matsci-parse 0.0.1 → 0.0.2

package/dist/main.js

@@ -1,24 +1,24 @@
-class S {
-  constructor(e, t, o = {}) {
-    this.speciesIndex = e, this.cart = t, this.props = o;
+class y {
+  constructor(e, s, i = {}) {
+    this.speciesIndex = e, this.cart = s, this.props = i;
   }
   getProp(e) {
     return this.props[e];
   }
-  setProp(e, t) {
-    this.props[e] = t;
+  setProp(e, s) {
+    this.props[e] = s;
   }
 }
-function I(n) {
-  return n.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
+function A(t) {
+  return t.sites.some((e) => Array.isArray(e.props.selectiveDynamics));
 }
-class x {
+class S {
   constructor({
     lattice: e,
-    species: t,
-    sites: o
+    species: s,
+    sites: i
   }) {
-    this.lattice = this._validateLattice(e), this.species = this._validateSpecies(t), this.sites = this._validateSites(o);
+    this.lattice = this._validateLattice(e), this.species = this._validateSpecies(s), this.sites = this._validateSites(i);
   }
   // ---------- Simple methods ----------
   get numSites() {
@@ -36,8 +36,8 @@ class x {
   get elements() {
     return this.species;
   }
-  addSite(e, t) {
-    this._validateSpeciesIndex(e), this.sites.push(new S(e, t));
+  addSite(e, s) {
+    this._validateSpeciesIndex(e), this.sites.push(new y(e, s));
   }
   removeSite(e) {
     this.sites.splice(e, 1);
@@ -46,27 +46,27 @@ class x {
   _validateLattice(e) {
     if (!Array.isArray(e) || e.length !== 3)
       throw new Error("Lattice must be a 3x3 matrix");
-    return e.forEach((t) => {
-      if (!Array.isArray(t) || t.length !== 3)
+    return e.forEach((s) => {
+      if (!Array.isArray(s) || s.length !== 3)
         throw new Error("Lattice vectors must be length 3");
     }), e;
   }
   _validateSpecies(e) {
     if (!Array.isArray(e)) throw new Error("Species must be an array");
-    return e.forEach((t) => {
-      if (typeof t != "string")
+    return e.forEach((s) => {
+      if (typeof s != "string")
         throw new Error("Species entries must be strings");
     }), e;
   }
   _validateSites(e) {
     if (!Array.isArray(e)) throw new Error("Sites must be an array");
-    return e.map((t) => {
-      if (t instanceof S) return t;
-      if (typeof t == "object" && typeof t.speciesIndex == "number" && Array.isArray(t.cart) && t.cart.length === 3)
-        return this._validateSpeciesIndex(t.speciesIndex), new S(
-          t.speciesIndex,
-          t.cart,
-          t.props ?? {}
+    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 ?? {}
         );
       throw new Error(
         "Each site must be a Site instance or a valid site object"
@@ -78,177 +78,288 @@ class x {
       throw new Error("speciesIndex out of bounds");
   }
 }
-function A(n) {
-  const e = [], t = I(n);
-  e.push("Generated by CrystalStructure"), e.push("1.0"), n.lattice.forEach((s) => {
-    e.push(s.map((p) => p.toFixed(10)).join(" "));
+function I(t) {
+  return t.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(" "));
   });
-  const o = Array.from(
-    new Set(n.sites.map((s) => n.species[s.speciesIndex]))
-  ), i = o.map(
-    (s) => n.sites.filter((p) => n.species[p.speciesIndex] === s).length
+  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
   );
-  return e.push(o.join(" ")), e.push(i.join(" ")), t && e.push("Selective dynamics"), e.push("Cartesian"), o.forEach((s) => {
-    n.sites.filter((p) => n.species[p.speciesIndex] === s).forEach((p) => {
-      const a = p.cart.map((h) => h.toFixed(10)).join(" ");
-      if (t) {
-        const d = (Array.isArray(p.props?.selectiveDynamics) ? p.props.selectiveDynamics : [!0, !0, !0]).map((u) => u ? "T" : "F").join(" ");
-        e.push(`${a} ${d}`);
+  return e.push(i.join(" ")), e.push(o.join(" ")), s && e.push("Selective dynamics"), e.push("Cartesian"), i.forEach((n) => {
+    t.sites.filter((c) => t.species[c.speciesIndex] === n).forEach((c) => {
+      const l = c.cart.map((u) => u.toFixed(10)).join(" ");
+      if (s) {
+        const m = (Array.isArray(c.props?.selectiveDynamics) ? c.props.selectiveDynamics : [!0, !0, !0]).map((p) => p ? "T" : "F").join(" ");
+        e.push(`${l} ${m}`);
       } else
-        e.push(a);
+        e.push(l);
     });
   }), e.join(`
 `);
 }
-function j(n) {
