Parse CIF text and return a Crystal object. Uses the first data_ block found.

Evaluate a symmetry-operation expression such as "-x+1/2, y, -z+1/4" for given fractional coordinate values.

Generate CIF text from a Crystal object. Only the identity symmetry operation is written (P1 description).

Build LatticeParams from three Cartesian lattice vectors.

Convert angles to lattice vectors using the standard crystallographic convention. a-vector lies along x-axis, b-vector in the xy-plane.

Convert fractional coordinates to Cartesian.

Convert Cartesian coordinates to fractional.

Unit cell volume in ų

Apply minimum image convention to a displacement vector. Returns the shortest-image equivalent of (dx, dy, dz) under PBC.

Type: (LatticeParams | null)

Type: (string | null)

Type: (number | null)

Type: Map<number, {x: number, y: number, z: number}>

Marker so code can distinguish Crystal from Molecule

Add an atom using fractional coordinates. Also stores Cartesian position for rendering. Throws a RangeError if any coordinate is NaN or non-finite, preventing invalid geometry from entering the scene graph.

Get stored fractional coordinates of an atom (or null).

Return fractional coordinates for an atom, falling back to computing them from the stored Cartesian position via lattice.cartToFrac() when the fracCoords cache has no entry. Unlike getFrac(), this method always returns a valid coordinate object and never returns null.

Wrap all atoms into the unit cell [0, 1). Updates both fracCoords and Cartesian positions.

Generate a supercell by repeating the unit cell na × nb × nc times.

Convenience wrapper: repeat na × nb × nc times along a, b, c axes. Delegates to generateSupercellMatrix for consistency.

Generate a supercell using a general 3×3 integer transformation matrix S.

Convention (row form, same as ASE/pymatgen): new_a = S[0][0]*a + S[0][1]*b + S[0][2]*c new_b = S[1][0]*a + S[1][1]*b + S[1][2]*c new_c = S[2][0]*a + S[2][1]*b + S[2][2]*c

Fractional coordinate transformation: f_new = (S^T)^{-1} * f_old

The resulting supercell contains |det(S)| × (original atom count) atoms.

Type: (THREE.LineSegments | null)

Type: Array<THREE.Object3D>

Type: Array<THREE.Mesh>

Elements that are polyhedra centres (empty = all with CN ≥ 3)

Draw (or redraw) the unit cell box for the given crystal. The parallelepiped has its origin at (0, 0, 0).

Render semi-transparent ghost atoms in the first shell of neighbouring cells (±1 in each lattice direction) for the given crystal.

Render semi-transparent coordination polyhedra. Each atom whose element is in polyhedralElements (or all atoms with CN ≥ 3 if the list is empty) is used as a polyhedron centre; its bonded neighbours form the vertices.

For crystal structures, neighbour positions are obtained via the minimum-image convention so that face-sharing polyhedra across PBC look correct.

Enable / disable polyhedral rendering.

Draw a semi-transparent Miller plane for the given (hkl) indices and register it in activePlanes. If a plane with identical indices already exists it is silently ignored (no duplicates). The plane colour is chosen automatically from a fixed palette based on the current number of active planes before the new entry is added, keeping the colour assignment consistent even if planes are added in different orders.

Remove all Miller-index label sprites from the scene and release their GPU and CPU resources (texture, material, and the off-screen canvas). Call this before hiding Miller labels or before destroying the renderer.

Redraw all crystal-specific overlays for the current active molecule. Should be called after rebuildScene().

Import SMILES string

Update current molecule from MolBlock, preserving 3D coordinates if possible

Update molecule from 2D editor MolBlock Generates fresh 3D coordinates as per user request.

Import SDF/MolBlock string

Export molecule as XYZ format

Helper: Convert Deuterium (H with isotope 2) to Dummy atom (X) in MolBlock Used to fix hydrogen addition for dummy atoms.

Helper: Convert atoms to MolBlock (V2000)

Helper: Convert atoms to XYZ string

Export current molecule as SMILES

Export molecule as SDF

Helper: Get disconnected fragments (arrays of atoms)

Helper: Convert atoms to OCL Molecule

Export molecule as SVG using OCL

Export molecule as PNG Data URL (Async)

Convert atoms to JSON format

Download XYZ file

Load XYZ from file input

Import XYZ string

Import a CIF file and load it as the active crystal structure.

Export the active crystal structure as CIF text.

Download the active structure as a .cif file.

