matterviz 0.3.4 → 0.3.6

package/dist/src/lib/structure/bonding.ts

@@ -0,0 +1,944 @@
+// Bonding algorithms for structure visualization
+
+import { element_data } from '$lib/element'
+import type { Vec3 } from '$lib/math'
+import * as math from '$lib/math'
+import type { AnyStructure, BondOrder, BondPair, Site, StructureBond } from '$lib/structure'
+
+type SpatialGrid = Map<string, number[]>
+
+const element_lookup = new Map(element_data.map((el) => [el.symbol, el]))
+const covalent_radii: Map<string, number> = new Map(
+  element_data.flatMap((el) =>
+    el.covalent_radius === null ? [] : [[el.symbol, el.covalent_radius]],
+  ),
+)
+
+const is_zero_cell_shift = (cell_shift: Vec3 | undefined): boolean =>
+  cell_shift === undefined || cell_shift.every((val) => val === 0)
+
+const format_cell_shift = (cell_shift: Vec3 | undefined): string => {
+  if (cell_shift === undefined || is_zero_cell_shift(cell_shift)) return ``
+  return `@${cell_shift.join(`,`)}`
+}
+
+const negate_cell_shift = (cell_shift: Vec3): Vec3 => [
+  cell_shift[0] === 0 ? 0 : -cell_shift[0],
+  cell_shift[1] === 0 ? 0 : -cell_shift[1],
+  cell_shift[2] === 0 ? 0 : -cell_shift[2],
+]
+
+const canonical_self_bond_shift = (cell_shift: Vec3): Vec3 => {
+  const first_non_zero = cell_shift.find((val) => val !== 0)
+  return first_non_zero !== undefined && first_non_zero < 0
+    ? negate_cell_shift(cell_shift)
+    : cell_shift
+}
+
+const normalize_bond_endpoints = (
+  site_idx_1: number,
+  site_idx_2: number,
+  cell_shift?: Vec3,
+): Pick<StructureBond, `site_idx_1` | `site_idx_2` | `cell_shift`> => {
+  if (site_idx_1 === site_idx_2) {
+    const ordered = { site_idx_1, site_idx_2 }
+    if (cell_shift === undefined || is_zero_cell_shift(cell_shift)) return ordered
+    return { ...ordered, cell_shift: canonical_self_bond_shift(cell_shift) }
+  }
+  const ordered =
+    site_idx_1 < site_idx_2
+      ? { site_idx_1, site_idx_2 }
+      : { site_idx_1: site_idx_2, site_idx_2: site_idx_1 }
+  if (cell_shift === undefined || is_zero_cell_shift(cell_shift)) return ordered
+  return {
+    ...ordered,
+    cell_shift: site_idx_1 < site_idx_2 ? cell_shift : negate_cell_shift(cell_shift),
+  }
+}
+
+export const normalize_structure_bond = (
+  site_idx_1: number,
+  site_idx_2: number,
+  order: BondOrder,
+  cell_shift?: Vec3,
+): StructureBond => {
+  const bond = normalize_bond_endpoints(site_idx_1, site_idx_2, cell_shift)
+  return { ...bond, order }
+}
+
+export const get_bond_key = (idx_1: number, idx_2: number, cell_shift?: Vec3): string => {
+  const normalized = normalize_bond_endpoints(idx_1, idx_2, cell_shift)
+  return `${normalized.site_idx_1}-${normalized.site_idx_2}${format_cell_shift(
+    normalized.cell_shift,
+  )}`
+}
+
+export type BondEditState = {
+  added_bonds: StructureBond[]
+  removed_bonds: StructureBond[]
+  bond_order_overrides: StructureBond[]
+}
+
+export type BondEditAction =
+  | `added`
+  | `already-visible`
+  | `deleted-added`
+  | `deleted-calculated`
+  | `not-visible`
+  | `ordered-added`
+  | `ordered-calculated`
+  | `restored`
+
+export type BondEditResult = {
+  action: BondEditAction
+  changed: boolean
+  state: BondEditState
+}
+
+export type BondKeyTarget = Pick<StructureBond, `site_idx_1` | `site_idx_2` | `cell_shift`>
+type BondOrderTarget = BondKeyTarget & {
+  bond_order?: BondOrder
+  order?: BondOrder
+}
+
+export const BOND_ORDER_OPTIONS: { order: BondOrder; label: string }[] = [
+  { order: 1, label: `Single` },
+  { order: 1.5, label: `1.5` },
+  { order: 2, label: `Double` },
+  { order: 3, label: `Triple` },
+  { order: `aromatic`, label: `Aromatic` },
+]
+
+const site_image_shift = (sites: Site[] | undefined, site_idx: number): Vec3 => {