-  const e = n.trim().split(/\r?\n/).map((l) => l.trim()).filter((l) => l.length > 0);
-  let t = 0;
-  t++;
-  const o = parseFloat(e[t++]), i = [];
-  for (let l = 0; l < 3; l++)
+function T(t) {
+  let e = 0;
+  e++;
+  const s = parseFloat(t[e++]), i = [];
+  for (let h = 0; h < 3; h++)
     i.push(
-      e[t++].split(/\s+/).map((y) => parseFloat(y) * o)
+      t[e++].split(/\s+/).map((f) => parseFloat(f) * s)
     );
-  let s = e[t].trim(), p;
-  /^[A-Za-z]/.test(s) && (p = s.split(/\s+/), t++);
-  const a = e[t++].split(/\s+/).map(Number);
-  p || (p = a.map((l, y) => `X${y + 1}`));
-  let h = !1;
-  e[t]?.toLowerCase().startsWith("s") && (h = !0, t++);
-  const u = e[t++].toLowerCase().startsWith("d"), m = [];
-  return p.forEach((l, y) => {
-    for (let r = 0; r < a[y]; r++) {
-      const c = e[t++].split(/\s+/).map(Number);
-      let f;
-      u ? f = [
-        c[0] * i[0][0] + c[1] * i[1][0] + c[2] * i[2][0],
-        c[0] * i[0][1] + c[1] * i[1][1] + c[2] * i[2][1],
-        c[0] * i[0][2] + c[1] * i[1][2] + c[2] * i[2][2]
-      ] : f = c.slice(0, 3);
-      let w = {};
-      if (h) {
-        const g = e[t - 1].split(/\s+/).slice(3, 6).map((v) => v.toUpperCase() === "T");
-        g.length === 3 && (w.selectiveDynamics = g);
+  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${f + 1}`));
+  let l = !1;
+  t[e]?.toLowerCase().startsWith("s") && (l = !0, e++);
+  const m = t[e++].toLowerCase().startsWith("d"), p = [];
+  return n.forEach((h, f) => {
+    for (let _ = 0; _ < c[f]; _++) {
+      const r = t[e++].split(/\s+/).map(Number);
+      let d;
+      m ? d = [
+        r[0] * i[0][0] + r[1] * i[1][0] + r[2] * i[2][0],
+        r[0] * i[0][1] + r[1] * i[1][1] + r[2] * i[2][1],
+        r[0] * i[0][2] + r[1] * i[1][2] + r[2] * i[2][2]
+      ] : d = r.slice(0, 3);
+      const g = {};
+      if (l) {
+        const x = r.slice(3, 6).map((a) => a === 1);
+        x.length === 3 && (g.selectiveDynamics = x);
       }
-      m.push(new S(y, f, w));
+      p.push(new y(f, d, g));
     }
-  }), new x({
-    lattice: i,
-    species: p,
-    sites: m
-  });
+  }), {
+    structure: new S({ lattice: i, species: n, sites: p }),
+    linesConsumed: e
+  };
+}
+function P(t) {
+  const e = I(t);
+  return T(e).structure;
 }
-function C(n) {
+function R(t) {
   const e = [];
-  return e.push("CRYSTAL"), e.push("PRIMVEC"), n.lattice.forEach((t) => {
-    e.push(t.map((o) => o.toFixed(10)).join(" "));
-  }), e.push("PRIMCOORD"), e.push(`${n.numSites} 1`), n.sites.forEach((t) => {
-    const o = n.species[t.speciesIndex];
-    e.push(`${o} ${t.cart.map((i) => i.toFixed(10)).join(" ")}`);
+  return e.push("CRYSTAL"), e.push("PRIMVEC"), t.lattice.forEach((s) => {
+    e.push(s.map((i) => i.toFixed(10)).join(" "));
+  }), e.push("PRIMCOORD"), e.push(`${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 D(n) {
-  const e = n.trim().split(/\r?\n/).map((a) => a.trim()).filter((a) => a.length > 0), t = [], o = [], i = [];
-  let s = 0;
-  for (; s < e.length && e[s].toUpperCase() !== "PRIMVEC"; ) s++;
-  if (s === e.length) throw new Error("PRIMVEC block not found in XSF");
-  s++;
-  for (let a = 0; a < 3; a++)
-    t.push(e[s++].split(/\s+/).map(Number));
-  for (; s < e.length && e[s].toUpperCase() !== "PRIMCOORD"; ) s++;
-  if (s === e.length) throw new Error("PRIMCOORD block not found in XSF");
-  s++;
-  const [p] = e[s++].split(/\s+/).map(Number);
-  for (let a = 0; a < p; a++) {
-    const h = e[s++].split(/\s+/), d = h[0], u = h.slice(1, 4).map(Number);
-    let m = o.indexOf(d);
-    m === -1 && (o.push(d), m = o.length - 1), i.push(new S(m, u));
-  }
-  return new x({ lattice: t, species: o, sites: i });
-}
-function F(n) {
-  const e = [], t = n.sites.length;
-  e.push(String(t));
-  const o = I(n), i = n.lattice, s = [
-    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(" "), p = [
+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));
+  }
+  return new S({ lattice: s, species: i, 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]
+  ].join(" "), c = [
     "species:S:1",
     "pos:R:3",
-    o ? "selectiveDynamics:L:3" : null
+    i ? "selectiveDynamics:L:3" : null
   ].filter(Boolean).join(":");
-  e.push(`Lattice="${s}" Properties=${p}`);
-  for (const a of n.sites) {
