Molecule Structure Viewer
Open a local MOL or SDF file conforming to this viewer's bounded BIOVIA CTfile Formats 2020 V2000 subset. Inspect atoms and bonds, switch among up to eight SDF records, and rotate a projection only when actual z coordinates are present. Warnings expose unsupported elements and limited interpretation; they do not assess chemical validity.
Key features
- Parse fixed-width V2000 atom and bond coordinates and optional M CHG values
- Choose among up to eight SDF records without submitting the file
- Inspect a 2D drawing or rotate provided 3D x/y/z coordinates
- Select atom and bond details with keyboard-operable controls
- Show unsupported element, stereo, isotope, omitted data, and coarse over-valence warnings
- Download the selected original MOL block, coordinate SVG, or versioned JSON report
How to use
- Choose a .mol or .sdf file, paste source text with the matching format, or load the independently authored water example.
- If an SDF contains several records, select one record. Read its source atom and bond counts and any visible warnings.
- Use 2D or, where z coordinates vary, 3D. Move yaw and pitch sliders to rotate only the supplied coordinates.
- Select atom and bond buttons to inspect indices, elements, charge, coordinates, order, and unrendered stereo flags.
- Download an SVG drawing, the chosen V2000 MOL block, or a JSON report. Unsupported or damaged input leaves the current view unchanged.
Use cases
- Review a small local V2000 MOL graph in a teaching activity
- Compare 2D layout and provided 3D coordinates without generating a conformer
- Inspect multiple records from an SDF collection
- Identify unsupported symbols or unrendered stereo before using specialist software
Frequently asked questions
Does this calculate a 3D structure from a 2D file?
No. The 3D control is enabled only when at least one input atom has a nonzero z coordinate. It rotates an orthographic projection of the supplied coordinates. It does not generate, optimize, measure or certify a conformer.
Which CTfile features are supported?
This is a deliberately limited BIOVIA CTfile Formats 2020 V2000 viewer: fixed-width atom coordinates, element labels, simple 1–3 and aromatic 4 bonds, legacy atom charge codes and M CHG. V3000, query lists and bonds, R groups, Sgroups and other property lines are rejected. SDF data fields are not interpreted.
What do valence and stereo warnings mean?
A valence warning only compares the visible bond-order sum of selected neutral elements with a coarse nominal maximum. Missing implied hydrogens, charges, aromaticity, resonance and unusual valence are not analyzed. Stereo flags are retained as numbers but stereochemistry is not drawn or verified. Neither warning proves validity or invalidity.
What happens to an unsupported element?
A well-formed element-like symbol outside this viewer's common display set remains labeled in amber and is listed as unsupported. The tool does not infer its properties or valence. Pseudo-atoms and query atom symbols are rejected rather than silently treated as elements.
Is the downloaded MOL the same as the uploaded SDF?
The MOL download contains the selected record's original header, atom, bond and accepted M CHG lines through M END. It excludes SDF data fields and other records, which are reported as omitted. SVG and JSON are viewer exports, not replacements for a complete chemistry exchange format.
Is this safe for medical, toxicity or chemical decisions?
No. This is a local coordinate and graph display for learning. It makes no assessment of compound identity, chemistry, biological effect, toxicity, safety or suitability for synthesis. Use specialist validated tools for those decisions.
Privacy
Files are parsed in this browser tab. No molecular content is automatically sent to this site's server or a third party. Downloaded files stay on your device; there is no automatic saving.
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