+  const site = sites?.[site_idx]
+  const orig_site_idx = site?.properties?.orig_site_idx
+  if (typeof orig_site_idx !== `number`) return [0, 0, 0]
+  const orig_site = sites?.[orig_site_idx]
+  if (!site?.abc || !orig_site?.abc) return [0, 0, 0]
+  return [
+    Math.round(site.abc[0] - orig_site.abc[0]),
+    Math.round(site.abc[1] - orig_site.abc[1]),
+    Math.round(site.abc[2] - orig_site.abc[2]),
+  ]
+}
+
+const original_site_idx = (sites: Site[] | undefined, site_idx: number): number => {
+  const orig_site_idx = sites?.[site_idx]?.properties?.orig_site_idx
+  return typeof orig_site_idx === `number` ? orig_site_idx : site_idx
+}
+
+export const canonicalize_bond_target = (
+  bond: BondKeyTarget,
+  sites: Site[] | undefined,
+): BondKeyTarget => {
+  const shift_1 = site_image_shift(sites, bond.site_idx_1)
+  const shift_2 = site_image_shift(sites, bond.site_idx_2)
+  const base_shift = bond.cell_shift ?? [0, 0, 0]
+  const cell_shift: Vec3 = [
+    base_shift[0] + shift_2[0] - shift_1[0],
+    base_shift[1] + shift_2[1] - shift_1[1],
+    base_shift[2] + shift_2[2] - shift_1[2],
+  ]
+  return normalize_bond_endpoints(
+    original_site_idx(sites, bond.site_idx_1),
+    original_site_idx(sites, bond.site_idx_2),
+    cell_shift,
+  )
+}
+
+const bond_key_for = (bond: BondKeyTarget): string =>
+  get_bond_key(bond.site_idx_1, bond.site_idx_2, bond.cell_shift)
+
+const matches_bond_key = (bond: BondKeyTarget, key: string): boolean =>
+  bond_key_for(bond) === key
+
+const replace_bond = (bonds: StructureBond[], next_bond: StructureBond): StructureBond[] => {
+  const key = bond_key_for(next_bond)
+  return [...bonds.filter((bond) => !matches_bond_key(bond, key)), next_bond]
+}
+
+const remove_bond_key = (bonds: StructureBond[], key: string): StructureBond[] =>
+  bonds.filter((bond) => !matches_bond_key(bond, key))
+
+const includes_bond_key = (bonds: BondKeyTarget[], key: string): boolean =>
+  bonds.some((bond) => matches_bond_key(bond, key))
+
+const get_bond_order = (bond: BondOrderTarget | undefined): BondOrder =>
+  bond?.bond_order ?? bond?.order ?? 1
+
+const find_bond_by_key = <BondType extends BondKeyTarget>(
+  bonds: BondType[],
+  key: string,
+): BondType | undefined => bonds.find((bond) => matches_bond_key(bond, key))
+
+const make_bond_record = (bond: BondKeyTarget, order: BondOrder): StructureBond =>
+  normalize_structure_bond(bond.site_idx_1, bond.site_idx_2, order, bond.cell_shift)
+
+export function has_visible_bond(
+  edit_state: BondEditState,
+  bond: BondKeyTarget,
+  calculated_bonds: BondOrderTarget[],
+): boolean {
+  const key = bond_key_for(bond)
+  if (includes_bond_key(edit_state.removed_bonds, key)) {
+    return false
+  }
+  if (includes_bond_key(edit_state.added_bonds, key)) return true
+  return includes_bond_key(calculated_bonds, key)
+}
+
+export function add_or_restore_bond(
+  edit_state: BondEditState,
+  bond: BondKeyTarget,
+  calculated_bonds: BondOrderTarget[],
+  order: BondOrder,
+): BondEditResult {
+  const record = make_bond_record(bond, order)
+  const key = bond_key_for(record)
+  const removed_bond = find_bond_by_key(edit_state.removed_bonds, key)
+  if (removed_bond) {
+    return {
+      action: `restored`,
+      changed: true,
+      state: {
+        ...edit_state,
+        added_bonds: remove_bond_key(edit_state.added_bonds, key),
+        removed_bonds: remove_bond_key(edit_state.removed_bonds, key),
+        bond_order_overrides:
+          removed_bond.order === order
+            ? remove_bond_key(edit_state.bond_order_overrides, key)
+            : replace_bond(edit_state.bond_order_overrides, record),
+      },
+    }
+  }
+  if (has_visible_bond(edit_state, record, calculated_bonds)) {
