// import {MolfileAtoms} from './mol-atoms';
// import {MolfileBonds} from './mol-bonds';
// import {RGroupHandler} from './r-group-handler';

// export class MolfileWrapper {
//   constructor(molfileV2K: string, private monomerSymbol: string) {
//     const lines = molfileV2K.split('\n');

//     // TODO: port to consts
//     const atomCountIdx = {begin: 0, end: 3};
//     const bondCountIdx = {begin: 3, end: 6};
//     const countsLineIdx = 3;
//     const atomBlockIdx = 4;

//     const atomCount = parseInt(lines[countsLineIdx].substring(atomCountIdx.begin, atomCountIdx.end));
//     const bondCount = parseInt(lines[countsLineIdx].substring(bondCountIdx.begin, bondCountIdx.end));

//     const atomLines = lines.slice(atomBlockIdx, atomBlockIdx + atomCount);
//     this.atoms = new MolfileAtoms(atomLines);

//     const bondLines = lines.slice(atomBlockIdx + atomCount, atomBlockIdx + atomCount + bondCount);
//     this.bonds = new MolfileBonds(bondLines);

//     this.rGroups = new RGroupHandler(lines, this.atoms, this.bonds);

//     this.shiftMonomerToDefaultPosition();
//   }

//   private atoms: MolfileAtoms;
//   private bonds: MolfileBonds;
//   private rGroups: RGroupHandler;

//   deleteBondLineWithSpecifiedRGroup(rGroupId: number): void {
//     this.rGroups.deleteBondLineWithSpecifiedRGroup(rGroupId);
//   }

//   shiftCoordinates(shift: {x: number, y: number}): void {
//     this.atoms.shift(shift);
//   }

//   rotateCoordinates(angle: number): void {
//     this.atoms.rotate(angle);
//   }

//   getBondLines(): string[] {
//     return this.bonds.getBondLines();
//   }

//   getAtomLines(): string[] {
//     return this.atoms.atomLines;
//   }

//   removeRGroups(rGroupIds: number[]): void {
//     this.rGroups.removeRGroups(rGroupIds);
//   }

//   replaceRGroupWithAttachmentAtom(rGroupId: number, externalAtom: number): void {
//     this.rGroups.replaceRGroupWithAttachmentAtom(rGroupId, externalAtom);
//   }

//   getAttachmentAtomByRGroupId(rgroupId: number): number {
//     return this.rGroups.getAttachmentAtomIdByRGroupId(rgroupId);
//   }

//   private shiftR1GroupToOrigin(): void {
//     const r1Idx = this.rGroups.getAtomicIdx(1);
//     if (r1Idx === null)
//       throw new Error(`Cannot find R1 group for monomer ${this.monomerSymbol}`);
//     const {x, y} = this.atoms.atomCoordinates[r1Idx];
//     this.atoms.shift({x: -x, y: -y});
//   }

//   private alignR2AlongX(): void {
//     const r2Idx = this.rGroups.getAtomicIdx(2);
//     if (r2Idx === null)
//       throw new Error(`Cannot find R2 group for monomer ${this.monomerSymbol}`);
//     const r2Coordinates = this.atoms.atomCoordinates[r2Idx];
//     const tan = r2Coordinates.y / r2Coordinates.x;
//     const angle = Math.atan(tan);
//     if (isNaN(angle))
//       throw new Error(`Cannot calculate angle for R2 group for monomer ${this.monomerSymbol}`);
//     this.rotateCoordinates(-angle);
//   }

//   private shiftMonomerToDefaultPosition(): void {
//     this.shiftR1GroupToOrigin();
//     const r2Idx = this.rGroups.getAtomicIdx(2);
//     if (r2Idx !== null)
//       this.alignR2AlongX();
//   }

//   shiftBonds(shift: number): void {
//     this.bonds.shift(shift);
//   }

//   capRGroups(capGroupElements: string[]): void {
//     this.rGroups.capRGroups(capGroupElements);
//   }
// }