matsci-parse 0.0.3 → 0.1.1

package/dist/main.js

@@ -1,319 +1,457 @@
-class y {
-  constructor(e, s, i = {}) {
-    this.speciesIndex = e, this.cart = s, this.props = i;
+class x {
+  constructor(e, t, n = {}) {
+    this.speciesIndex = e, this.cart = t, this.props = n;
   }
   getProp(e) {
     return this.props[e];
   }
-  setProp(e, s) {
-    this.props[e] = s;
+  setProp(e, t) {
+    this.props[e] = t;
   }
 }
-function A(t) {
-  return t.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
+function C(s) {
+  return s.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
 }
-class S {
+function E(s) {
+  return s * Math.PI / 180;
+}
+function $(s, e) {
+  return s.map(
+    (t) => t[0] * e[0] + t[1] * e[1] + t[2] * e[2]
+  );
+}
+function T(s, e, t, n, o, i) {
+  const a = E(n), c = E(o), h = E(i), m = [s, 0, 0], p = [
+    e * Math.cos(h),
+    e * Math.sin(h),
+    0
+  ], u = t * Math.cos(c), l = t * (Math.cos(a) - Math.cos(c) * Math.cos(h)) / Math.sin(h), d = Math.sqrt(t * t - u * u - l * l);
+  return [m, p, [u, l, d]];
+}
+function L(s, e) {
+  const [t, n, o] = e;
+  return [
+    s[0] * t[0] + s[1] * n[0] + s[2] * o[0],
+    s[0] * t[1] + s[1] * n[1] + s[2] * o[1],
+    s[0] * t[2] + s[1] * n[2] + s[2] * o[2]
+  ];
+}
+class w {
+  /**
+   * Creates a new CrystalStructure.
+   *
+   * @param props - Object containing lattice, species, and sites
+   * @param props.lattice - 3x3 array of Cartesian lattice vectors
+   * @param props.species - List of chemical species
+   * @param props.sites - List of Site instances or objects with speciesIndex and Cartesian coordinates
+   *
+   * @throws Will throw an error if lattice is not 3x3, species is not an array of strings, or sites are invalid
+   */
   constructor({
     lattice: e,
-    species: s,
-    sites: i
+    species: t,
+    sites: n
   }) {
-    this.lattice = this._validateLattice(e), this.species = this._validateSpecies(s), this.sites = this._validateSites(i);
+    this.lattice = this._validateLattice(e), this.species = this._validateSpecies(t), this.sites = this._validateSites(n);
   }
   // ---------- Simple methods ----------
+  /** Number of sites in the structure */
   get numSites() {
     return this.sites.length;
   }
+  /**
+   * Returns the site at the specified index.
+   * @param i - Site index
+   */
   site(e) {
     return this.sites[e];
   }
+  /**
+   * Returns the Cartesian coordinates of a site.
+   * @param i - Site index
+   */
   cartCoords(e) {
     return this.sites[e].cart;
   }
+  /**
+   * Returns the chemical species of a site.
+   * @param i - Site index
+   */
   siteSpecies(e) {
     return this.species[this.sites[e].speciesIndex];
   }
+  /** Returns the array of elements (species) in the structure */
   get elements() {
     return this.species;
   }
-  addSite(e, s) {
-    this._validateSpeciesIndex(e), this.sites.push(new y(e, s));
+  /**
+   * Adds a new site to the crystal.
+   * If the species is not already in the structure, it is added automatically.
+   *
+   * @param species - Name of the species
+   * @param cart - Cartesian coordinates of the new site
+   * @param position - Optional index at which to insert the site. Defaults to appending at the end.
+   */
+  addSite(e, t, n) {
+    let o = this.species.indexOf(e);
+    o === -1 && (this.species.push(e), o = this.species.length - 1);
+    const i = new x(o, t);
+    n === void 0 || n >= this.sites.length ? this.sites.push(i) : n < 0 ? this.sites.unshift(i) : this.sites.splice(n, 0, i);
   }
+  /**
+   * Removes a site from the crystal.
+   * Automatically removes species from the species array if no other site uses it.
+   * Updates speciesIndex for remaining sites if necessary.
