3dmol/src/parsers/utils/areConnected.ts

JavaScript/TypeScript molecular visualization library

import { AtomSpec } from "specs";
import { bondLength } from "./bondLength";
import { ParserOptionsSpec } from "parsers/ParserOptionsSpec";

const cations = new Set(["Na","K","Ca","Mg","Mn","Sr"]);

/*
 * Return true if atom1 and atom2 are probably bonded to each other based on distance alone
 */
export function areConnected(atom1: AtomSpec, atom2: AtomSpec, options: ParserOptionsSpec) {
  if(options && options.unboundCations && (cations.has(atom1.elem) || cations.has(atom2.elem))) {
    return false;
  }
  let maxsq = bondLength(atom1.elem) + bondLength(atom2.elem);
  maxsq += 0.25; // fudge factor, especially important for md frames, also see 1i3d
  maxsq *= maxsq;

  let xdiff = atom1.x - atom2.x;
  xdiff *= xdiff;
  if (xdiff > maxsq) return false;
  let ydiff = atom1.y - atom2.y;
  ydiff *= ydiff;
  if (ydiff > maxsq) return false;
  let zdiff = atom1.z - atom2.z;
  zdiff *= zdiff;
  if (zdiff > maxsq) return false;

  const distSquared = xdiff + ydiff + zdiff;

  if (
    isNaN(distSquared) ||
    distSquared < 0.5 ||
    distSquared > maxsq ||
    (atom1.altLoc !== atom2.altLoc && atom1.altLoc.trim() !== "" && atom2.altLoc.trim() !== "")
  )
    return false;

    
  return true;
}