+    return { action: `already-visible`, changed: false, state: edit_state }
+  }
+  return {
+    action: `added`,
+    changed: true,
+    state: {
+      ...edit_state,
+      added_bonds: replace_bond(edit_state.added_bonds, record),
+      bond_order_overrides: remove_bond_key(edit_state.bond_order_overrides, key),
+    },
+  }
+}
+
+export function delete_bond(
+  edit_state: BondEditState,
+  bond: BondKeyTarget,
+  calculated_bonds: BondOrderTarget[],
+): BondEditResult {
+  const record = make_bond_record(bond, 1)
+  const key = bond_key_for(record)
+  if (includes_bond_key(edit_state.added_bonds, key)) {
+    return {
+      action: `deleted-added`,
+      changed: true,
+      state: {
+        ...edit_state,
+        added_bonds: remove_bond_key(edit_state.added_bonds, key),
+        bond_order_overrides: remove_bond_key(edit_state.bond_order_overrides, key),
+      },
+    }
+  }
+  const calculated = find_bond_by_key(calculated_bonds, key)
+  if (!calculated || includes_bond_key(edit_state.removed_bonds, key)) {
+    return { action: `not-visible`, changed: false, state: edit_state }
+  }
+  return {
+    action: `deleted-calculated`,
+    changed: true,
+    state: {
+      ...edit_state,
+      removed_bonds: replace_bond(edit_state.removed_bonds, {
+        ...record,
+        order: get_bond_order(calculated),
+      }),
+      bond_order_overrides: remove_bond_key(edit_state.bond_order_overrides, key),
+    },
+  }
+}
+
+export function set_bond_order(
+  edit_state: BondEditState,
+  bond: BondKeyTarget,
+  calculated_bonds: BondOrderTarget[],
+  order: BondOrder,
+): BondEditResult {
+  const record = make_bond_record(bond, order)
+  const key = bond_key_for(record)
+  const calculated = find_bond_by_key(calculated_bonds, key)
+  if (calculated) {
+    const visible_order = get_bond_order(calculated)
+    const has_existing_edit =
+      includes_bond_key(edit_state.added_bonds, key) ||
+      includes_bond_key(edit_state.removed_bonds, key) ||
+      includes_bond_key(edit_state.bond_order_overrides, key)
+    const next_overrides =
+      order === visible_order
+        ? remove_bond_key(edit_state.bond_order_overrides, key)
+        : replace_bond(edit_state.bond_order_overrides, record)
+    const next_state = {
+      added_bonds: remove_bond_key(edit_state.added_bonds, key),
+      removed_bonds: remove_bond_key(edit_state.removed_bonds, key),
+      bond_order_overrides: next_overrides,
+    }
+    return {
+      action: `ordered-calculated`,
+      changed: has_existing_edit || order !== visible_order,
+      state: next_state,
+    }
+  }
+  return {
+    action: `ordered-added`,
+    changed: true,
+    state: {
+      ...edit_state,
+      added_bonds: replace_bond(edit_state.added_bonds, record),
+      bond_order_overrides: remove_bond_key(edit_state.bond_order_overrides, key),
+    },
+  }
+}
+
+export const merge_bond_edits = (
+  base_bonds: StructureBond[],
+  added: StructureBond[],
+  removed: StructureBond[],
+  overrides: StructureBond[],
+): StructureBond[] => {
+  const key_for = (bond: StructureBond): string =>
+    get_bond_key(bond.site_idx_1, bond.site_idx_2, bond.cell_shift)
+  const normalize_record = (bond: StructureBond): StructureBond =>
+    normalize_structure_bond(bond.site_idx_1, bond.site_idx_2, bond.order, bond.cell_shift)
+  const removed_keys = new Set(removed.map(key_for))
+  const merged = new Map(
+    base_bonds
+      .filter((bond) => !removed_keys.has(key_for(bond)))
+      .map((bond) => [key_for(bond), normalize_record(bond)]),
+  )
+  // Apply additions before overrides so user-set bond orders win even if
+  // callers accidentally pass overlapping edit lists.