+   *
+   * @param index - Index of the site to remove
+   *
+   * @throws Will throw an error if index is out of bounds
+   */
   removeSite(e) {
-    this.sites.splice(e, 1);
+    if (e < 0 || e >= this.sites.length)
+      throw new Error("siteIndex out of bounds");
+    const n = this.sites.splice(e, 1)[0].speciesIndex;
+    this.sites.some(
+      (i) => i.speciesIndex === n
+    ) || (this.species.splice(n, 1), this.sites.forEach((i) => {
+      i.speciesIndex > n && (i.speciesIndex -= 1);
+    }));
+  }
+  /**
+   * Replaces the species of a site at the given index.
+   * Internally calls `removeSite` and `addSite` to ensure species array cleanup
+   * and proper indexing. The site’s coordinates are preserved.
+   *
+   * @param siteIndex - Index of the site to replace
+   * @param newSpecies - Name of the new species
+   *
+   * @throws Will throw an error if siteIndex is out of bounds
+   */
+  replaceSite(e, t) {
+    if (e < 0 || e >= this.sites.length)
+      throw new Error("siteIndex out of bounds");
+    const n = [...this.sites[e].cart];
+    this.removeSite(e), this.addSite(t, n, e);
+  }
+  /**
+   * Returns a new CrystalStructure transformed by a linear matrix.
+   *
+   * Can be used for uniform scaling, diagonal scaling, or applying a full 3x3 transformation matrix.
+   *
+   * @param scale - Transformation to apply:
+   *   - single number: uniform scaling along all axes
+   *   - 3-element array: diagonal scaling [sx, sy, sz]
+   *   - 3x3 matrix: full linear transformation
+   * @returns A new CrystalStructure instance with transformed lattice and sites
+   *
+   * @throws Will throw an error if scale is not a number, a 3-element array, or a 3x3 matrix
+   */
+  applyLatticeTransformation(e) {
+    let t;
+    if (typeof e == "number")
+      t = [
+        [e, 0, 0],
+        [0, e, 0],
+        [0, 0, e]
+      ];
+    else if (Array.isArray(e) && e.length === 3 && e.every((i) => typeof i == "number"))
+      t = [
+        [e[0], 0, 0],
+        [0, e[1], 0],
+        [0, 0, e[2]]
+      ];
+    else if (Array.isArray(e) && e.length === 3 && e.every((i) => Array.isArray(i) && i.length === 3))
+      t = e;
+    else
+      throw new Error(
+        "Scale must be a number, a 3-element array, or a 3x3 matrix"
+      );
+    const n = this.lattice.map(
+      (i) => $(t, i)
+    ), o = this.sites.map((i) => {
+      const a = $(
+        t,
+        i.cart
+      );
+      return new x(i.speciesIndex, a, i.props);
+    });
+    return new w({
+      lattice: n,
+      species: [...this.species],
+      sites: o
+    });
   }
   // ---------- Internal validation ----------
+  /**
+   * Validates that the lattice is a 3x3 array of Cartesian vectors.
+   * @throws Will throw an error if lattice is invalid
+   */
   _validateLattice(e) {
     if (!Array.isArray(e) || e.length !== 3)
       throw new Error("Lattice must be a 3x3 matrix");
-    return e.forEach((s) => {
-      if (!Array.isArray(s) || s.length !== 3)
+    return e.forEach((t) => {
+      if (!Array.isArray(t) || t.length !== 3)
         throw new Error("Lattice vectors must be length 3");
     }), e;
   }
+  /**
+   * Validates that species is an array of strings.
+   * @throws Will throw an error if species array is invalid
+   */
   _validateSpecies(e) {
     if (!Array.isArray(e)) throw new Error("Species must be an array");
-    return e.forEach((s) => {
-      if (typeof s != "string")
+    return e.forEach((t) => {
+      if (typeof t != "string")
         throw new Error("Species entries must be strings");
     }), e;
   }
+  /**
+   * Validates the sites array, ensuring each site is a Site instance or a valid object.
