mirror of
https://github.com/molstar/molstar.git
synced 2026-06-04 21:34:23 +08:00
27af73f97f
* 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>
66 lines
2.2 KiB
YAML
66 lines
2.2 KiB
YAML
site_name: Mol* Developer Documentation
|
|
theme:
|
|
name: material
|
|
|
|
# 404 page
|
|
static_templates:
|
|
- 404.html
|
|
|
|
# Necessary for search to work properly
|
|
include_search_page: false
|
|
search_index_only: true
|
|
|
|
# Default values, taken from mkdocs_theme.yml
|
|
language: en
|
|
font:
|
|
text: Roboto
|
|
code: Roboto Mono
|
|
favicon: assets/favicon.png
|
|
icon:
|
|
logo: logo
|
|
markdown_extensions:
|
|
- pymdownx.highlight
|
|
- pymdownx.superfences
|
|
- pymdownx.arithmatex:
|
|
generic: true
|
|
# Scripts for rendering Latex equations (in addition to pymdownx.arithmatex):
|
|
extra_javascript:
|
|
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
|
|
nav:
|
|
- 'index.md'
|
|
- Plugin:
|
|
- Creating Instance: 'plugin/instance.md'
|
|
- Examples: plugin/examples.md
|
|
- Custom Library: 'plugin/custom-library.md'
|
|
- Selections: 'plugin/selections.md'
|
|
- Superposition: 'plugin/superposition.md'
|
|
- Viewer State: 'plugin/viewer-state.md'
|
|
- Data State: 'plugin/data-state.md'
|
|
- File Formats: 'plugin/file-formats.md'
|
|
- CIF Schemas: 'plugin/cif-schemas.md'
|
|
- Managers:
|
|
- Markdown Extensions: 'plugin/managers/markdown-extensions.md'
|
|
- State Transforms:
|
|
- Custom Trajectory: 'plugin/transforms/custom-trajectory.md'
|
|
- Custom Conformation: 'plugin/transforms/custom-conformation.md'
|
|
- Data Access Tools:
|
|
- 'data-access-tools/model-server.md'
|
|
- Volume Server:
|
|
- Overview: 'data-access-tools/volume-server/index.md'
|
|
- Examples: 'data-access-tools/volume-server/examples.md'
|
|
- How it Works: 'data-access-tools/volume-server/how-it-works.md'
|
|
- Data Format: 'data-access-tools/volume-server/response-data-format.md'
|
|
- 'data-access-tools/plugin-state-server.md'
|
|
- 'data-access-tools/convert-to-bcif.md'
|
|
- 'data-access-tools/create-ccd-table.md'
|
|
- 'data-access-tools/extract-ccd-ions.md'
|
|
- Extensions:
|
|
- MolViewSpec: 'extensions/mvs/index.md'
|
|
- wwPDB StructConn: 'extensions/struct-conn.md'
|
|
- Tunnels: 'extensions/tunnels.md'
|
|
- Interactions: 'extensions/interactions.md'
|
|
- Misc:
|
|
- Interesting PDB entries: misc/interesting-pdb-entries.md
|
|
- Exporting component data: misc/exporting-components.md
|
|
repo_url: https://github.com/molstar/docs
|