Glossary

Short definitions for terms used across these docs. Molkit-specific terms come first, then general chemistry terms you may see while drawing.

Molkit terms

Abbreviation A compact label for a common group (Me, Ph, Boc, and so on) drawn from Molkit’s abbreviation library. You can place one as a label or full structure, collapse a drawn group into an abbreviation, and expand it back later. See Abbreviations.

Animation State (State Box) A keyframe snapshot of your content drawn inside its own framed region of the canvas. An animation is a sequence of states, and Molkit interpolates matched objects from one state to the next during playback. See Animation States.

Annotation Any non-structural object on the canvas: text, arrows, shapes, brackets, images, and projections. Annotations are stored separately from atoms and bonds.

Attachment / Anchor The link between an arrow endpoint and a target (atom, bond midpoint, lone pair, radical, or annotation edge), shown as a white square handle on the endpoint. An anchored endpoint carries a small accent dot inside the square and tracks its target when the target moves. See Straight Arrows.

Bow The curvature of a curved or spline arrow, measured as a percentage of the chord length. The Shape Properties panel has a Bow slider, and F flips the bow to the other side of the chord. See Curved Arrows.

Color Scheme The set of element and structure colors (bonds, atom labels, charges, background) applied to your drawing. It is independent of the structure preset. See Color Schemes.

Conformer (idealized) A 3D arrangement of a molecule generated from its 2D structure. The 3D viewer builds and shows an idealized conformer, which conveys shape and geometry but is not an experimental measurement. See 3D Structure Viewer.

Convert to paths An SVG export option that outlines atom-label text as vector geometry so no font is needed. The result renders the same everywhere but the text is no longer selectable. See SVG Export.

Crop A trim applied to an imported raster image. Double-click the image to enter crop mode, then drag the edge and corner handles; they snap to the image’s detected content edges unless Shift is held. See Canvas Handles.

Embedded chemistry metadata Per-atom and per-bond data (such as formula and structure details) written into data-mk-* attributes during SVG export, optionally enriched with PubChem data. See Export Metadata.

Emerge / Collapse The enter and exit behaviors for objects that exist in only one state of a transition. An unmatched object that is bonded to a matched atom slides out from that neighbor (emerge-from) or into it (collapse-into); otherwise it pops in or fades out. See Object Matching.

Flyout menu The small panel that opens off a toolbar button to expose its variants, such as the arrow tool’s straight, curved, and reaction options. See The Interface.

Functional Group A common chemistry group from Molkit’s functional-group library (OH, COOH, NO2, and so on), placeable as a label or as real atoms and bonds. See Abbreviations.

Group A bundle of layers combined with Ctrl+G so they select and move as one unit; Ctrl+Shift+G dissolves it again. See Layers & Groups.

Handle A small draggable control drawn on or near a selected object, such as resize squares, rotation handles, arrow endpoint squares, and Bezier controls. Handle shapes and colors follow shared conventions. See Canvas Handles.

Implicit Hydrogen A hydrogen that Molkit infers from an atom’s valence and draws automatically rather than as a separate atom. Formulas and molecular weights always count implicit hydrogens; SVG metadata export can optionally omit the per-atom counts.

Layer An object’s position in the canvas stacking order. Each connected molecule and each annotation is its own layer; reorder them with Ctrl+[ / Ctrl+] or from the Layers panel (F7). See Layers & Groups.

Lone Pair A pair of non-bonding valence electrons drawn as two dots beside an atom. Lone pairs are valid arrow attachment targets. See Lone Pairs.

Mechanism Arrow A curved arrow that depicts electron movement in a reaction mechanism. Arrows anchored to a donor and acceptor drive Molkit’s reaction choreography during animation. See Mechanism Arrows.

.mkit file Molkit’s native document format: a JSON file holding the entire document (structures, annotations, animation states, slides, settings, and metadata) in fully editable form. See .mkit Files.

Mobile-safe rendering An SVG export option that embeds a subsetted metric-compatible fallback font (Liberation Sans) so labels render the same on devices that may lack Arial. See Mobile-safe Export.

Net dipole A molecule’s overall bond-polarity vector, drawn over the structure as an arrow pointing toward the negative end with a plus mark at the positive end. Switched on for a whole molecule from the Object Properties panel. See Net Dipole.