+   * @throws Will throw an error if sites array is invalid
+   */
   _validateSites(e) {
     if (!Array.isArray(e)) throw new Error("Sites must be an array");
-    return e.map((s) => {
-      if (s instanceof y) return s;
-      if (typeof s == "object" && typeof s.speciesIndex == "number" && Array.isArray(s.cart) && s.cart.length === 3)
-        return this._validateSpeciesIndex(s.speciesIndex), new y(
-          s.speciesIndex,
-          s.cart,
-          s.props ?? {}
+    return e.map((t) => {
+      if (t instanceof x) return t;
+      if (typeof t == "object" && typeof t.speciesIndex == "number" && Array.isArray(t.cart) && t.cart.length === 3)
+        return this._validateSpeciesIndex(t.speciesIndex), new x(
+          t.speciesIndex,
+          t.cart,
+          t.props ?? {}
         );
       throw new Error(
         "Each site must be a Site instance or a valid site object"
       );
     });
   }
+  /**
+   * Validates that a species index is within bounds.
+   * @throws Will throw an error if index is out of range
+   */
   _validateSpeciesIndex(e) {
     if (e < 0 || e >= this.species.length)
       throw new Error("speciesIndex out of bounds");
   }
 }
-function I(t) {
-  return t.split(/\r?\n/).map((e) => e.trim()).filter(Boolean);
+function F(s) {
+  return s.split(/\r?\n/).map((e) => e.trim()).filter(Boolean);
 }
-function D(t) {
-  const e = [], s = A(t);
-  e.push("Generated by matsci-parse"), e.push("1.0"), t.lattice.forEach((n) => {
-    e.push(n.map((c) => c.toFixed(10)).join(" "));
+function P(s, e = 6) {
+  const t = [], n = C(s);
+  t.push("Generated by matsci-parse"), t.push("1.0"), s.lattice.forEach((a) => {
+    t.push(a.map((c) => c.toFixed(e)).join(" "));
   });
-  const i = Array.from(
-    new Set(t.sites.map((n) => t.species[n.speciesIndex]))
-  ), o = i.map(
-    (n) => t.sites.filter((c) => t.species[c.speciesIndex] === n).length
+  const o = Array.from(
+    new Set(s.sites.map((a) => s.species[a.speciesIndex]))
+  ), i = o.map(
+    (a) => s.sites.filter((c) => s.species[c.speciesIndex] === a).length
   );
-  return e.push(i.join(" ")), e.push(o.join(" ")), s && e.push("Selective dynamics"), e.push("Cartesian"), i.forEach((n) => {
-    t.sites.filter((c) => t.species[c.speciesIndex] === n).forEach((c) => {
-      const l = c.cart.map((u) => u.toFixed(10)).join(" ");
-      if (s) {
-        const m = (Array.isArray(c.props?.selectiveDynamics) ? c.props.selectiveDynamics : [!0, !0, !0]).map((p) => p ? "T" : "F").join(" ");
-        e.push(`${l} ${m}`);
+  return t.push(o.join(" ")), t.push(i.join(" ")), n && t.push("Selective dynamics"), t.push("Cartesian"), o.forEach((a) => {
+    s.sites.filter((c) => s.species[c.speciesIndex] === a).forEach((c) => {
+      const h = c.cart.map((m) => m.toFixed(e)).join(" ");
+      if (n) {
+        const p = (Array.isArray(c.props?.selectiveDynamics) ? c.props.selectiveDynamics : [!0, !0, !0]).map((u) => u ? "T" : "F").join(" ");
+        t.push(`${h} ${p}`);
       } else
-        e.push(l);
+        t.push(h);
     });
-  }), e.join(`
+  }), t.join(`
 `);
 }
-function T(t) {
+function j(s) {
   let e = 0;
   e++;
-  const s = parseFloat(t[e++]), i = [];
-  for (let h = 0; h < 3; h++)
-    i.push(
-      t[e++].split(/\s+/).map((f) => parseFloat(f) * s)
