parameter to Cartoon representation
+- Add ``SdfFormat`` and update SDF parser to be able to parse data headers according to spec (hopefully :)) #230
+- Fix mononucleotides detected as polymer components (#229)
+- Set default outline scale back to 1
+- Improved DCD reader cell angle handling (interpret near 0 angles as 90 deg)
+- Handle more residue/atom names commonly used in force-fields
+- Add USDZ support to ``geo-export`` extension.
+- Fix ``includeParent`` support for multi-instance bond visuals.
+- Add ``operator`` Loci granularity, selecting everything with the same operator name.
+- Prefer ``_label_seq_id`` fields in secondary structure assignment.
+- Support new EMDB API (https://www.ebi.ac.uk/emdb/api/entry/map/[EMBD-ID]) for EM volume contour levels.
+- ``Canvas3D`` tweaks:
+    - Update ``forceDraw`` logic.
+    - Ensure the scene is re-rendered when viewport size changes.
+    - Support ``noDraw`` mode in ``PluginAnimationLoop``.
+
+## [v2.1.0] - 2021-07-05
+
+- Add parameter for to display aromatic bonds as dashes next to solid cylinder/line.
+- Add backbone representation
+- Fix outline in orthographic mode and set default scale to 2.
+
+## [v2.0.7] - 2021-06-23
+
+- Add ability to specify ``volumeIndex`` in ``Viewer.loadVolumeFromUrl`` to better support Volume Server inputs.
+- Support in-place reordering for trajectory ``Frame.x/y/z`` arrays for better memory efficiency.
+- Fixed text CIF encoder edge cases (most notably single whitespace not being escaped).
+
+## [v2.0.6] - 2021-06-01
+
+- Add glTF (GLB) and STL support to ``geo-export`` extension.
+- Protein crosslink improvements
+    - Change O-S bond distance to allow for NOS bridges (doi:10.1038/s41586-021-03513-3)
+    - Added NOS-bridges query & improved disulfide-bridges query
+- Fix #178: ``IndexPairBonds`` for non-single residue structures (bug due to atom reordering).
+- Add volumetric color smoothing for MolecularSurface and GaussianSurface representations (#173)
+- Fix nested 3d grid lookup that caused results being overwritten in non-covalent interactions computation.
+- Basic implementation of ``BestDatabaseSequenceMapping`` (parse from CIF, color theme, superposition).
+- Add atom id ranges support to Selection UI.
+
+## [v2.0.5] - 2021-04-26
+
+- Ability to pass ``Canvas3DContext`` to ``PluginContext.fromCanvas``.
+- Relative frame support for ``Canvas3D`` viewport.
+- Fix bug in screenshot copy UI.
+- Add ability to select residues from a list of identifiers to the Selection UI.
+- Fix SSAO bugs when used with ``Canvas3D`` viewport.
+- Support for  full pausing (no draw) rendering: ``Canvas3D.pause(true)``.
+- Add ``MeshBuilder.addMesh``.
+- Add ``Torus`` primitive.
+- Lazy volume loading support.
+- [Breaking] ``Viewer.loadVolumeFromUrl`` signature change.
+    - ``loadVolumeFromUrl(url, format, isBinary, isovalues, entryId)`` => ``loadVolumeFromUrl({ url, format, isBinary }, isovalues, { entryId, isLazy })``
+- Add ``TextureMesh`` support to ``geo-export`` extension.
+
+## [v2.0.4] - 2021-04-20
+
+- [WIP] Mesh export extension
+- ``Structure.eachAtomicHierarchyElement`` (#161)
+- Fixed reading multi-line values in SDF format
+- Fixed Measurements UI labels (#166)
+
+## [v2.0.3] - 2021-04-09
+
+- Add support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
+- [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
+- [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.
+
+## [v2.0.2] - 2021-03-29
+
+- Add ``Canvas3D.getRenderObjects``.
+- [WIP] Animate state interpolating, including model trajectories
+- Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
+- Fix VolumeFromDensityServerCif transform label
+
+## [v2.0.1] - 2021-03-23
+
+- Exclude tsconfig.commonjs.tsbuildinfo from npm bundle
+
+## [v2.0.0] - 2021-03-23
+
+Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.

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.