MOL import coordinates and hydrogen presentation

Implementation notes and historical checks. Open the visual guide →.

When you open a MOL file with 3D coordinates, ReShiki keeps them, so you can tilt the molecule. Ordinary hydrogens become H counts; hydrogens with an isotope, charge, map number or stereo stay as atoms. Save as a .rsk file to keep the 3D shape. MOL export keeps it too, except for Haworth drawings.

Use it

1. Open a V2000 or V3000 MOL file, or paste MOL text into Import.
2. Select the molecule and use 3D tilt (right-click menu or tool palette) to turn it. The atoms keep their original 3D positions.
3. Save as a .rsk file to keep the coordinates and stereo for later.

Limits

• Import keeps the coordinates exactly; it does not clean up, minimize or generate a conformer.
• Hydrogens that are charged, isotope-labeled, radical, isolated, bridging, bound to a metal, mapped or annotated stay as drawn atoms. So do hydrogens whose removal would change stereo.
• MOL export keeps the 3D coordinates of heavy atoms and marks the file as 3D. Hydrogens folded into counts are not written as atoms. If the 3D shape no longer matches the drawn stereo, for example after you edit a wedge, export writes a flat 2D drawing and says so.
• If anything in the file fails validation, nothing is imported.

Implementation notes

The canvas conversion is uniform: X is multiplied by 28, Y is inverted and multiplied by 28, and Z is multiplied by 28. .rsk drawing storage uses f32, so only the corresponding numeric rounding is expected. Import retains nonzero Z even when it is below the parser’s threshold for assigning stereo from a 3D conformer. Retained depth lets the selection tilt controls rotate the original conformation. The source molecular tags and double-bond controls remain authoritative when the projection becomes edge-on. Explicit unknown double stereo is stored as any; a source wavy single bond remains a chemical unknown rather than projection paint. Both survive rotation and reopen without inventing an assigned configuration.

Ordinary terminal neutral, nonisotopic H attached by a single bond to a supported main-group atom becomes an explicit-H count on its parent atom. It contributes to the same chemical formula without crowding the drawing. The shared graph operation adjusts neighbor parity and stereo controls; the import adapter checks composition and CIP descriptors before publishing the result. Kept source indices remap stable IDs, XYZ and annotations together. The lossless raw MOL parser is unchanged.

Unknown H or bond stereochemistry is protected. Unsupported non-tetrahedral removal cases retain their H. Any graph, coordinate, annotation or stereo validation failure returns an error before publishing a partial drawing. Existing 2D inputs without removable explicit H retain their current drawing.

.rsk save/reopen retains XYZ and the stereo controls.

MOL export keeps the 3D coordinates of drawings that have depth, such as imported 3D MOL files and 3D optimize… results, and marks the file as 3D. A drawing qualifies when an exported atom has a depth above 0.001 Å. 2D drawings export as 2D, unchanged. Haworth drawings export as 2D because their depth is drawing perspective. RXN export keeps the 3D coordinates of each participant by the same rule. If the 3D coordinates no longer match the drawn stereochemistry, for example after wedges were edited, export writes a 2D depiction instead and shows this notice: “Exported as 2D because the 3D coordinates no longer match the drawn stereochemistry”.

Import folds ordinary hydrogens into counts, so a re-exported 3D file holds the heavy atoms and any hydrogens that stayed explicit. Export does not invent hydrogen positions.

The 2D depiction can omit a wavy single-bond unknown marker while leaving that center unassigned; .rsk files keep the marker. Explicit unknown double stereo is checked through MOL export as well.

Regression inputs and independent executable checks are described in the fixture README.