simpledit 0.0.0 | Documentation

simpledit

0.0.0

FileIOManager ▸
- Instance members
- #importXYZ
- #exportXYZ
- #atomsToXYZ
- #atomsToJSON
- #downloadXYZ
- #loadXYZFile
GeometryController ▸
- Instance members
- #bindGeometrySliders
- #bindBondLengthSlider
- #bindAngleSlider
- #bindDihedralSlider
- #setBondLength
- #setAngle
- #setDihedral
- #getMovingFragment
calculateDistance
calculateAngle
calculateDihedral
getNewPositionsForBondLength
getNewPositionsForAngle
getNewPositionsForDihedral
getCenterOfMass
getRotatedPositions
getTranslatedPositions
calculateSmartOffset
RenderManager ▸
- Instance members
- #createAtomMesh
- #createBondMesh
- #getElementColor
- #getElementRadius
- #updateAtomColors
- #updateBondMeshes
- #rebuildScene
- #updateAtomVisuals
- #updateBondVisuals
SelectionManager ▸
- Instance members
- #clearSelection
- #selectAtom
- #deselectAtom
- #selectByIndices
- #selectRange
- #selectAll
- #invertSelection
- #getSelectedAtoms
- #getSelectionCount
- #getSelectionOrder
- #setSelectionMode
- #cycleSelectionMode
- #updateSelectionStatus
- #clearSelectionStatus
- #updateHighlights
UIManager ▸
ErrorHandler ▸
- Static members
- .error
- .success
- .warning
- .info
- .logError
- .validateParams
- .validateNumber
- .validatePositive
LabelRenderer ▸
- Instance members
- #init
- #markDirty
- #markAllDirty
- #scheduleUpdate
- #updateDirtyLabels
- #getScreenPosition
- #updateAllLabels
- #cancelUpdate
- #dispose
Vector3Pool ▸
- Instance members
- #get
- #getSet
- #resize

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FileIOManager

Manages file import/export operations Handles XYZ format and coordinate conversions

new FileIOManager(editor: any)

Parameters

editor (any)

Instance Members

▸ importXYZ(xyzString)

Import XYZ format string

importXYZ(xyzString: string): Object

Parameters

xyzString (string) XYZ format data

Returns

Object: Result object

▸ exportXYZ()

Export molecule as XYZ format

exportXYZ(): (string | null)

Returns

(string | null): XYZ format string or null on error

▸ atomsToXYZ(atoms)

Convert atoms array to XYZ string

atomsToXYZ(atoms: Array<Object>): string

Parameters

atoms (Array<Object>) Array of atom objects

Returns

string: XYZ format string

▸ atomsToJSON(atoms)

Convert atoms to JSON format

atomsToJSON(atoms: Array<Object>): string

Parameters

atoms (Array<Object>) Array of atom objects

Returns

string: JSON string

▸ downloadXYZ()

Download XYZ file

downloadXYZ()

▸ loadXYZFile(file)

Load XYZ from file input

loadXYZFile(file: File): Promise<Object>

Parameters

file (File) File object

Returns

Promise<Object>: Result object

GeometryController

Controls geometry manipulation sliders and operations Handles bond length, angle, and dihedral adjustments

new GeometryController(editor: any)

Parameters

editor (any)

Instance Members

▸ bindGeometrySliders()

Bind geometry slider events

bindGeometrySliders()

▸ bindBondLengthSlider()

Bind bond length slider

bindBondLengthSlider()

▸ bindAngleSlider()

Bind angle slider

bindAngleSlider()

▸ bindDihedralSlider()

Bind dihedral slider

bindDihedralSlider()

▸ setBondLength(targetDist)

Set bond length between two selected atoms

setBondLength(targetDist: number): Object

Parameters

targetDist (number) Target distance in Angstroms

Returns

Object: Result object

▸ setAngle(targetAngle)

Set angle between three selected atoms

setAngle(targetAngle: number): Object

Parameters

targetAngle (number) Target angle in degrees

Returns

Object: Result object

▸ setDihedral(targetAngle)

Set dihedral angle between four selected atoms

setDihedral(targetAngle: number): Object

Parameters

targetAngle (number) Target dihedral in degrees

Returns

Object: Result object

▸ getMovingFragment(pivot, direction)

Get moving fragment for geometry operation

getMovingFragment(pivot: Object, direction: Object): Set

Parameters

pivot (Object) Pivot atom

direction (Object) Direction atom

Returns

Set: Set of atoms to move

calculateDistance

Calculate distance between two points

calculateDistance(p1: THREE.Vector3, p2: THREE.Vector3): number

Parameters

p1 (THREE.Vector3)

p2 (THREE.Vector3)

