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.
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>
Overhaul User Manual pages: exhaustive walkthrough, fix stale version/license
Stale: wiki manual was frozen at v1.9.7 / Apache-2.0 license and missing
whole sections present in the real app (Move Group, Move Selected Atoms,
Constrained Optimization, Planarize, 3D conversion mode details, Settings
Other tab, 3D Atom Info index base, aromatic ring style, right-click quick
optimizer). Replaced with the current source-of-truth content mirrored
from python_molecular_editor/manual/manual.md (v4.5, kept in sync with the
app) and updated to 4.5.1 / GPL-3.0.
Added: a Settings section with full default-value tables read from
utils/default_settings.py, and a Menu Reference table cross-checked
against ui/main_window_init.py. Keyboard-Shortcuts/Using-Plugins/
Official-Plugins/File-Formats-and-Import-Export/Command-Line-Options are
now linked instead of duplicated, per the new dedicated pages another
agent is adding. JP page kept in sync with natural (non-machine-translated)
Japanese.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Created User Manual JP (markdown)