Object Matching The pairing of each atom, bond, and annotation in one animation state with its counterpart in the next, so matched objects tween smoothly. The Match Editor lets you inspect and correct pairings. See Object Matching.

Orbital Lobe An annotation that draws an atomic or hybrid orbital shape (s, p, d, sp/sp2/sp3, or a pi overlap) on an atom, or freestanding on the canvas. See Orbital Lobes.

Page One sheet of a paged document. Page Setup switches the document from the infinite canvas to fixed pages with a chosen paper size, orientation, and margins. See Page Setup & Pages.

Projection A real set of atoms and bonds linked to an annotation that draws them in a canonical style (Fischer, Newman, Haworth, or chair). The atoms stay ordinary and select, move, count, and export like any others. See How Projections Work.

Properties panel The docked panel on the right that shows editing controls for the current selection, such as Shape Properties for arrows and shapes or Projection Properties for a projection.

Radical A single unpaired electron drawn as one dot beside an atom. Radicals are arrow attachment targets and can drive radical-pairing choreography in animations. See Radicals.

Reaction Choreography Molkit’s automatic detection of reaction events (bond breaking and forming, electron motion) between adjacent animation states, which it sequences into timed sub-animations instead of a plain crossfade. See Reaction Choreography.

Smart Guides Alignment helpers that snap a dragged object to the edges, centers, and spacing of nearby objects and match bond lengths. They are on by default; toggle them with Ctrl+;. See Arrange and Select Tool.

Spline Arrow A curved arrow built from anchor points with paired Bezier tangent handles, supporting interior waypoints. Most curved arrows in Molkit use the spline geometry. See Curved Arrows.

Squiggle A wavy line annotation, drawn free-floating or anchored across the end of a bond as a cut-off mark showing that the structure continues. Reached from the Bond tool flyout. See Squiggle Line.

Structure Preset A named bundle of drawing defaults (bond length, fonts, aromatic display, arrow proportions, and more) applied in one step. Molkit ships Traditional, Compact, and Textbook. It is separate from the color scheme. See Structure Presets.

Tab An open document in Molkit. Opening a .mkit file loads it into a new tab, and you can apply a preset across all open tabs. See Tabs and Autosave.

Theme Light or dark appearance. The editor itself is fixed light; the place light and dark matter is the theme-aware SVG export, which adapts the saved file to the viewer’s color-scheme setting. See Theme.

Chemistry terms

Chair projection A drawing of a six-membered ring in its chair conformation, the lowest-energy shape of cyclohexane, showing axial and equatorial positions. See Chair Conformations.

E/Z stereochemistry A naming system for double-bond geometry. Z (zusammen) means the two higher-priority groups are on the same side; E (entgegen) means opposite sides. See Stereo Labels.

Fischer projection A flat drawing of a chiral molecule with horizontal bonds toward the viewer and vertical bonds away, used for sugars and amino acids. See Fischer Projections.

Formal charge The charge assigned to an atom by comparing its valence electrons to the bonds and lone pairs drawn on it. See Charges.

Haworth projection A three-quarter view of a cyclic sugar (pyranose or furanose) drawn as a flat ring with substituents above and below the plane. See Haworth Projections.

InChI The IUPAC International Chemical Identifier, a structured text string that encodes a molecule’s composition and connectivity for database lookup.

Kekule vs aromatic circle Two ways to draw an aromatic ring. Kekule style uses alternating single and double bonds; the aromatic-circle style draws a single inscribed circle to represent the delocalized electrons. Molkit’s preset controls which style aromatic rings use.

Molecular weight vs exact mass Molecular weight is the average mass using natural isotopic abundances; exact (monoisotopic) mass uses the most abundant isotope of each element. See ChemCalc.

Newman projection A view straight down a carbon-carbon bond, showing the front and back atoms’ substituents as spokes to compare staggered and eclipsed arrangements. See Newman Projections.

R/S stereochemistry The Cahn-Ingold-Prelog system for naming a chiral center. After ranking the four groups by priority, R means clockwise and S counterclockwise when viewed with the lowest priority pointing away. See Stereo Labels.

SMILES Simplified Molecular Input Line Entry System, a compact text notation for a molecular structure (for example c1ccccc1 for benzene). Molkit imports and exports SMILES. See SMILES.

Valence The number of bonds an atom forms, used by Molkit to infer implicit hydrogens and to flag bonding that exceeds the expected count.