Refactor remaining files in parser/utils

src/parsers/utils/assignBonds.ts

@@ -21,15 +21,28 @@ const OFFSETS = [
 ];
 const MAX_BOND_LENGTH = 4.95; // (largest bond length, Cs) 2.25 * 2 * 1.1 (fudge factor)
 
-export function assignBonds(atoms: string | any[]) {
+export function assignBonds(atoms: AtomSpec[]) {
   // Assign bonds - yuck, can't count on connect records
 
   for (let i = 0, n = atoms.length; i < n; i++) {
     // Don't reindex if atoms are already indexed
     if (!atoms[i].index) atoms[i].index = i;
   }
 
-  const grid = {};
+  const grid: {
+    x: {
+      y: {
+        z: AtomSpec[];
+      };
+    };
+  } = {
+    x: {
+      y: {
+        z: [],
+      },
+    },
+  };
+
   for (let index = 0; index < atoms.length; index++) {
     const atom = atoms[index];
     const x = Math.floor(atom.x / MAX_BOND_LENGTH);
@@ -76,7 +89,7 @@ export function assignBonds(atoms: string | any[]) {
         }
       }
     }
-  };
+  }
 
   for (let xg in grid) {
     const x = parseInt(xg);

src/parsers/utils/assignPDBBonds.ts

@@ -1,22 +1,21 @@
 // This is optimized for proteins where it is assumed connected atoms are on the same or next residue
 
+import { AtomSpec } from "specs";
 import { areConnected } from "./areConnected";
 import { assignBonds } from "./assignBonds";
 import { standardResidues } from "./standardResidues";
 
-
-/** 
+/**
  * @param {AtomSpec[]}
  *            atomsarray
-*/
+ */
 
-export function assignPDBBonds(atomsarray: string | any[]) {
+export function assignPDBBonds(atomsarray: AtomSpec[]) {
   // assign bonds - yuck, can't count on connect records
-  var protatoms: any[] = [];
-  var hetatoms: any[] = [];
-  var i: number, n: number;
-  for (i = 0, n = atomsarray.length; i < n; i++) {
-    var atom: any = atomsarray[i];
+  const protatoms: Array<AtomSpec> = [];
+  const hetatoms: Array<AtomSpec> = [];
+  for (let i = 0, n = atomsarray.length; i < n; i++) {
+    const atom = atomsarray[i];
     atom.index = i;
     if (atom.hetflag || !standardResidues.has(atom.resn)) hetatoms.push(atom);
     else protatoms.push(atom);
@@ -25,18 +24,18 @@ export function assignPDBBonds(atomsarray: string | any[]) {
   assignBonds(hetatoms);
 
   // sort by resid
-  protatoms.sort(function (a: any, b: any) {
-    if (a.chain != b.chain) return a.chain < b.chain ? -1 : 1;
+  protatoms.sort(function (a, b) {
+    if (a.chain !== b.chain) return a.chain < b.chain ? -1 : 1;
     return a.resi - b.resi;
   });
 
   // for identifying connected residues
-  var currentResi = -1;
-  var reschain = -1;
-  var lastResConnected: boolean;
+  let currentResi = -1;
+  let reschain = -1;
+  let lastResConnected: boolean;
 
-  for (i = 0, n = protatoms.length; i < n; i++) {
-    var ai = protatoms[i];
+  for (let i = 0, n = protatoms.length; i < n; i++) {
+    const ai = protatoms[i];
 
     if (ai.resi !== currentResi) {
       currentResi = ai.resi;
@@ -47,12 +46,10 @@ export function assignPDBBonds(atomsarray: string | any[]) {
 
     ai.reschain = reschain;
 
-    for (var j = i + 1; j < protatoms.length; j++) {
-      var aj = protatoms[j];
-      if (aj.chain != ai.chain) break;
-      if (aj.resi - ai.resi > 1)
-        // can't be connected
-        break;
+    for (let j = i + 1; j < protatoms.length; j++) {
+      const aj = protatoms[j];
+      if (aj.chain !== ai.chain || aj.resi - ai.resi > 1) break;
+
       if (areConnected(ai, aj)) {
         if (ai.bonds.indexOf(aj.index) === -1) {
           // only add if not already there