+  for (const bond of added) {
+    if (!removed_keys.has(key_for(bond))) merged.set(key_for(bond), normalize_record(bond))
+  }
+  for (const bond of overrides) {
+    if (!removed_keys.has(key_for(bond))) merged.set(key_for(bond), normalize_record(bond))
+  }
+  return [...merged.values()]
+}
+
+const is_record = (value: unknown): value is Record<string, unknown> =>
+  typeof value === `object` && value !== null
+
+export function normalize_bond_order(order: unknown): BondOrder | null {
+  if (order === `aromatic`) return order
+  if (order === 1 || order === 1.5 || order === 2 || order === 3) return order
+  return null
+}
+
+function normalize_cell_shift(cell_shift: unknown): Vec3 | undefined | null {
+  if (cell_shift === undefined) return undefined
+  if (!Array.isArray(cell_shift) || cell_shift.length !== 3) return null
+  return cell_shift.some((val) => typeof val !== `number` || !Number.isInteger(val))
+    ? null
+    : [cell_shift[0], cell_shift[1], cell_shift[2]]
+}
+
+function lattice_translation(structure: AnyStructure, cell_shift: Vec3 | undefined): Vec3 {
+  if (cell_shift === undefined || is_zero_cell_shift(cell_shift)) return [0, 0, 0]
+  if (!(`lattice` in structure)) {
+    throw new Error(`Explicit bond cell_shift requires a crystal lattice`)
+  }
+  const [shift_a, shift_b, shift_c] = cell_shift
+  const [vec_a, vec_b, vec_c] = structure.lattice.matrix
+  return math.add(
+    math.scale(vec_a, shift_a),
+    math.scale(vec_b, shift_b),
+    math.scale(vec_c, shift_c),
+  )
+}
+
+export function structure_bond_to_bond_pair(
+  structure: AnyStructure,
+  bond: StructureBond,
+): BondPair {
+  const { site_idx_1, site_idx_2, order, cell_shift } = bond
+  const site_1 = structure.sites[site_idx_1]
+  const site_2 = structure.sites[site_idx_2]
+  if (!site_1 || !site_2) {
+    throw new Error(
+      `Cannot create bond pair for invalid site indices ${site_idx_1}, ${site_idx_2}`,
+    )
+  }
+  const pos_1 = site_1.xyz
+  const pos_2 = math.add(site_2.xyz, lattice_translation(structure, cell_shift))
+  return {
+    pos_1,
+    pos_2,
+    site_idx_1,
+    site_idx_2,
+    bond_length: math.euclidean_dist(pos_1, pos_2),
+    strength: 1,
+    bond_order: order,
+    cell_shift,
+    transform_matrix: compute_bond_transform(pos_1, pos_2),
+  }
+}
+
+export function get_explicit_bond_metadata(structure: AnyStructure): StructureBond[] {
+  const raw_bonds = structure.properties?.bonds
+  if (raw_bonds === undefined) return []
+  if (!Array.isArray(raw_bonds)) {
+    console.warn(`Ignoring structure.properties.bonds because it is not an array`)
+    return []
+  }
+
+  const explicit_bonds = new Map<string, StructureBond>()
+  for (const [entry_idx, raw_bond] of raw_bonds.entries()) {
+    if (!is_record(raw_bond)) {
+      console.warn(`Ignoring invalid explicit bond at index ${entry_idx}: expected object`)
+      continue
+    }
+    const { order } = raw_bond
+    const site_idx_1 = raw_bond.site_idx_1
+    const site_idx_2 = raw_bond.site_idx_2
+    if (
+      typeof site_idx_1 !== `number` ||
+      typeof site_idx_2 !== `number` ||
+      !Number.isInteger(site_idx_1) ||
+      !Number.isInteger(site_idx_2)
+    ) {
+      console.warn(
+        `Ignoring invalid explicit bond at index ${entry_idx}: site indices must be integers`,
+      )
+      continue
+    }
+    if (
+      site_idx_1 < 0 ||
+      site_idx_2 < 0 ||
+      site_idx_1 >= structure.sites.length ||
+      site_idx_2 >= structure.sites.length
+    ) {
+      console.warn(
+        `Ignoring invalid explicit bond at index ${entry_idx}: site indices ${
+          site_idx_1
+        }, ${site_idx_2} are out of range for ${structure.sites.length} sites`,
+      )
+      continue
+    }
+    const bond_order = normalize_bond_order(order)
+    if (bond_order === null) {
+      console.warn(
+        `Ignoring invalid explicit bond at index ${entry_idx}: unsupported order ${String(
+          order,
+        )}`,
+      )
+      continue
+    }
+    const cell_shift = normalize_cell_shift(raw_bond.cell_shift)
+    if (cell_shift === null) {
+      console.warn(
+        `Ignoring invalid explicit bond at index ${entry_idx}: cell_shift must be three integers`,
+      )
+      continue
+    }
