Roadmap#

This page is public on purpose. It captures planning intent, not a set of commitments.

MolSysViewer — ROADMAP (Unified and Definitive)#

Last updated: 2025-11

This unified roadmap consolidates prior planning notes into a single place.

Phase 0 — Architecture Reset (Completed)#

Achievements#

  • Full migration away from legacy JupyterLab-extension code.

  • Adoption of anywidget for modern rendering.

  • Build system based on TypeScript + esbuild.

  • Full control of the Mol* runtime via initViewerAsync.

  • Corrected Mol* initialization sequencing.

  • Robust, asynchronous Python ↔ JavaScript messaging.

  • First working custom shapes (transparent spheres).

Phase 1 — Core Features (Active)#

1. Molecule Input#

  • [x] Load PDB/mmCIF strings

  • [x] Load from remote URLs

  • [ ] Load native MolSysMT systems

  • [ ] Load multi-frame trajectories

2. Shape System (v1)#

  • [x] Transparent sphere

  • [x] add_sphere() Python API

  • [x] add_spheres() vectorized API

  • [ ] Point primitives (billboards)

  • [ ] Arrows

  • [ ] Cylinders

  • [ ] Mesh loading

  • [ ] Text labels

3. Scene Management (v1)#

  • [ ] Object tagging (tag=)

  • [ ] viewer.clear(tag=...)

  • [ ] Camera utilities

  • [ ] Visibility toggles for custom objects

Phase 1.5 — Immediate Next Steps#

(Previously in NEXT_STEPS.md, now formalized)

Shape Grouping#

  • tag= parameter

  • Tag registry

  • clear(tag=...) implementation

New Shape Primitives#

  • Billboards / points

  • Arrows

  • Cylinders

  • Mesh importers

  • 3D labels

Camera Utilities#

  • center_on()

  • focus_on_sphere()

  • fit_to_bbox()

Rendering Engine Enhancements#

  • Vectorized add_spheres inside JS

  • Efficient multi-sphere representations

  • Internal shape manager (IDs, delete, visibility)

  • Debugging tools: logging, HUD text, performance stats

Phase 2 — Integration with the uibcdf Ecosystem#

TopoMT Integration#

  • [ ] Alpha-sphere rendering

  • [ ] Pocket surfaces

  • [ ] Cavity rims and mouth borders

  • [ ] Feature-based color schemes

PharmacophoreMT Integration#

  • [ ] Pharmacophoric spheres

  • [ ] Donor/acceptor arrow glyphs

  • [ ] Aromatic ring discs

  • [ ] Exclusion volumes

MolSysMT Integration#

  • [ ] Load MolSysMT systems directly

  • [ ] Shared selections/highlights

  • [ ] Trajectory stepping (previous, next, play, loop)

Phase 3 — UX / UI Enhancements#

  • [ ] Scene inspector panel

  • [ ] Prebuilt color palettes

  • [ ] Text overlays for annotations

  • [ ] Screenshot export

  • [ ] Scene serialization to JSON

Phase 4 — Structure Module#

Numerical Functions (get_*)#

  • [ ] Distances

  • [ ] Angles

  • [ ] Dihedrals

  • [ ] Neighbors / contacts

  • [ ] Radius of gyration

  • [ ] PCA

  • [ ] Transformations (rotate, center, align)

Visual Functions (show_*)#

  • [ ] Show distances

  • [ ] Show angles

  • [ ] Show dihedrals

  • [ ] Show neighbors

  • [ ] Show principal axes

Phase 5 — Hbonds & Topology Module#

Hydrogen Bonds#

  • [ ] get_hbonds()

  • [ ] show_hbonds()

Topology#

  • [ ] get_bonds()

  • [ ] show_bonds()

  • [ ] Integration with MolSysMT topology tools

Phase 6 — Advanced Shape Primitives#

  • [ ] Planes

  • [ ] Advanced meshes

  • [ ] Volumetric representations

  • [ ] Scalar fields (e.g., ESP, density)

Phase 7 — Engines & Performance#

Multi-Engine Support#

  • "molsysmt" (default scientific engine)

  • "molstar" (ultrafast mass distance operations)

  • "numpy"

  • "numba"

  • "cupy" (GPU acceleration, future)

Benchmarking Suite#

  • Load times

  • Render performance

  • Shape scalability

Phase 8 — Documentation, Tests & Demos#

  • Comprehensive tutorials

  • API reference

  • Example Jupyter notebooks

  • Integration with MolSysMT, TopoMT, PharmacophoreMT

  • Unit tests and visual tests

Long-Term Vision#

MolSysViewer aims to become the central visualization engine of the uibcdf ecosystem.

Legacy Notes#

(Useful concepts preserved from older roadmaps)

  • Scene inspector panel

  • Clipping planes

  • Regional highlighting

  • JS → Python callbacks

  • Animation systems (time-driven)

  • Volume rendering

Current Status (Summary)#

MolSysViewer stands on a solid, modern, extensible foundation and is ready to grow into a fully capable visualization and analysis platform.