import { Vector3, Matrix4 } from "../WebGL";
import { assignBonds } from "./utils/assignBonds";
import { anumToSymbol } from "./utils/anumToSymbol";
import { ParserOptionsSpec } from "./ParserOptionsSpec";
/**
* @param {string}
* str
* @param {ParserOptionsSpec}
* options
* @category Parsers
*/
export function CUBE(str: string, options: ParserOptionsSpec) {
options = options || {};
var atoms: any[][] & Record<string, any> = [[]];
var lines = str.split(/\r?\n/);
var assignbonds = options.assignBonds === undefined ? true : options.assignBonds;
if (lines.length < 6)
return atoms;
var lineArr = lines[2].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var natoms = Math.abs(parseFloat(lineArr[0]));
let cryst: Record<string, any> = {};
var origin = cryst.origin = new Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]));
lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
lineArr = lines[3].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
// might have to convert from bohr units to angstroms
// there is a great deal of confusion here:
// n>0 means angstroms: http://www.gaussian.com/g_tech/g_ur/u_cubegen.htm
// n<0 means angstroms: http://paulbourke.net/dataformats/cube/
// always assume bohr: openbabel source code
// always assume angstrom: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/cubeplugin.html
// we are going to go with n<0 means angstrom - note this is just the first n
var convFactor = ((lineArr[0] as any) > 0) ? 0.529177 : 1;
origin.multiplyScalar(convFactor);
var nX = Math.abs((lineArr[0] as any));
var xVec = new Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]))
.multiplyScalar(convFactor);
lineArr = lines[4].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var nY = Math.abs((lineArr[0] as any));
var yVec = new Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]))
.multiplyScalar(convFactor);
lineArr = lines[5].replace(/^\s+/, "").replace(/\s+/g, " ").split(" ");
var nZ = Math.abs((lineArr[0] as any));
var zVec = new Vector3(parseFloat(lineArr[1]),
parseFloat(lineArr[2]), parseFloat(lineArr[3]))
.multiplyScalar(convFactor);
cryst.size = {x:nX, y:nY, z:nZ};
cryst.unit = new Vector3(xVec.x, yVec.y, zVec.z);
if (xVec.y != 0 || xVec.z != 0 || yVec.x != 0 || yVec.z != 0 || zVec.x != 0
|| zVec.y != 0) {
//need a transformation matrix
cryst.matrix4 = new Matrix4(xVec.x, yVec.x, zVec.x, 0, xVec.y, yVec.y, zVec.y, 0, xVec.z, yVec.z, zVec.z, 0, 0,0,0,1);
// include translation in matrix
let t = new Matrix4().makeTranslation(origin.x, origin.y, origin.z);
cryst.matrix4 = cryst.matrix4.multiplyMatrices(t,cryst.matrix4);
cryst.matrix = cryst.matrix4.matrix3FromTopLeft();
// all translation and scaling done by matrix, so reset origin and unit
cryst.origin = new Vector3(0,0,0);
cryst.unit = new Vector3(1,1,1);
}
atoms.modelData = [{cryst:cryst}];
// Extract atom portion; send to new GLModel...
lines = lines.splice(6, natoms);
var start = atoms[atoms.length-1].length;
var end = start + lines.length;
for (var i = start; i < end; ++i) {
var atom: Record<string, any> = {};
atom.serial = i;
var line = lines[i - start];
var tokens = line.replace(/^\s+/, "").replace(/\s+/g, " ").split(
" ");
atom.elem = anumToSymbol[tokens[0]];
atom.x = parseFloat(tokens[2]) * convFactor;
atom.y = parseFloat(tokens[3]) * convFactor;
atom.z = parseFloat(tokens[4]) * convFactor;
atom.hetflag = true;
atom.bonds = [];
atom.bondOrder = [];
atom.properties = {};
atoms[atoms.length-1].push(atom);
}
if(assignbonds) {
for (let i = 0; i < atoms.length; i++)
assignBonds(atoms[i]);
}
return atoms;
};