+  const t = parseFloat(s[e++]), n = [];
+  for (let u = 0; u < 3; u++)
+    n.push(
+      s[e++].split(/\s+/).map((l) => parseFloat(l) * t)
     );
-  let o = t[e].trim(), n;
-  /^[A-Za-z]/.test(o) && (n = o.split(/\s+/), e++);
-  const c = t[e++].split(/\s+/).map(Number);
-  n || (n = c.map((h, f) => `X${f + 1}`));
-  let l = !1;
-  t[e]?.toLowerCase().startsWith("s") && (l = !0, e++);
-  const m = t[e++].toLowerCase().startsWith("d"), p = [];
-  return n.forEach((h, f) => {
-    for (let _ = 0; _ < c[f]; _++) {
-      const r = t[e++].split(/\s+/).map(Number);
-      let d;
-      m ? d = [
-        r[0] * i[0][0] + r[1] * i[1][0] + r[2] * i[2][0],
-        r[0] * i[0][1] + r[1] * i[1][1] + r[2] * i[2][1],
-        r[0] * i[0][2] + r[1] * i[1][2] + r[2] * i[2][2]
-      ] : d = r.slice(0, 3);
+  let o = s[e].trim(), i;
+  /^[A-Za-z]/.test(o) && (i = o.split(/\s+/), e++);
+  const a = s[e++].split(/\s+/).map(Number);
+  i || (i = a.map((u, l) => `X${l + 1}`));
+  let c = !1;
+  s[e]?.toLowerCase().startsWith("s") && (c = !0, e++);
+  const m = s[e++].toLowerCase().startsWith("d"), p = [];
+  return i.forEach((u, l) => {
+    for (let d = 0; d < a[l]; d++) {
+      const r = s[e++].split(/\s+/).map(Number);
+      let f;
+      m ? f = [
+        r[0] * n[0][0] + r[1] * n[1][0] + r[2] * n[2][0],
+        r[0] * n[0][1] + r[1] * n[1][1] + r[2] * n[2][1],
+        r[0] * n[0][2] + r[1] * n[1][2] + r[2] * n[2][2]
+      ] : f = r.slice(0, 3);
       const g = {};
-      if (l) {
-        const x = r.slice(3, 6).map((a) => a === 1);
-        x.length === 3 && (g.selectiveDynamics = x);
+      if (c) {
+        const y = r.slice(3, 6).map((_) => _ === 1);
+        y.length === 3 && (g.selectiveDynamics = y);
       }
-      p.push(new y(f, d, g));
+      p.push(new x(l, f, g));
     }
   }), {
-    structure: new S({ lattice: i, species: n, sites: p }),
+    structure: new w({ lattice: n, species: i, sites: p }),
     linesConsumed: e
   };
 }
-function P(t) {
-  const e = I(t);
-  return T(e).structure;
+function R(s) {
+  const e = F(s);
+  return j(e).structure;
 }
-function R(t) {
-  const e = [];
-  return e.push("CRYSTAL"), e.push("PRIMVEC"), t.lattice.forEach((s) => {
-    e.push(s.map((i) => i.toFixed(10)).join(" "));
-  }), e.push("PRIMCOORD"), e.push(`${t.numSites} 1`), t.sites.forEach((s) => {
-    const i = t.species[s.speciesIndex];
-    e.push(`${i} ${s.cart.map((o) => o.toFixed(10)).join(" ")}`);
-  }), e.join(`
+function W(s, e = 6) {
+  const t = [];
+  return t.push("CRYSTAL"), t.push("PRIMVEC"), s.lattice.forEach((n) => {
+    t.push(n.map((o) => o.toFixed(e)).join(" "));
+  }), t.push("PRIMCOORD"), t.push(`${s.numSites} 1`), s.sites.forEach((n) => {
+    const o = s.species[n.speciesIndex];
+    t.push(
+      `${o} ${n.cart.map((i) => i.toFixed(e)).join(" ")}`
+    );
+  }), t.join(`
 `);
 }
-function W(t) {
-  const e = I(t), s = [], i = [], o = [];
-  let n = 0;
-  for (; n < e.length && e[n].toUpperCase() !== "PRIMVEC"; ) n++;
-  if (n === e.length) throw new Error("PRIMVEC block not found in XSF");
-  n++;
-  for (let l = 0; l < 3; l++)
-    s.push(e[n++].split(/\s+/).map(Number));
-  for (; n < e.length && e[n].toUpperCase() !== "PRIMCOORD"; ) n++;
-  if (n === e.length) throw new Error("PRIMCOORD block not found in XSF");