Returns

number: Distance in Angstroms

calculateAngle

Calculate angle between three points (p1-p2-p3)

calculateAngle(p1: THREE.Vector3, p2: THREE.Vector3, p3: THREE.Vector3): number

Parameters

p1 (THREE.Vector3)

p2 (THREE.Vector3) Vertex

p3 (THREE.Vector3)

Returns

number: Angle in degrees

calculateDihedral

Calculate dihedral angle (p1-p2-p3-p4)

calculateDihedral(p1: THREE.Vector3, p2: THREE.Vector3, p3: THREE.Vector3, p4: THREE.Vector3): number

Parameters

p1 (THREE.Vector3)

p2 (THREE.Vector3)

p3 (THREE.Vector3)

p4 (THREE.Vector3)

Returns

number: Dihedral angle in degrees

getNewPositionsForBondLength

Calculate new positions for bond length adjustment Moves 'movingAtoms' to satisfy target distance between atom1 and atom2

getNewPositionsForBondLength(pos1: THREE.Vector3, pos2: THREE.Vector3, movingAtomPositions: Array<THREE.Vector3>, targetDist: number): Array<THREE.Vector3>

Parameters

pos1 (THREE.Vector3) Position of fixed atom

pos2 (THREE.Vector3) Position of moving atom (pivot)

movingAtomPositions (Array<THREE.Vector3>) Positions of all atoms to move (including pos2)

targetDist (number) Target distance

Returns

Array<THREE.Vector3>: New positions for moving atoms

getNewPositionsForAngle

Calculate new positions for bond angle adjustment Rotates 'movingAtoms' around axis (pivot-normal) to satisfy target angle p1-pivot-p3

getNewPositionsForAngle(p1: THREE.Vector3, pivot: THREE.Vector3, p3: THREE.Vector3, movingAtomPositions: Array<THREE.Vector3>, targetAngleDegrees: number): Array<THREE.Vector3>

Parameters

p1 (THREE.Vector3) Fixed atom position

pivot (THREE.Vector3) Pivot atom position (vertex)

p3 (THREE.Vector3) Moving atom position (defines current angle)

movingAtomPositions (Array<THREE.Vector3>) Atoms to rotate

targetAngleDegrees (number) Target angle in degrees

Returns

Array<THREE.Vector3>: New positions

getNewPositionsForDihedral

Calculate new positions for dihedral angle adjustment Rotates 'movingAtoms' around axis p2-p3

getNewPositionsForDihedral(p1: THREE.Vector3, p2: THREE.Vector3, p3: THREE.Vector3, p4: THREE.Vector3, movingAtomPositions: Array<THREE.Vector3>, targetDihedralDegrees: number): Array<THREE.Vector3>

Parameters

p1 (THREE.Vector3)

p2 (THREE.Vector3) Axis start

p3 (THREE.Vector3) Axis end

p4 (THREE.Vector3)

movingAtomPositions (Array<THREE.Vector3>) Atoms to rotate

targetDihedralDegrees (number) Target dihedral

Returns

Array<THREE.Vector3>: New positions

getCenterOfMass

Calculate center of mass of atoms

getCenterOfMass(atoms: Array<Object>): THREE.Vector3

Parameters

atoms (Array<Object>) Array of atom objects with position property

Returns

THREE.Vector3: Center of mass

getRotatedPositions

Get positions rotated by Euler angles (degrees) around (0,0,0)

getRotatedPositions(positions: Array<THREE.Vector3>, xDeg: number, yDeg: number, zDeg: number): Array<THREE.Vector3>

Parameters

positions (Array<THREE.Vector3>)

xDeg (number)

yDeg (number)

zDeg (number)

Returns

Array<THREE.Vector3>:

getTranslatedPositions

Get translated positions

getTranslatedPositions(positions: Array<THREE.Vector3>, x: number, y: number, z: number): Array<THREE.Vector3>

Parameters

positions (Array<THREE.Vector3>)

x (number)

y (number)

z (number)

Returns

Array<THREE.Vector3>:

calculateSmartOffset

Calculate smart offset to avoid overlap

calculateSmartOffset(incomingAtoms: Array<Object>, currentAtoms: Array<Object>, minDistance: number): THREE.Vector3

Parameters

incomingAtoms (Array<Object>) Atoms to add

currentAtoms (Array<Object>) Existing atoms

minDistance (number) Minimum distance required

Returns

THREE.Vector3: Offset vector

RenderManager

Manages 3D rendering of atoms and bonds Handles mesh creation, color management, and scene updates

new RenderManager(editor: any)

