Merge pull request #785 from prajwalkulkarni/refactor-lammpstrj

refactor: LAMMPSTRJ.ts
3dmol · May 19, 2024 · 841f8d1 · 841f8d1
2 parents cb602bd + efbf907
commit 841f8d1
Showing 1 changed file with 20 additions and 19 deletions.
diff --git a/src/parsers/LAMMPSTRJ.ts b/src/parsers/LAMMPSTRJ.ts
@@ -1,3 +1,4 @@
+import { AtomSpec } from "specs";
 import { ParserOptionsSpec } from "./ParserOptionsSpec";
 import { assignBonds } from "./utils/assignBonds";
 
@@ -6,10 +7,7 @@ import { assignBonds } from "./utils/assignBonds";
  * 
  * @category Parsers
 */
-
-export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
-  var atoms: any[] = [];
-  var dic:any = {
+const dic: Record<string,string> = {
     id: "serial",
     type: "atom",
     element: "elem",
@@ -28,10 +26,13 @@ export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
     zs: "z",
     zsu: "z",
   };
-  var lines = str.split(/\r?\n|\r/);
-  var offset = 0;
-  var atomCount = 0;
-  var start = 0;
+
+export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
+  const atoms: AtomSpec[][] = [];
+  const lines = str.split(/\r?\n|\r/);
+  let offset = 0;
+  let atomCount = 0;
+  let start = 0;
   while (start < lines.length - 9) {
     for (var j = start; j < lines.length; j++) {
       if (lines[j].match(/ITEM: NUMBER OF ATOMS/))
@@ -41,19 +42,19 @@ export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
         break;
       }
     }
-    var types = lines[offset - 1].replace("ITEM: ATOMS ", "").split(" ");
+    const types = lines[offset - 1].replace("ITEM: ATOMS ", "").split(" ");
     atoms.push([]);
     for (let j = offset; j < offset + atomCount; j++) {
-      var atom: Record<string, any> = {};
-      var properties: any = {};
-      var tokens = lines[j].split(" ");
-      for (var k = 0; k < tokens.length; k++) {
-        var prop = dic[types[k]];
-        if (prop != undefined) {
-          if (prop == "serial") atom[prop] = parseInt(tokens[k]);
-          else if (prop == "x" || prop == "y" || prop === "z")
+      const atom: AtomSpec = {};
+      const properties = {};
+      const tokens = lines[j].split(" ");
+      for (let k = 0; k < tokens.length; k++) {
+        const prop = dic[types[k]];
+        if (prop !== undefined) {
+          if (prop === "serial") atom[prop] = parseInt(tokens[k]);
+          else if (prop === "x" || prop === "y" || prop === "z")
             atom[prop] = parseFloat(tokens[k]);
-          else if (prop == "charge" || prop == "radius")
+          else if (prop === "charge" || prop === "radius")
             properties[prop] = parseFloat(tokens[k]);
           else atom[prop] = tokens[k];
         }
@@ -66,7 +67,7 @@ export function LAMMPSTRJ(str: string, options: ParserOptionsSpec) {
     start = offset + atomCount - 1;
   }
   if (options.assignBonds) {
-    for (var i = 0; i < atoms.length; i++) assignBonds(atoms[i], options);
+    for (let i = 0; i < atoms.length; i++) assignBonds(atoms[i], options);
   }
   return atoms;
 }