Chemdraw style addition

[iribirii]

Summary

This PR adds a new chemdraw rendering preset and associated renderer changes to approximate a Chemdraw-style 2D line diagram, while reusing xyzrender’s existing graph and SVG pipeline.

• Introduces a chemdraw preset that removes atom circles, draws uniform thin bonds, and labels non‑carbon atoms with bold element symbols.
• Adjusts the renderer so Chemdraw labels use CPK colours and bonds are positioned to avoid overlapping the text, including special handling for aromatic bonds.
• Adds documentation and example figures for the new Chemdraw style (caffeine and bimp).

Details

Preset and configuration

• Added src/xyzrender/presets/chemdraw.json:
  • chemdraw_style: true to toggle Chemdraw-specific behaviour in the renderer.
  • White background, black bonds (bond_width tuned for line diagrams).
  • No gradients, fog enabled (depth cueing preserved).
  • Larger label_font_size for legible element symbols.
• Extended RenderConfig with:
  • chemdraw_style: bool = False (default off), set from presets/JSON via the existing config machinery.

Atom rendering (Chemdraw mode)

• In render_svg:
  • When cfg.chemdraw_style is True:
    • No atom circles are drawn.
    • Carbon atoms: implied, no label.
    • Non-carbon atoms: drawn as bold text at the projected atom position using a sans-serif font.
      • Base colour comes from the same CPK palette used for standard rendering.
      • If fog is enabled, the label colour is blended with the fog colour (blend_fog) for consistent depth fading.
      • Hydrogen labels are forced to black (#000000) to stay visible on light backgrounds.
  • The existing index-label logic (cfg.show_indices) remains unchanged and is only active when explicitly requested.

Bond rendering and placement

• Bond endpoints:

  • All bonds still use 3D radii to determine start/end points, then project to 2D.
  • In Chemdraw mode:
    • For carbon atoms, the effective radius is forced to zero so bonds meet at the carbon centre.
    • For non-carbon atoms, the effective radius is max(original_radius, k * label_font_size / scale) (with an empirical factor), so the bond endpoint moves further away from the atom as labels get larger, reducing overlap with text.

• Uniform thickness:

  • In Chemdraw mode, all covalent bonds (single, double, aromatic) use a uniform, slightly thinner stroke width (e.g. bond_width * 0.6), independent of bond order. This keeps the visual style consistent.

• Aromatic bonds (special handling):

  • Non-Chemdraw styles retain the original behaviour: two parallel lines displaced symmetrically, with one dashed toward the ring centre.
  • In Chemdraw mode, aromatic bonds are drawn as:
    • One solid line centred on the bond (no perpendicular offset), visually like a single bond.
    • One dashed line:
      • Offset further toward the ring centre using the perpendicular direction (px, py) and gap.
      • Shortened at both ends by trimming a fraction of the bond length along the bond direction, so it doesn’t run into atom labels or other bonds.
    • Both components use the uniform Chemdraw stroke width.

Documentation and examples

• README.md:
  • Updated the Presets table to include a Chemdraw-style column with examples/images/caffeine_chemdraw.svg.
  • Added a CLI example:

    xyzrender caffeine.xyz --config chemdraw -o caffeine_chemdraw.svg

• Example images:
  • examples/images/caffeine_chemdraw.svg and examples/images/bimp_chemdraw.svg generated with the new preset.

Future work / known limitations

This PR focuses on the core Chemdraw-like look (hidden C–H, labelled heteroatoms, uniform thin bonds, aromatic styling, CPK-coloured labels). There are still several refinements that could be tackled in follow-up PRs:

• Double/triple bond layout:

  • Current Chemdraw mode keeps multiple lines but does not yet optimize spacing/length per bond order to match Chemdraw conventions (e.g. inside vs outside bonds, asymmetric placement).
  • Refining these layouts—especially around heteroatoms and in crowded aromatic systems—would further improve readability.

• More precise label–bond interaction:

  • The current label clearance is based on a simple mapping from font size to effective radius.
  • A more geometry-aware solution (e.g. using measured text extents or adaptive trimming per bond/label pair) could reduce edge cases where long labels are close to bonds.

• Additional presets / variations:

  • Variants for black-and-white export (no CPK colours), or thinner stroke widths for dense structures, could be added as separate presets built on top of this Chemdraw mode.

I’m happy to iterate on any of these in subsequent PRs if you’d like to refine the Chemdraw style further.

[codecov-commenter]

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Codecov Report

❌ Patch coverage is 61.73913% with 44 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/xyzrender/skeletal.py	55.07%	22 Missing and 9 partials ⚠️
src/xyzrender/api.py	18.18%	6 Missing and 3 partials ⚠️
src/xyzrender/cli.py	0.00%	3 Missing ⚠️
src/xyzrender/renderer.py	96.66%	0 Missing and 1 partial ⚠️

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