+    if (site_idx_1 === site_idx_2 && is_zero_cell_shift(cell_shift)) {
+      console.warn(`Ignoring invalid explicit bond at index ${entry_idx}: endpoints match`)
+      continue
+    }
+    if (
+      cell_shift !== undefined &&
+      !is_zero_cell_shift(cell_shift) &&
+      !(`lattice` in structure)
+    ) {
+      console.warn(
+        `Ignoring invalid explicit bond at index ${entry_idx}: cell_shift requires a crystal lattice`,
+      )
+      continue
+    }
+
+    const key = get_bond_key(site_idx_1, site_idx_2, cell_shift)
+    if (explicit_bonds.has(key)) {
+      console.warn(
+        `Duplicate explicit bond definition at index ${entry_idx} for site indices ${
+          site_idx_1
+        }, ${site_idx_2} with order ${bond_order}; will overwrite the previous entry`,
+      )
+    }
+    explicit_bonds.set(
+      key,
+      normalize_structure_bond(site_idx_1, site_idx_2, bond_order, cell_shift),
+    )
+  }
+  return [...explicit_bonds.values()]
+}
+
+export function apply_explicit_bond_metadata(
+  structure: AnyStructure,
+  bonds: BondPair[],
+): BondPair[] {
+  const explicit_bonds = get_explicit_bond_metadata(structure)
+  if (explicit_bonds.length === 0) return bonds
+
+  const explicit_by_key = new Map(
+    explicit_bonds.map((bond) => [
+      get_bond_key(bond.site_idx_1, bond.site_idx_2, bond.cell_shift),
+      bond,
+    ]),
+  )
+  const merged = bonds.map((bond) => {
+    const key = get_bond_key(bond.site_idx_1, bond.site_idx_2, bond.cell_shift)
+    const explicit = explicit_by_key.get(key)
+    if (!explicit) return bond
+    explicit_by_key.delete(key)
+    return { ...bond, bond_order: explicit.order }
+  })
+
+  for (const explicit_bond of explicit_by_key.values()) {
+    merged.push(structure_bond_to_bond_pair(structure, explicit_bond))
+  }
+
+  return merged
+}
+
+export function scale_and_offset_bond_matrix(
+  transform_matrix: Float32Array,
+  offset: number,
+  radius_scale: number,
+): Float32Array {
+  const matrix = new Float32Array(transform_matrix)
+  // Column-major 4x4 layout: 0-2 are the right vector, 8-10 are the forward
+  // vector. Scale orientation columns for cylinder radius, not translation.
+  for (const matrix_idx of [0, 1, 2, 8, 9, 10]) {
+    matrix[matrix_idx] *= radius_scale
+  }
+
+  const right_len = Math.hypot(matrix[0], matrix[1], matrix[2]) || 1
+  const offset_dir: Vec3 = [
+    matrix[0] / right_len,
+    matrix[1] / right_len,
+    matrix[2] / right_len,
+  ]
+  matrix[12] += offset_dir[0] * offset
+  matrix[13] += offset_dir[1] * offset
+  matrix[14] += offset_dir[2] * offset
+  return matrix
+}
+
+export function get_bond_render_matrices(
+  bond: BondPair,
+  bond_thickness: number,
+): Float32Array[] {
+  const order = bond.bond_order ?? 1
+  const gap = bond_thickness * 1.8
+  const offsets_and_scales: [number, number][] =
+    order === 2
+      ? [
+          [-gap / 2, 0.65],
+          [gap / 2, 0.65],
+        ]
+      : order === 3
+        ? [
+            [-gap, 0.55],
+            [0, 0.55],
+            [gap, 0.55],
+          ]
+        : order === 1.5 || order === `aromatic`
+          ? [
+              [-gap / 2, 0.75],
+              [gap / 2, 0.4],
+            ]
+          : []
+  return offsets_and_scales.length === 0
+    ? [bond.transform_matrix]
+    : offsets_and_scales.map(([offset, radius_scale]) =>
+        scale_and_offset_bond_matrix(bond.transform_matrix, offset, radius_scale),
+      )
+}
+
+// Get the species with highest occupancy from a site.
+const get_majority_species = (site: Site) =>
+  (site.species ?? []).reduce(
+    (max_species, species) => (species.occu > max_species.occu ? species : max_species),
+    site.species?.[0] ?? { element: ``, occu: -1 },
+  )
+
+// Helper to extract numeric index from site properties
+function get_orig_idx(site: Site, fallback: number): number {
+  const props = site.properties
+  if (!props) return fallback
+
+  const raw = props.orig_unit_cell_idx ?? props.orig_site_idx
+  if (raw === undefined) return fallback
+
+  const num = Number(raw)
+  return Number.isFinite(num) ? num : fallback
+}
+
+// Compute 4x4 transformation matrix for bond cylinder between two positions.
+// Uses Y-up, right-handed coordinate system convention for Three.js compatibility.
