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Trim the hit/snap row back to a name Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Document the 4.7 .pmeraw guard and the renamed 2D hit/snap setting Opening a .pmeraw file now always asks for confirmation (Cancel is the default) because the format is a pickle, and Ctrl+S on a file opened from .pmeraw redirects to Save As instead of writing the pickle back. Covered in the user manual, the file-format reference and the shortcut table. The 2D settings table also gets the setting's 4.7.0 name, Atom Hit / Snap Distance, and what it actually controls beyond bond snapping. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Document the user template's first atom Placing a user template on an existing atom merges that atom with the template's first atom and overwrites its element, charge and radical (4.8.0), so which atom was drawn first when the template was saved is now user-visible behaviour. The ghost preview marks it with a pale blue circle. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Chain end snapping follows the shared bond snapping distance
Drop pinned version numbers from the wiki so pages do not go stale
Chain tool: the end joins the atom under the cursor
Say exactly what the chain badge counts: carbons added, not bonds
Document the alkyl chain tool in both user manuals Covers where the -(-)n- button lives on the template toolbar, that the drag distance sets the chain length while the axis snaps to 15 deg steps, that the repeat count is previewed at the cursor, and how starting or ending the drag on an existing atom behaves.
Finish menu-breadcrumb style cleanup in Tips-for-2D-to-3D-conversion Two remaining backtick+escaped-arrow spots missed by the earlier pass. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Fix Docker install page: contradicted other pages by calling itself "recommended" Installation-for-Windows/macOS/Linux all label moleditpy-installer as the recommended method; Installation-with-Docker(-JP) claimed Docker was "the recommended method for running moleditpy", which contradicts them. Reframed as an alternative for isolated/reproducible environments. Also fixes doubled-bracket links ([[text](url)](url) -> [text](url)), strips bold markers from headings, sentence-cases headings, adds See also. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Sentence-case headings and add See also to Raspberry Pi troubleshooting page Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Apply house style to remaining Tips pages; fix Official-Plugins link Tips-for-2D-to-3D-conversion(-JP): retitle to match page name, sentence-case headings, See also section. Tips-for-working-with-Dummy-Atoms: rewrite in house style, verified PLUGIN_SUPPORTED_MOLEDITPY_VERSION against the actual XYZ_Editor plugin source, fix the dead Official-Plugins link. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Apply house style to JP counterparts of 3D-editing and force-field Tips pages Mirrors the EN structure: sentence-case headings, bold UI breadcrumbs, opening paragraph, See also section; fixes an anchor link that pointed at User-Manual-JP's old heading text. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Apply house style to Tips-for-3D-editing and force-field-selection pages Sentence-case headings, bold UI breadcrumbs instead of backtick+escaped arrows, opening paragraph, See also section. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Apply house style to Shortcut-* pages (titles, headings, See also) Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Apply house style to installation pages and Keyboard Shortcuts title Strip bold-markdown headings (## **X** -> ## X), sentence-case headings, match H1 title to page name, add See also sections to the three Installation-for-* pages. Rename Keyboard-Shortcuts.md's H1 to match its page name. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Rewrite User Manual to mirror main repo's manual/manual.md structure Reorders sections to match the published manual (Plugin System with 9.1-9.3 subsections before Keyboard Shortcuts, dropping the wiki-only Menu Reference section that didn't exist in the source doc), fixes the version to 4.5.1 (main repo's manual.md still says "4.5"), replaces the stale `python -m moleditpy_installer` invocation with the actual console script `moleditpy-installer` (per pyproject.toml [project.scripts]), applies house style (bold UI breadcrumbs, code spans, tables), embeds the manual's own screenshots via raw.githubusercontent.com, and fixes the Official-Plugins links to point at the moleditpy-plugins wiki. JP counterpart rewritten to match structure exactly. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Reorder Troubleshooting Common Issues for end users; fix broken plugin-page links Task 1: move OpenGL/VTK, Qt-platform-plugin, and log-file diagnostics to a trailing Advanced/diagnostic section; lead with first-launch slowness, 3D-view crashes, plugin failures, and a new file import/export table. Task 2: replace links to Official-Plugins/Plugin-CIF-Viewer (pages that no longer exist in this wiki) with links to the moleditpy-plugins wiki, in Using-Plugins(-JP) and File-Formats-and-Import-Export(-JP). Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Move plugin pages to the plugins wiki; rebuild the index The per-plugin guides and the catalogue documented moleditpy-plugins, not the editor, so they now live in that repository's own wiki and this Home page links to it. Using Plugins stays here: it is about the plugin system, which is part of the application rather than any particular plugin. Home.md now indexes every page in the wiki, including the ones added yesterday that were never linked (Keyboard Shortcuts, File Formats, Command-Line Options, Using Plugins, Troubleshooting), and marks which pages have a Japanese counterpart. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add PMEFF plugin walkthrough page Full force-field-term breakdown, PMEFF Settings dialog, Metal Geometry Override window, optimizer details, and the two Analysis-menu diagnostics (Single-Point Energy, Minimum Check), grounded in the moleditpy_pmeff-plugin v1.4.0 source. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add CIF Viewer plugin walkthrough page Full 4-tab control-panel walkthrough (Structure, Supercell, Ellipsoids, Cell/Axes) and a typical workflow, grounded in the moleditpy_cif_viewer v1.3.0 source. Confirms the bond-cutoff cap and disorder-group bonding fixes are already in this version. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add Gaussian Input Generator Pro plugin walkthrough page Full dialog and Route Builder walkthrough (6 tabs including the 3D-viewer-driven ModRedundant Constraints/Scan picker and Link1 chained-job support) and a typical workflow, grounded in the moleditpy_gaussian_input_generator_pro v1.1.2 source. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add PySCF Calculator plugin walkthrough page Full Calculation/Visualization tab walkthrough (job types, methods, basis sets, Scan Configuration dialog, Orbital Energy Diagram, Thermodynamic Properties dialog) and a typical workflow, grounded in the moleditpy_pyscf-calculator v3.3.2 source. Notes the macOS/Linux/WSL-only OS restriction (no native PySCF Windows build). Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add ORCA Result Analyzer plugin walkthrough page Full hub-window walkthrough covering all analysis windows (SCF Trace, MO Analysis + Compare MOs, Optimization/Scan, Forces, Atomic Charges, Dipole, Frequencies, Thermochemistry, TDDFT, NMR, Bond Analysis, Post-HF) and a typical workflow, grounded in the moleditpy_orca_result_analyzer_plugin v3.13.3 source. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add ORCA Input Generator Pro plugin walkthrough page Full dialog/tab walkthrough (main dialog + Keyword Builder's 6 tabs including the 3D-viewer-driven Constraints/Scan picker) and a typical workflow, grounded in the moleditpy_orca_input_generator_pro v3.4.4 source. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add Official Plugins catalogue page (English) Full catalogue of every visible plugin in moleditpy-plugins' REGISTRY/plugins.json, grouped by category, with menu locations, features, requirements, and versions grounded in the registry and each plugin's source. Links out to six dedicated deep-dive pages for the larger plugins. Notes retired plugins/_old entries and the hidden-but-not-retired orca_nics_analyzer registry entry. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add Japanese counterparts for Command-Line Options, File Formats, Using Plugins, and Troubleshooting wiki pages Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Cross-link Raspberry Pi troubleshooting to the Linux install page Verified the MSAA/Wayland workaround is still accurate: grepped the app source for SetMultiSamples/QT_QPA_PLATFORM/raspberry — no hits, so the "disable MSAA to fix root cause" suggestion is still an open dev TODO, not already implemented. Added a pointer to Installation-for-Linux and a note that the workaround still needs to be applied manually. JP kept in sync. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Expand force-field tips with backend/menu locations; fix stale dummy-atom version claim Tips-for-force-field-selection: added where the force field is actually chosen (Settings > 3D Optimization Settings, Constrained Optimization dropdown, Optimize 3D right-click), the full RDKit vs Open Babel force field lists (GAFF/Ghemical are Open Babel-only), the Linux caveat (moleditpy-linux has no Open Babel), and the automatic MMFF->UFF fallback behavior for unsupported elements. JP kept in sync. Tips-for-working-with-Dummy-Atoms: "MoleditPy: Version 2 or higher" was meaningless boilerplate (current release is 4.5.1). Replaced with the XYZ Editor plugin's actual declared compatibility range (PLUGIN_SUPPORTED_MOLEDITPY_VERSION = ">=4.0.0, <5.0.0", checked against moleditpy-plugins/plugins/XYZ_Editor/xyz_editor.py) and linked to the new Using-Plugins/Official-Plugins pages. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Add File Formats, Troubleshooting, and Using Plugins wiki pages (EN) Grounded in ui/io_logic.py, ui/export_logic.py, ui/string_importers.py, plugins/plugin_manager.py, plugins/plugin_manager_window.py, and the moleditpy-linux OBABEL_AVAILABLE hardcode. JP counterparts follow in a separate commit. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>