Parameters

editor (any)

Instance Members

▸ createAtomMesh(atom)

Create mesh for an atom

createAtomMesh(atom: Object): THREE.Mesh

Parameters

atom (Object) Atom object

Returns

THREE.Mesh: Atom mesh

▸ createBondMesh(bond)

Create mesh for a bond

createBondMesh(bond: Object): THREE.Mesh

Parameters

bond (Object) Bond object

Returns

THREE.Mesh: Bond mesh

▸ getElementColor(element)

Get color for an element based on current scheme

getElementColor(element: string): number

Parameters

element (string) Element symbol

Returns

number: Color hex value

▸ getElementRadius(element)

Get radius for an element

getElementRadius(element: string): number

Parameters

element (string) Element symbol

Returns

number: Radius in Angstroms

▸ updateAtomColors()

Update colors for all atoms based on current color scheme

updateAtomColors()

▸ updateBondMeshes()

Update bond meshes

updateBondMeshes()

▸ rebuildScene()

Rebuild entire scene from scratch

rebuildScene()

▸ updateAtomVisuals(atom)

Update single atom's visuals

updateAtomVisuals(atom: Object)

Parameters

atom (Object) Atom to update

▸ updateBondVisuals()

Update bond visuals

updateBondVisuals()

SelectionManager

Manages atom selection state and UI Handles selection highlighting, order tracking, and status updates

new SelectionManager(editor: any)

Parameters

editor (any)

Instance Members

▸ clearSelection()

Clear all selections

clearSelection()

▸ selectAtom(atom, add)

Select an atom

selectAtom(atom: Object, add: boolean)

Parameters

atom (Object) Atom to select

add

(boolean
            = false)

Whether to add to selection or replace

▸ deselectAtom(atom)

Deselect an atom

deselectAtom(atom: Object)

Parameters

atom (Object) Atom to deselect

▸ selectByIndices(indices)

Select atoms by indices

selectByIndices(indices: Array<number>)

Parameters

indices (Array<number>) Atom indices to select

▸ selectRange(start, end)

Select atoms in a range (inclusive)

selectRange(start: number, end: number)

Parameters

start (number) Start index

end (number) End index

▸ selectAll()

Select all atoms

selectAll()

▸ invertSelection()

Invert selection

invertSelection()

▸ getSelectedAtoms()

Get selected atoms

getSelectedAtoms(): Array<Object>

Returns

Array<Object>: Array of selected atoms

▸ getSelectionCount()

Get selection count

getSelectionCount(): number

Returns

number: Number of selected atoms

▸ getSelectionOrder()

Get selection order (for geometry operations)

getSelectionOrder(): Array<Object>

Returns

Array<Object>: Array of atoms in selection order

▸ setSelectionMode(mode)

Update selection mode

setSelectionMode(mode: string)

Parameters

mode (string) 'lasso' or 'rectangle'

▸ cycleSelectionMode()

Cycle through selection modes

cycleSelectionMode()

▸ updateSelectionStatus()

Update selection status display

updateSelectionStatus()

▸ clearSelectionStatus()

Clear selection status display

clearSelectionStatus()

▸ updateHighlights()

Update highlights for all atoms (refresh visual state)

updateHighlights()

UIManager

Manages UI interactions, modals, and labels Handles toolbar events, periodic table, coordinate editor, and atom labels

new UIManager(editor: any)

Parameters

editor (any)

Instance Members

▸ bindToolbarEvents()

Bind all toolbar button events

bindToolbarEvents()

▸ bindModeButtons()

Bind mode selection buttons (edit/select/move)

bindModeButtons()

▸ bindViewButtons()

Bind view control buttons

bindViewButtons()

▸ bindLabelButton()

Bind label toggle button

bindLabelButton()

▸ bindExportButton()

Bind export PNG button

bindExportButton()

▸ bindMoleculeButtons()

Bind molecule management buttons

bindMoleculeButtons()

▸ updateLabelButtonText()

Update label button text to reflect current mode

updateLabelButtonText()

▸ openPeriodicTable(callback)

Open periodic table modal

openPeriodicTable(callback: function)

Parameters

callback (function) Callback function when element is selected

▸ closePeriodicTable()

Close periodic table modal

closePeriodicTable()

▸ openCoordinateEditor()

Open coordinate editor modal

openCoordinateEditor()

▸ closeCoordinateEditor()

Close coordinate editor modal

closeCoordinateEditor()

▸ toggleMaximize(element)

Toggle modal maximize

toggleMaximize(element: HTMLElement)