+export function compute_bond_transform(pos_1: Vec3, pos_2: Vec3): Float32Array {
+  const [dx, dy, dz] = math.subtract(pos_2, pos_1)
+  const height = Math.hypot(dx, dy, dz)
+
+  if (height < 1e-10) {
+    return new Float32Array([1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1])
+  }
+
+  const [dir_x, dir_y, dir_z] = [dx / height, dy / height, dz / height]
+  let [m00, m01, m02, m10, m11, m12, m20, m21, m22] = [0, 0, 0, 0, 0, 0, 0, 0, 0]
+
+  // Special case: bond pointing straight up (+Y)
+  if (Math.abs(dir_y - 1.0) < 1e-10) {
+    ;[m00, m01, m02, m10, m11, m12, m20, m21, m22] = [1, 0, 0, 0, 1, 0, 0, 0, 1]
+  } else if (Math.abs(dir_y + 1.0) < 1e-10) {
+    // Special case: bond pointing straight down (-Y)
+    ;[m00, m01, m02, m10, m11, m12, m20, m21, m22] = [1, 0, 0, 0, -1, 0, 0, 0, 1]
+  } else {
+    // General case: construct orthonormal basis (right, dir, up)
+    // Right vector: perpendicular to dir in XZ plane
+    const [rx, rz] = [-dir_z, dir_x]
+    const r_len = Math.hypot(rx, rz)
+    const [right_x, right_z] = [rx / r_len, rz / r_len]
+    // Up vector: cross product of dir and right
+    const [up_x, up_y, up_z] = [
+      dir_y * right_z,
+      dir_z * right_x - dir_x * right_z,
+      -dir_y * right_x,
+    ]
+    ;[m00, m01, m02, m10, m11, m12, m20, m21, m22] = [
+      right_x,
+      dir_x,
+      up_x,
+      0,
+      dir_y,
+      up_y,
+      right_z,
+      dir_z,
+      up_z,
+    ]
+  }
+
+  // Position at midpoint between the two atoms
+  const [px, py, pz] = [
+    (pos_1[0] + pos_2[0]) / 2,
+    (pos_1[1] + pos_2[1]) / 2,
+    (pos_1[2] + pos_2[2]) / 2,
+  ]
+
+  return new Float32Array([
+    // Return flattened column-major 4x4 matrix for Three.js
+    m00,
+    m10,
+    m20,
+    0,
+    m01 * height,
+    m11 * height,
+    m21 * height,
+    0,
+    m02,
+    m12,
+    m22,
+    0,
+    px,
+    py,
+    pz,
+    1,
+  ])
+}
+
+// Build spatial grid by dividing 3D space into cubic cells.
+function build_spatial_grid(sites: Site[], cell_size: number): SpatialGrid {
+  const grid: SpatialGrid = new Map()
+  for (let idx = 0; idx < sites.length; idx++) {
+    const [x, y, z] = sites[idx].xyz.map((coord) => Math.floor(coord / cell_size))
+    const key = `${x},${y},${z}`
+    const cell = grid.get(key)
+    if (cell) cell.push(idx)
+    else grid.set(key, [idx])
+  }
+  return grid
+}
+
+// Get all site indices in 3x3x3 cube of cells around position.
+function get_neighbors_from_grid(pos: Vec3, grid: SpatialGrid, cell_size: number): number[] {
+  const [cx, cy, cz] = [
+    Math.floor(pos[0] / cell_size),
+    Math.floor(pos[1] / cell_size),
+    Math.floor(pos[2] / cell_size),
+  ]
+  const neighbors: number[] = []
+  for (let dx = -1; dx <= 1; dx++) {
+    for (let dy = -1; dy <= 1; dy++) {
+      for (let dz = -1; dz <= 1; dz++) {
+        const cell = grid.get(`${cx + dx},${cy + dy},${cz + dz}`)
+        if (cell) neighbors.push(...cell)
+      }
+    }
+  }
+  return neighbors
+}
+
+// Setup spatial decomposition for structures with >50 atoms.
+function setup_spatial_grid(sites: Site[], cutoff: number) {
+  const use_grid = sites.length > 50
+  return use_grid ? { grid: build_spatial_grid(sites, cutoff), cell_size: cutoff } : null
+}
+
+// Get candidate neighbor indices using spatial grid or all sites.
+const get_candidates = (
+  pos: Vec3,
+  sites: Site[],
+  spatial: ReturnType<typeof setup_spatial_grid>,
+): number[] =>
+  spatial
+    ? get_neighbors_from_grid(pos, spatial.grid, spatial.cell_size)
+    : Array.from({ length: sites.length }, (_, idx) => idx)
+
+export const BONDING_STRATEGIES = { electroneg_ratio, solid_angle } as const
+export type BondingStrategy = keyof typeof BONDING_STRATEGIES
+export type BondingAlgo = (typeof BONDING_STRATEGIES)[BondingStrategy]
+
+// Electronegativity-based bonding with chemical preferences.
+// This algorithm considers electronegativity differences between atoms, metal/nonmetal
+// properties, and distance to determine bond strength. Bonds are only created if the
+// computed strength exceeds the strength_threshold parameter (default: 0.3).