-    const h = n.species[a.speciesIndex], [d, u, m] = a.cart;
-    let l = `${h} ${d.toFixed(10)} ${u.toFixed(10)} ${m.toFixed(10)}`;
-    if (o) {
-      const y = Array.isArray(a.props?.selectiveDynamics) ? a.props.selectiveDynamics : [!0, !0, !0];
-      l += " " + y.map((r) => r ? "T" : "F").join(" ");
+  e.push(`Lattice="${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(" ");
     }
-    e.push(l);
+    e.push(f);
   }
   return e.join(`
 `);
 }
-function L(n) {
-  const e = n.trim().split(/\r?\n/).map((r) => r.trim()).filter((r) => r.length > 0);
-  let t = 0;
-  const o = parseInt(e[t++], 10);
-  if (!Number.isFinite(o))
+function X(t) {
+  const e = I(t);
+  let s = 0;
+  const i = parseInt(e[s++], 10);
+  if (!Number.isFinite(i))
     throw new Error("Invalid XYZ: first line must be atom count");
-  const i = e[t++], s = {}, p = /(\w+)=(".*?"|\S+)/g;
-  for (const r of i.matchAll(p)) {
-    let c = r[2];
-    c.startsWith('"') && (c = c.slice(1, -1)), s[r[1]] = c;
-  }
-  let a;
-  if (s.Lattice) {
-    const r = s.Lattice.split(/\s+/).map(Number);
+  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;
+  }
+  let l;
+  if (n.Lattice) {
+    const r = n.Lattice.split(/\s+/).map(Number);
     if (r.length !== 9) throw new Error("Invalid Lattice in extended XYZ");
-    a = [
+    l = [
       [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 h = 0, d = 1, u = null;
-  if (s.Properties) {
-    const r = s.Properties.split(":");
-    let c = 0;
-    for (let f = 0; f < r.length; f += 3) {
-      const w = r[f], g = parseInt(r[f + 2], 10);
-      w === "species" && (h = c), w === "pos" && (d = c), w === "selectiveDynamics" && (u = c), c += g;
+  let u = 0, m = 1, p = null;
+  if (n.Properties) {
+    const r = n.Properties.split(":");
+    let d = 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 m = [], l = /* @__PURE__ */ new Map(), y = [];
-  for (let r = 0; r < o; r++) {
-    const c = e[t++].split(/\s+/), f = c[h];
-    l.has(f) || (l.set(f, m.length), m.push(f));
-    const w = l.get(f), g = c.slice(d, d + 3).map(Number), v = {};
-    if (u !== null) {
-      const E = c.slice(u, u + 3).map((b) => b.toUpperCase() === "T");
-      E.length === 3 && (v.selectiveDynamics = E);
+  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 = {};
+    if (p !== null) {
+      const v = d.slice(p, p + 3).map((w) => w.toUpperCase() === "T");
+      v.length === 3 && (b.selectiveDynamics = v);
     }
-    y.push(new S(w, g, v));
+    _.push(new y(x, a, b));
+  }
+  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]
+  ];
+}
+function F(t, e) {
+  return t[0] * e[0] + t[1] * e[1] + t[2] * e[2];
+}
+function M(t) {
+  return Math.sqrt(F(t, t));
+}
+function $(t) {
+  return t * 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)
+    throw new Error("Singular lattice matrix");
+  const c = [
+    [
+      (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
+    ],
+    [
+      (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
+    ],
+    [
+      (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
+    ]
+  ];
+  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]
+  ];
+}
+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
+    _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   ${m.toFixed(6)}
+
+    loop_
+    _atom_site_label
+    _atom_site_type_symbol
+    _atom_site_fract_x
+    _atom_site_fract_y
+    _atom_site_fract_z
+`;
+  return t.sites.forEach((h, f) => {
+    const _ = t.species[h.speciesIndex], r = L(h.cart, t.lattice);
+    p += `${_}${f + 1} ${_} ${r[0].toFixed(6)} ${r[1].toFixed(
+      6
+    )} ${r[2].toFixed(6)}
+`;
+  }), p;
+}
+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));
   }
-  return new x({ lattice: a, species: m, sites: y });
+  return new S({ lattice: h, species: f, sites: _ });
 }
 export {
-  x as CrystalStructure,
-  S as Site,
-  j as poscarToStructure,
-  A as structureToPoscar,
-  C as structureToXsf,
-  F as structureToXyz,
-  D as xsfToStructure,
-  L as xyzToStructure
+  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
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "matsci-parse",
-  "version": "0.0.1",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/main.js",
   "module": "dist/main.js",