Parameters

element (HTMLElement) Modal element

▸ exportPNG()

Export current view as PNG

exportPNG()

▸ showError(message)

Show error message to user

showError(message: string)

Parameters

message (string) Error message

▸ showSuccess(message)

Show success message to user

showSuccess(message: string)

Parameters

message (string) Success message

▸ createAtomLabel(atom)

Create label element for an atom

createAtomLabel(atom: Object): HTMLElement

Parameters

atom (Object) Atom object

Returns

HTMLElement: Label element

▸ updateAtomLabelText(atom, label)

Update label text for an atom

updateAtomLabelText(atom: Object, label: HTMLElement)

Parameters

atom (Object) Atom object

label

(HTMLElement
            = null)

Label element (optional, will find if not provided)

▸ updateAllLabels()

Update all atom labels

updateAllLabels()

▸ updateLabelPositions()

Update label positions (2D screen coordinates)

updateLabelPositions()

ErrorHandler

Centralized error handling utility Provides consistent error/success response format across the application

new ErrorHandler()

Static Members

▸ error(message, details)

Create a standard error response

error(message: string, details: any): Object

Parameters

message (string) User-friendly error message

details

(any
            = null)

Optional error details for debugging

Returns

Object: Error response object

▸ success(message, data)

Create a standard success response

success(message: string, data: any): Object

Parameters

message (string) Success message

data

(any
            = null)

Optional data to return

Returns

Object: Success response object

▸ warning(message)

Create a warning response

warning(message: string): Object

Parameters

message (string) Warning message

Returns

Object: Warning response object

▸ info(message)

Create an info response

info(message: string): Object

Parameters

message (string) Info message

Returns

Object: Info response object

▸ logError(context, error)

Log error to console (development only)

logError(context: string, error: (Error | string))

Parameters

context (string) Context where error occurred

error ((Error | string)) Error to log

▸ validateParams(params, required)

Validate required parameters

validateParams(params: Object, required: Array<string>): (Object | null)

Parameters

params (Object) Parameters to validate

required (Array<string>) Required parameter names

Returns

(Object | null): Error response if validation fails, null otherwise

▸ validateNumber(value, name)

Validate numeric value

validateNumber(value: any, name: string): (Object | null)

Parameters

value (any) Value to validate

name

(string
            = 'value')

Parameter name for error message

Returns

(Object | null): Error response if validation fails, null otherwise

▸ validatePositive(value, name)

Validate positive number

validatePositive(value: any, name: string): (Object | null)

Parameters

value (any) Value to validate

name

(string
            = 'value')

Parameter name for error message

Returns

(Object | null): Error response if validation fails, null otherwise

LabelRenderer

Optimized label rendering with dirty checking and RAF batching Reduces DOM updates from every frame to only when needed

new LabelRenderer()

Instance Members

▸ init(atoms, camera, canvas)

Initialize renderer with references

init(atoms: Array<Object>, camera: THREE.Camera, canvas: HTMLCanvasElement)

Parameters

atoms (Array<Object>) Atoms array

camera (THREE.Camera) Camera for projection

canvas (HTMLCanvasElement) Canvas for size

▸ markDirty(atomIndex)

Mark a specific label as dirty (needs update)

markDirty(atomIndex: number)

Parameters

atomIndex (number) Index of atom whose label needs update

▸ markAllDirty()

Mark all labels as dirty

markAllDirty()

▸ scheduleUpdate()

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

scheduleUpdate()

▸ updateDirtyLabels()

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

updateDirtyLabels()

▸ getScreenPosition(atom)

Get screen position for an atom

getScreenPosition(atom: Object): (Object | null)

Parameters

atom (Object) Atom with mesh

Returns

(Object | null): {x, y} screen coordinates or null

▸ updateAllLabels()

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

updateAllLabels()

▸ cancelUpdate()

Cancel any pending update

cancelUpdate()

▸ dispose()

Cleanup

dispose()

Vector3Pool

Object pool for THREE.Vector3 to reduce garbage collection Reuses Vector3 instances instead of creating new ones

new Vector3Pool(size: any)

Parameters

size

(any
            = 100)

Instance Members

▸ get()

Get a vector from the pool

get(): THREE.Vector3

Returns

THREE.Vector3: Reusable vector (reset to 0,0,0)

▸ getSet(x, y, z)

Get a vector and set its values

getSet(x: number, y: number, z: number): THREE.Vector3

Parameters

x (number)

y (number)

z (number)

Returns

THREE.Vector3:

▸ resize(newSize)

Resize pool

resize(newSize: number)

Parameters

newSize (number)