+export function electroneg_ratio(
+  structure: AnyStructure,
+  {
+    electronegativity_threshold = 1.7, // Max electronegativity difference for bonding
+    max_distance_ratio = 2.0, // Max distance as multiple of sum of covalent radii
+    min_bond_dist = 0.4, // Minimum bond distance in Angstroms
+    metal_metal_penalty = 0.7, // Strength penalty for metal-metal bonds
+    metal_nonmetal_bonus = 1.5, // Strength bonus for metal-nonmetal bonds
+    similar_electronegativity_bonus = 1.2, // Bonus for similar electronegativity
+    same_species_penalty = 0.5, // Penalty for bonds between same element
+    strength_threshold = 0.3, // Minimum bond strength to include in results
+  } = {},
+): BondPair[] {
+  const { sites } = structure
+  if (sites.length < 2) return []
+
+  const bonds: BondPair[] = []
+  const min_dist_sq = min_bond_dist ** 2
+  const closest = new Map<number, number>()
+
+  const props = sites.map((site) => {
+    const majority = get_majority_species(site)
+    const elem = majority.element
+    const data = element_lookup.get(elem)
+    return {
+      element: elem,
+      electroneg: data?.electronegativity ?? 2.0,
+      is_metal: data?.metal ?? false,
+      is_nonmetal: data?.nonmetal ?? false,
+      radius: elem ? covalent_radii.get(elem) : undefined,
+    }
+  })
+
+  let max_radius = 0
+  for (const radius of covalent_radii.values()) {
+    if (radius > max_radius) max_radius = radius
+  }
+  const max_cutoff = max_radius * 2 * max_distance_ratio
+  const spatial = setup_spatial_grid(sites, max_cutoff)
+
+  // Two-pass approach to ensure symmetry between original and image atoms:
+  // 1. Collect all potential bonds and determine closest neighbor distance for each unique atom (orig_idx)
+  // 2. Filter bonds based on penalties using the fully populated closest distances
+
+  interface PotentialBond {
+    site_idx_1: number
+    site_idx_2: number
+    dist: number
+    expected_dist: number
+    base_strength: number
+    orig_idx_a: number
+    orig_idx_b: number
+  }
+
+  const potential_bonds: PotentialBond[] = []
+
+  for (let idx_a = 0; idx_a < sites.length - 1; idx_a++) {
+    const [x1, y1, z1] = sites[idx_a].xyz
+    const props_a = props[idx_a]
+
+    for (const idx_b of get_candidates(sites[idx_a].xyz, sites, spatial)) {
+      if (idx_b <= idx_a) continue
+
+      const [x2, y2, z2] = sites[idx_b].xyz
+      const props_b = props[idx_b]
+
+      const [dx, dy, dz] = [x2 - x1, y2 - y1, z2 - z1]
+      const dist_sq = dx * dx + dy * dy + dz * dz
+      const dist = Math.sqrt(dist_sq)
+
+      if (dist_sq < min_dist_sq || !props_a.radius || !props_b.radius) continue
+
+      const expected = props_a.radius + props_b.radius
+      if (dist > expected * max_distance_ratio) continue
+
+      const electroneg_diff = Math.abs(props_a.electroneg - props_b.electroneg)
+      const electroneg_balance = electroneg_diff / (props_a.electroneg + props_b.electroneg)
+
+      let bond_strength = 1.0
+      if (props_a.is_metal && props_b.is_metal) {
+        bond_strength *= metal_metal_penalty
+      } else if (
+        (props_a.is_metal && props_b.is_nonmetal) ||
+        (props_a.is_nonmetal && props_b.is_metal)
+      ) {
+        bond_strength *= metal_nonmetal_bonus
+        if (electroneg_diff > electronegativity_threshold) bond_strength *= 1.3
+      } else if (electroneg_diff < 0.5) {
+        bond_strength *= similar_electronegativity_bonus
+      }
+
+      const dist_weight = Math.exp(-((dist / expected - 1) ** 2) / 0.18)
+      const electroneg_weight = 1.0 - 0.3 * electroneg_balance
+      let strength = bond_strength * dist_weight * electroneg_weight
+
+      if (props_a.element === props_b.element) strength *= same_species_penalty
+
+      // If raw strength is already too low, we can skip early
+      // (penalty will only reduce it further)
+      if (strength <= strength_threshold) continue
+
+      // Use helper logic to handle both supercell and image atoms with robust normalization
+      const orig_idx_a = get_orig_idx(sites[idx_a], idx_a)
+      const orig_idx_b = get_orig_idx(sites[idx_b], idx_b)
+
+      // Update closest known normalized distance (dist / expected) for original atoms
+      // Normalized distance handles atoms of different sizes better than raw distance
+      // (e.g. C-H is short but C-C is longer; we don't want C-H to penalize C-C just because H is small)