-  n++;
-  const [c] = e[n++].split(/\s+/).map(Number);
-  for (let l = 0; l < c; l++) {
-    const u = e[n++].split(/\s+/), m = u[0], p = u.slice(1, 4).map(Number);
-    let h = i.indexOf(m);
-    h === -1 && (i.push(m), h = i.length - 1), o.push(new y(h, p));
+function O(s) {
+  const e = F(s), t = [], n = [], o = [];
+  let i = 0;
+  for (; i < e.length && e[i].toUpperCase() !== "PRIMVEC"; ) i++;
+  if (i === e.length) throw new Error("PRIMVEC block not found in XSF");
+  i++;
+  for (let c = 0; c < 3; c++)
+    t.push(e[i++].split(/\s+/).map(Number));
+  for (; i < e.length && e[i].toUpperCase() !== "PRIMCOORD"; ) i++;
+  if (i === e.length) throw new Error("PRIMCOORD block not found in XSF");
+  i++;
+  const [a] = e[i++].split(/\s+/).map(Number);
+  for (let c = 0; c < a; c++) {
+    const h = e[i++].split(/\s+/), m = h[0], p = h.slice(1, 4).map(Number);
+    let u = n.indexOf(m);
+    u === -1 && (n.push(m), u = n.length - 1), o.push(new x(u, p));
   }
-  return new S({ lattice: s, species: i, sites: o });
+  return new w({ lattice: t, species: n, sites: o });
 }
-function O(t) {
-  const e = [], s = t.sites.length;
-  e.push(String(s));
-  const i = A(t), o = t.lattice, n = [
-    o[0][0],
-    o[1][0],
-    o[2][0],
-    o[0][1],
-    o[1][1],
-    o[2][1],
-    o[0][2],
-    o[1][2],
-    o[2][2]
+function X(s, e = 6) {
+  const t = [], n = s.sites.length;
+  t.push(String(n));
+  const o = C(s), i = s.lattice, a = [
+    i[0][0],
+    i[1][0],
+    i[2][0],
+    i[0][1],
+    i[1][1],
+    i[2][1],
+    i[0][2],
+    i[1][2],
+    i[2][2]
   ].join(" "), c = [
     "species:S:1",
     "pos:R:3",
-    i ? "selectiveDynamics:L:3" : null
+    o ? "selectiveDynamics:L:3" : null
   ].filter(Boolean).join(":");
-  e.push(`Lattice="${n}" Properties=${c}`);
-  for (const l of t.sites) {
-    const u = t.species[l.speciesIndex], [m, p, h] = l.cart;
-    let f = `${u} ${m.toFixed(10)} ${p.toFixed(10)} ${h.toFixed(10)}`;
-    if (i) {
-      const _ = Array.isArray(l.props?.selectiveDynamics) ? l.props.selectiveDynamics : [!0, !0, !0];
-      f += " " + _.map((r) => r ? "T" : "F").join(" ");
+  t.push(`Lattice="${a}" Properties=${c}`);
+  for (const h of s.sites) {
+    const m = s.species[h.speciesIndex], [p, u, l] = h.cart;
+    let d = `${m} ${p.toFixed(e)} ${u.toFixed(e)} ${l.toFixed(e)}`;
+    if (o) {
+      const r = Array.isArray(h.props?.selectiveDynamics) ? h.props.selectiveDynamics : [!0, !0, !0];
+      d += " " + r.map((f) => f ? "T" : "F").join(" ");
     }
-    e.push(f);
+    t.push(d);
   }
-  return e.join(`
+  return t.join(`
 `);
 }
-function X(t) {
-  const e = I(t);
-  let s = 0;
-  const i = parseInt(e[s++], 10);
-  if (!Number.isFinite(i))
+function N(s) {
+  const e = F(s);
+  let t = 0;
+  const n = parseInt(e[t++], 10);
+  if (!Number.isFinite(n))
     throw new Error("Invalid XYZ: first line must be atom count");
-  const o = e[s++], n = {}, c = /(\w+)=(".*?"|\S+)/g;
-  for (const r of o.matchAll(c)) {
-    let d = r[2];
-    d.startsWith('"') && (d = d.slice(1, -1)), n[r[1]] = d;
+  const o = e[t++], i = {}, a = /(\w+)=(".*?"|\S+)/g;
+  for (const r of o.matchAll(a)) {
+    let f = r[2];
+    f.startsWith('"') && (f = f.slice(1, -1)), i[r[1]] = f;
   }
-  let l;
-  if (n.Lattice) {