Import a POSCAR / CONTCAR file.

Export the active crystal structure as POSCAR text.

Download the active structure as POSCAR.

Bind geometry slider events

Bind bond length slider

Bind bond length slider and input

Bind angle slider and input

Bind dihedral slider and input

Set bond length between two selected atoms

Set angle between three selected atoms

Set dihedral angle between four selected atoms

Get moving fragment specifically for dihedral rotation This version starts BFS from neighbors of axisEnd, not from axisEnd itself

Get moving fragment for geometry operation

Initialize JSME in the specified container

Set molecule in JSME

Get molecule from JSME as MolBlock

Get molecule from JSME as JME string

Get molecule from JSME as SMILES

Initialize OCL Editor in the specified container

Set molecule from MolBlock

Set molecule from MolBlock

Get MolBlock from editor

Initialize OCL resources

Generate 3D coordinates for a SMILES string or Molecule object

Convert MolBlock to SMILES

Add hydrogens to a SMILES string (2D)

Parse POSCAR/CONTCAR content into a Crystal object.

Convert three lattice vectors to LatticeParams (a, b, c, alpha, beta, gamma).

Generate POSCAR text (VASP 5 format, Direct coordinates).

Initialize RDKit module

Get RDKit instance, loading if necessary

Convert SMILES to MolBlock (V3000) with 3D coordinates

Generate 2D SVG for a molecule

Convert MolBlock to SMILES

Create mesh for an atom

Create mesh for a bond

Get color for an element based on current scheme

Get radius for an element

Update colors for all atoms based on current color scheme

Update bond meshes

Rebuild entire scene from scratch

Update single atom's visuals

Update bond visuals

Update bond visuals

Set atom scale

Set bond scale

Clear all selections

Select an atom

Toggle selection of an atom

Deselect an atom

Select atoms by indices

Select atoms in a range (inclusive)

Select all atoms

Invert selection

Get selected atoms

Get selection count

Get selection order (for geometry operations)

Update selection mode

Cycle through selection modes

Update selection status display

Clear selection status display

Update highlights for all atoms (refresh visual state)

Delete selected atoms

Start selection drag

Update selection drag

End selection drag

Generate a surface slab from a bulk crystal by cleaving along the (hkl) plane. The method constructs a new orthorhombic-like unit cell whose c axis is perpendicular to the surface, stacks the requested number of atomic layers, and adds a vacuum region. The slab cell matrix is checked for singularity before inversion; degenerate in-plane vectors raise an explicit Error rather than producing silently wrong coordinates.

Bind all toolbar button events

Bind mode selection buttons (edit/select/move)

Bind Edit submode buttons (manual/smart)

Update Edit submode button UI

Bind Select submode buttons (lasso/rectangle)

Bind Move submode buttons (translate/orbit/trackball)

Update Select submode button UI

Update Move submode button UI

Bind view control buttons

Bind label toggle button

Bind export PNG button

Bind console toggle button

Bind molecule management buttons

Bind sidebar toggle events

Bind undo/redo buttons

Bind periodic table events

Bind auto-bond button

Bind coordinate editor button

Bind JSME button

Bind bond threshold slider

Update label button text to reflect current mode

Open periodic table modal

Close periodic table modal

Render periodic table grid

Bind Functional Groups modal events

Open Functional Groups modal

Close Functional Groups modal

Render Functional Groups grid by category

Open coordinate editor modal

Close coordinate editor modal

Toggle maximize state of JSME modal

Open 2D Editor modal (JSME or OCL)

Load current 3D molecule into 2D editor with options

Switch active editor

Update editor visibility based on active state

Close JSME modal

Toggle modal maximize

Export current view as PNG

Show error message to user

Show success message to user

Create label element for an atom

Update label text for an atom

Update all atom labels

Update label positions (2D screen coordinates)

Update atom count display

Create a standard error response

Create a standard success response

Create a warning response

Create an info response

Log error to console (development only)

Validate required parameters

Validate numeric value

Validate positive number

Initialize renderer with references

Mark a specific label as dirty (needs update)

Mark all labels as dirty

Schedule a label update using requestAnimationFrame Ensures updates happen at most once per frame

Update only dirty labels in batched manner Separates DOM reads and writes to minimize reflow

Get screen position for an atom

Update all labels (fallback for full updates) Used when camera moves or all labels need refresh

Cancel any pending update

Cleanup

Get a vector from the pool

Get a vector and set its values

Resize pool