+      const norm_dist = dist / expected
+      const closest_dist_a = closest.get(orig_idx_a) ?? Infinity
+      if (norm_dist < closest_dist_a) closest.set(orig_idx_a, norm_dist)
+
+      const closest_dist_b = closest.get(orig_idx_b) ?? Infinity
+      if (norm_dist < closest_dist_b) closest.set(orig_idx_b, norm_dist)
+
+      potential_bonds.push({
+        site_idx_1: idx_a,
+        site_idx_2: idx_b,
+        dist,
+        expected_dist: expected,
+        base_strength: strength,
+        orig_idx_a,
+        orig_idx_b,
+      })
+    }
+  }
+
+  // Second pass: Apply penalties and filter
+  for (const bond of potential_bonds) {
+    const {
+      site_idx_1,
+      site_idx_2,
+      dist,
+      expected_dist,
+      base_strength,
+      orig_idx_a,
+      orig_idx_b,
+    } = bond
+
+    const closest_dist_a = closest.get(orig_idx_a) ?? Infinity
+    const closest_dist_b = closest.get(orig_idx_b) ?? Infinity
+    const norm_dist = dist / expected_dist
+
+    let strength = base_strength
+
+    // Apply penalty if this bond is much longer (relative to radii) than the closest known bond
+    if (norm_dist > closest_dist_a) {
+      strength *= Math.exp(-(norm_dist / closest_dist_a - 1) / 0.5)
+    }
+    if (orig_idx_b !== orig_idx_a && norm_dist > closest_dist_b) {
+      strength *= Math.exp(-(norm_dist / closest_dist_b - 1) / 0.5)
+    }
+
+    if (strength > strength_threshold) {
+      bonds.push({
+        pos_1: sites[site_idx_1].xyz,
+        pos_2: sites[site_idx_2].xyz,
+        site_idx_1,
+        site_idx_2,
+        bond_length: dist,
+        strength,
+        transform_matrix: compute_bond_transform(sites[site_idx_1].xyz, sites[site_idx_2].xyz),
+      })
+    }
+  }
+
+  return apply_explicit_bond_metadata(structure, bonds)
+}
+
+// Solid angle-based bonding using geometric proximity heuristics.
+// Inspired by Voronoi tessellation without having to actually compute Voronoi cells.
+// This algorithm computes bond strength based on the solid angle subtended by atoms
+// and their distance penalty. Bonds are only created if the computed strength exceeds
+// the strength_threshold parameter.
+export function solid_angle(
+  structure: AnyStructure,
+  {
+    min_solid_angle = 0.01,
+    min_face_area = 0.05,
+    max_distance = 5.0,
+    min_bond_dist = 0.4,
+    strength_threshold = 0.05,
+  } = {},
+): BondPair[] {
+  const { sites } = structure
+  if (sites.length < 2) return []
+
+  const bonds: BondPair[] = []
+  const min_dist_sq = min_bond_dist ** 2
+  const max_dist_sq = max_distance ** 2
+  const spatial = setup_spatial_grid(sites, max_distance)
+
+  for (let idx_a = 0; idx_a < sites.length - 1; idx_a++) {
+    const [x1, y1, z1] = sites[idx_a].xyz
+    const majority_a = get_majority_species(sites[idx_a])
+    const radius_a = majority_a.element ? covalent_radii.get(majority_a.element) : undefined
+
+    for (const idx_b of get_candidates(sites[idx_a].xyz, sites, spatial)) {
+      if (idx_b <= idx_a) continue
+
+      const [x2, y2, z2] = sites[idx_b].xyz
+      const majority_b = get_majority_species(sites[idx_b])
+      const radius_b = majority_b.element ? covalent_radii.get(majority_b.element) : undefined
+
+      const [dx, dy, dz] = [x2 - x1, y2 - y1, z2 - z1]
+      const dist_sq = dx * dx + dy * dy + dz * dz
+      const dist = Math.sqrt(dist_sq)
+
+      if (dist_sq < min_dist_sq || dist_sq > max_dist_sq || !radius_a || !radius_b) {
+        continue
+      }
+
+      const avg_radius = (radius_a + radius_b) / 2.0
+      const face_area = Math.PI * avg_radius * avg_radius
+      const bond_solid_angle = face_area / dist_sq
+
+      if (bond_solid_angle < min_solid_angle || face_area < min_face_area) continue
+
+      const dist_penalty = Math.exp(-((dist / (radius_a + radius_b) - 1) ** 2) / 0.4)
+      const angle_strength = Math.min(bond_solid_angle / (4.0 * Math.PI), 1.0)
+      const strength = angle_strength * dist_penalty
+
+      if (strength > strength_threshold) {
+        bonds.push({
+          pos_1: sites[idx_a].xyz,
+          pos_2: sites[idx_b].xyz,
+          site_idx_1: idx_a,
+          site_idx_2: idx_b,
+          bond_length: dist,
+          strength,
+          transform_matrix: compute_bond_transform(sites[idx_a].xyz, sites[idx_b].xyz),
+        })
+      }
+    }
+  }
+  return apply_explicit_bond_metadata(structure, bonds)
+}