-    const r = n.Lattice.split(/\s+/).map(Number);
+  let c;
+  if (i.Lattice) {
+    const r = i.Lattice.split(/\s+/).map(Number);
     if (r.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
-    l = [
+    c = [
       [r[0], r[3], r[6]],
       [r[1], r[4], r[7]],
       [r[2], r[5], r[8]]
     ];
   } else
     throw new Error("Lattice must be present in extended XYZ format");
-  let u = 0, m = 1, p = null;
-  if (n.Properties) {
-    const r = n.Properties.split(":");
-    let d = 0;
+  let h = 0, m = 1, p = null;
+  if (i.Properties) {
+    const r = i.Properties.split(":");
+    let f = 0;
     for (let g = 0; g < r.length; g += 3) {
-      const x = r[g], a = parseInt(r[g + 2], 10);
-      x === "species" && (u = d), x === "pos" && (m = d), x === "selectiveDynamics" && (p = d), d += a;
+      const y = r[g], _ = parseInt(r[g + 2], 10);
+      y === "species" && (h = f), y === "pos" && (m = f), y === "selectiveDynamics" && (p = f), f += _;
     }
   }
-  const h = [], f = /* @__PURE__ */ new Map(), _ = [];
-  for (let r = 0; r < i; r++) {
-    const d = e[s++].split(/\s+/), g = d[u];
-    f.has(g) || (f.set(g, h.length), h.push(g));
-    const x = f.get(g), a = d.slice(m, m + 3).map(Number), b = {};
+  const u = [], l = /* @__PURE__ */ new Map(), d = [];
+  for (let r = 0; r < n; r++) {
+    const f = e[t++].split(/\s+/), g = f[h];
+    l.has(g) || (l.set(g, u.length), u.push(g));
+    const y = l.get(g), _ = f.slice(m, m + 3).map(Number), S = {};
     if (p !== null) {
-      const v = d.slice(p, p + 3).map((w) => w.toUpperCase() === "T");
-      v.length === 3 && (b.selectiveDynamics = v);
+      const I = f.slice(p, p + 3).map((b) => b.toUpperCase() === "T");
+      I.length === 3 && (S.selectiveDynamics = I);
     }
-    _.push(new y(x, a, b));
+    d.push(new x(y, _, S));
   }
-  return new S({ lattice: l, species: h, sites: _ });
-}
-function E(t) {
-  return t * Math.PI / 180;
-}
-function C(t, e, s, i, o, n) {
-  const c = E(i), l = E(o), u = E(n), m = [t, 0, 0], p = [
-    e * Math.cos(u),
-    e * Math.sin(u),
-    0
-  ], h = s * Math.cos(l), f = s * (Math.cos(c) - Math.cos(l) * Math.cos(u)) / Math.sin(u), _ = Math.sqrt(s * s - h * h - f * f);
-  return [m, p, [h, f, _]];
-}
-function j(t, e) {
-  const [s, i, o] = e;
-  return [
-    t[0] * s[0] + t[1] * i[0] + t[2] * o[0],
-    t[0] * s[1] + t[1] * i[1] + t[2] * o[1],
-    t[0] * s[2] + t[1] * i[2] + t[2] * o[2]
-  ];
+  return new w({ lattice: c, species: u, sites: d });
 }
-function F(t, e) {
-  return t[0] * e[0] + t[1] * e[1] + t[2] * e[2];
+function v(s, e) {
+  return s[0] * e[0] + s[1] * e[1] + s[2] * e[2];
 }
-function M(t) {
-  return Math.sqrt(F(t, t));
+function A(s) {
+  return Math.sqrt(v(s, s));
 }
-function $(t) {
-  return t * 180 / Math.PI;
+function M(s) {
+  return s * 180 / Math.PI;
 }
-function L(t, e) {
-  const [s, i, o] = e, n = s[0] * (i[1] * o[2] - i[2] * o[1]) - s[1] * (i[0] * o[2] - i[2] * o[0]) + s[2] * (i[0] * o[1] - i[1] * o[0]);
-  if (Math.abs(n) < 1e-12)
+function D(s, e) {
+  const [t, n, o] = e, i = t[0] * (n[1] * o[2] - n[2] * o[1]) - t[1] * (n[0] * o[2] - n[2] * o[0]) + t[2] * (n[0] * o[1] - n[1] * o[0]);
+  if (Math.abs(i) < 1e-12)
     throw new Error("Singular lattice matrix");
-  const c = [
+  const a = [
     [
-      (i[1] * o[2] - i[2] * o[1]) / n,
-      (s[2] * o[1] - s[1] * o[2]) / n,
-      (s[1] * i[2] - s[2] * i[1]) / n
+      (n[1] * o[2] - n[2] * o[1]) / i,
+      (t[2] * o[1] - t[1] * o[2]) / i,
+      (t[1] * n[2] - t[2] * n[1]) / i
     ],
     [
-      (i[2] * o[0] - i[0] * o[2]) / n,
-      (s[0] * o[2] - s[2] * o[0]) / n,
-      (s[2] * i[0] - s[0] * i[2]) / n
+      (n[2] * o[0] - n[0] * o[2]) / i,
+      (t[0] * o[2] - t[2] * o[0]) / i,
+      (t[2] * n[0] - t[0] * n[2]) / i
     ],
     [
-      (i[0] * o[1] - i[1] * o[0]) / n,
-      (s[1] * o[0] - s[0] * o[1]) / n,
-      (s[0] * i[1] - s[1] * i[0]) / n
+      (n[0] * o[1] - n[1] * o[0]) / i,
+      (t[1] * o[0] - t[0] * o[1]) / i,
+      (t[0] * n[1] - t[1] * n[0]) / i
     ]
   ];
   return [
-    t[0] * c[0][0] + t[1] * c[1][0] + t[2] * c[2][0],
-    t[0] * c[0][1] + t[1] * c[1][1] + t[2] * c[2][1],
-    t[0] * c[0][2] + t[1] * c[1][2] + t[2] * c[2][2]
+    s[0] * a[0][0] + s[1] * a[1][0] + s[2] * a[2][0],
+    s[0] * a[0][1] + s[1] * a[1][1] + s[2] * a[2][1],
+    s[0] * a[0][2] + s[1] * a[1][2] + s[2] * a[2][2]
   ];
 }
-function N(t) {
-  const [e, s, i] = t.lattice, o = M(e), n = M(s), c = M(i), l = $(Math.acos(F(s, i) / (n * c))), u = $(Math.acos(F(e, i) / (o * c))), m = $(Math.acos(F(e, s) / (o * n)));
-  let p = `data_made_with_matsci-parse
+function z(s, e = 6) {
+  const [t, n, o] = s.lattice, i = A(t), a = A(n), c = A(o), h = M(Math.acos(v(n, o) / (a * c))), m = M(Math.acos(v(t, o) / (i * c))), p = M(Math.acos(v(t, n) / (i * a)));
+  let u = `data_made_with_matsci-parse
     _symmetry_space_group_name_H-M   'P 1'
     _symmetry_Int_Tables_number    1
 
-    _cell_length_a   ${o.toFixed(6)}
-    _cell_length_b   ${n.toFixed(6)}
-    _cell_length_c   ${c.toFixed(6)}
-    _cell_angle_alpha   ${l.toFixed(6)}
-    _cell_angle_beta    ${u.toFixed(6)}
-    _cell_angle_gamma   ${m.toFixed(6)}
+    _cell_length_a   ${i.toFixed(e)}
+    _cell_length_b   ${a.toFixed(e)}
+    _cell_length_c   ${c.toFixed(e)}
+    _cell_angle_alpha   ${h.toFixed(e)}
+    _cell_angle_beta    ${m.toFixed(e)}
+    _cell_angle_gamma   ${p.toFixed(e)}
 
     loop_
     _atom_site_label
@@ -322,44 +460,70 @@ function N(t) {
     _atom_site_fract_y
     _atom_site_fract_z
 `;
-  return t.sites.forEach((h, f) => {
-    const _ = t.species[h.speciesIndex], r = L(h.cart, t.lattice);
-    p += `${_}${f + 1} ${_} ${r[0].toFixed(6)} ${r[1].toFixed(
+  return s.sites.forEach((l, d) => {
+    const r = s.species[l.speciesIndex], f = D(l.cart, s.lattice);
+    u += `${r}${d + 1} ${r} ${f[0].toFixed(e)} ${f[1].toFixed(
       6
-    )} ${r[2].toFixed(6)}
+    )} ${f[2].toFixed(e)}
 `;
-  }), p;
+  }), u;
 }
-function z(t) {
-  const e = I(t);
-  let s = 0, i = 0, o = 0, n = 0, c = 0, l = 0;
-  const u = [];
-  let m = !1, p = [];
-  for (const a of e)
-    a.startsWith("_cell_length_a") ? s = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_length_b") ? i = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_length_c") ? o = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_angle_alpha") ? n = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_angle_beta") ? c = parseFloat(a.split(/\s+/)[1]) : a.startsWith("_cell_angle_gamma") ? l = parseFloat(a.split(/\s+/)[1]) : a.startsWith("loop_") ? (m = !0, p = []) : m && a.startsWith("_") ? p.push(a) : m && a && !a.startsWith("_") && u.push(a.split(/\s+/));
-  const h = C(s, i, o, n, c, l), f = [], _ = [], r = p.findIndex((a) => a.includes("fract_x")), d = p.findIndex((a) => a.includes("fract_y")), g = p.findIndex((a) => a.includes("fract_z")), x = p.findIndex((a) => a.includes("type_symbol"));
-  if (r < 0 || d < 0 || g < 0 || x < 0)
-    throw new Error("CIF missing required _atom_site columns");
-  for (const a of u) {
-    const b = [
-      parseFloat(a[r]),
-      parseFloat(a[d]),
-      parseFloat(a[g])
-    ], v = j(b, h);
-    let w = f.indexOf(a[x]);
-    w === -1 && (w = f.length, f.push(a[x])), _.push(new y(w, v));
+function V(s) {
+  const e = F(s);
+  let t = 0, n = 0, o = 0, i = 0, a = 0, c = 0;
+  const h = [], m = [];
+  let p = 0;
+  for (; p < e.length; ) {
+    const l = e[p].trim();
+    if (l.startsWith("_cell_length_a")) t = parseFloat(l.split(/\s+/)[1]);
+    else if (l.startsWith("_cell_length_b"))
+      n = parseFloat(l.split(/\s+/)[1]);
+    else if (l.startsWith("_cell_length_c"))
+      o = parseFloat(l.split(/\s+/)[1]);
+    else if (l.startsWith("_cell_angle_alpha"))
+      i = parseFloat(l.split(/\s+/)[1]);
+    else if (l.startsWith("_cell_angle_beta"))
+      a = parseFloat(l.split(/\s+/)[1]);
+    else if (l.startsWith("_cell_angle_gamma"))
+      c = parseFloat(l.split(/\s+/)[1]);
+    else if (l.startsWith("loop_")) {
+      p++;
+      const d = [];
+      for (; p < e.length && e[p].trim().startsWith("_"); )
+        d.push(e[p].trim()), p++;
+      if (d.some((r) => r.includes("_atom_site_"))) {
+        const r = d.findIndex((_) => _.includes("fract_x")), f = d.findIndex((_) => _.includes("fract_y")), g = d.findIndex((_) => _.includes("fract_z")), y = d.findIndex((_) => _.includes("type_symbol"));
+        if (r < 0 || f < 0 || g < 0 || y < 0)
+          throw new Error("CIF missing required _atom_site columns");
+        for (; p < e.length && e[p].trim() && !e[p].trim().startsWith("_") && !e[p].trim().startsWith("loop_"); ) {
+          const _ = e[p].trim().split(/\s+/), S = [
+            parseFloat(_[r]),
+            parseFloat(_[f]),
+            parseFloat(_[g])
+          ], I = L(
+            S,
+            T(t, n, o, i, a, c)
+          );
+          let b = h.indexOf(_[y]);
+          b === -1 && (b = h.length, h.push(_[y])), m.push(new x(b, I)), p++;
+        }
+        continue;
+      }
+    }
+    p++;
   }
-  return new S({ lattice: h, species: f, sites: _ });
+  const u = T(t, n, o, i, a, c);
+  return new w({ lattice: u, species: h, sites: m });
 }
 export {
-  S as CrystalStructure,
-  y as Site,
-  z as cifToStructure,
-  P as poscarToStructure,
-  N as structureToCif,
-  D as structureToPoscar,
-  R as structureToXsf,
-  O as structureToXyz,
-  W as xsfToStructure,
-  X as xyzToStructure
+  w as CrystalStructure,
+  x as Site,
+  V as cifToStructure,
+  R as poscarToStructure,
+  z as structureToCif,
+  P as structureToPoscar,
+  W as structureToXsf,
+  X as structureToXyz,
+  O as xsfToStructure,
+  N as xyzToStructure
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matsci-parse",
-  "version": "0.0.3",
+  "version": "0.1.1",
   "type": "module",
   "main": "dist/main.js",
   "module": "dist/main.js",