smiles-drawer/src/Vertex.js

A SMILES drawer and parser. Generate molecular structure depictions in pure JavaScript.

//@ts-check
const MathHelper = require('./MathHelper')
const ArrayHelper = require('./ArrayHelper')
const Vector2 = require('./Vector2')
const Atom = require('./Atom')

/** 
 * A class representing a vertex.
 * 
 * @property {Number} id The id of this vertex.
 * @property {Atom} value The atom associated with this vertex.
 * @property {Vector2} position The position of this vertex.
 * @property {Vector2} previousPosition The position of the previous vertex.
 * @property {Number|null} parentVertexId The id of the previous vertex.
 * @property {Number[]} children The ids of the children of this vertex.
 * @property {Number[]} spanningTreeChildren The ids of the children of this vertex as defined in the spanning tree defined by the SMILES.
 * @property {Number[]} edges The ids of edges associated with this vertex.
 * @property {Boolean} positioned A boolean indicating whether or not this vertex has been positioned.
 * @property {Number} angle The angle of this vertex.
 * @property {Number} dir The direction of this vertex.
 * @property {Number} neighbourCount The number of neighbouring vertices.
 * @property {Number[]} neighbours The vertex ids of neighbouring vertices.
 * @property {String[]} neighbouringElements The element symbols associated with neighbouring vertices.
 * @property {Boolean} forcePositioned A boolean indicating whether or not this vertex was positioned using a force-based approach.
 */

class Vertex {
  /**
   * The constructor for the class Vertex.
   *
   * @param {Atom} value The value associated with this vertex.
   * @param {Number} [x=0] The initial x coordinate of the positional vector of this vertex.
   * @param {Number} [y=0] The initial y coordinate of the positional vector of this vertex.
   */
  constructor(value, x = 0, y = 0) {
    this.id = null;
    this.value = value;
    this.position = new Vector2(x ? x : 0, y ? y : 0);
    this.previousPosition = new Vector2(0, 0);
    this.parentVertexId = null;
    this.children = Array();
    this.spanningTreeChildren = Array();
    this.edges = Array();
    this.positioned = false;
    this.angle = null;
    this.dir = 1.0;
    this.neighbourCount = 0;
    this.neighbours = Array();
    this.neighbouringElements = Array();
    this.forcePositioned = false;
  }

  /**
   * Set the 2D coordinates of the vertex.
   * 
   * @param {Number} x The x component of the coordinates.
   * @param {Number} y The y component of the coordinates.
   * 
   */
  setPosition(x, y) {
    this.position.x = x;
    this.position.y = y;
  }

  /**
   * Set the 2D coordinates of the vertex from a Vector2.
   * 
   * @param {Vector2} v A 2D vector.
   * 
   */
  setPositionFromVector(v) {
    this.position.x = v.x;
    this.position.y = v.y;
  }

  /**
   * Add a child vertex id to this vertex.
   * @param {Number} vertexId The id of a vertex to be added as a child to this vertex.
   */
  addChild(vertexId) {
    this.children.push(vertexId);
    this.neighbours.push(vertexId);

    this.neighbourCount++;
  }

  /**
   * Add a child vertex id to this vertex as the second child of the neighbours array,
   * except this vertex is the first vertex of the SMILE string, then it is added as the first.
   * This is used to get the correct ordering of neighbours for parity calculations.
   * If a hydrogen is implicitly attached to the chiral center, insert as the third child.
   * @param {Number} vertexId The id of a vertex to be added as a child to this vertex.
   * @param {Number} ringbondIndex The index of the ringbond.
   */
  addRingbondChild(vertexId, ringbondIndex) {
    this.children.push(vertexId);

    if (this.value.bracket) {
      let index = 1;

      if (this.id === 0 && this.value.bracket.hcount === 0) {
        index = 0;
      }
      
      if (this.value.bracket.hcount === 1 && ringbondIndex === 0) {
        index = 2;
      }

      if (this.value.bracket.hcount === 1 && ringbondIndex === 1) {
        if (this.neighbours.length < 3) {
          index = 2;
        } else {
          index = 3;
        }
      }

      if (this.value.bracket.hcount === null && ringbondIndex === 0) {
        index = 1;
      }

      if (this.value.bracket.hcount === null && ringbondIndex === 1) {
        if (this.neighbours.length < 3) {
          index = 1;
        } else {
          index = 2;
        }
      }
      
      this.neighbours.splice(index, 0, vertexId);
    } else {
      this.neighbours.push(vertexId);
    }

    this.neighbourCount++;
  }

  /**
   * Set the vertex id of the parent.
   * 
   * @param {Number} parentVertexId The parents vertex id.
   */
  setParentVertexId(parentVertexId) {
    this.neighbourCount++;
    this.parentVertexId = parentVertexId;
    this.neighbours.push(parentVertexId);
  }

  /**
   * Returns true if this vertex is terminal (has no parent or child vertices), otherwise returns false. Always returns true if associated value has property hasAttachedPseudoElements set to true.
   *
   * @returns {Boolean} A boolean indicating whether or not this vertex is terminal.
   */
  isTerminal() {
    if (this.value.hasAttachedPseudoElements) {
      return true;
    }

    return (this.parentVertexId === null && this.children.length < 2) || this.children.length === 0;
  }

  /**
   * Clones this vertex and returns the clone.
   *
   * @returns {Vertex} A clone of this vertex.
   */
  clone() {
    let clone = new Vertex(this.value, this.position.x, this.position.y);
    clone.id = this.id;
    clone.previousPosition = new Vector2(this.previousPosition.x, this.previousPosition.y);
    clone.parentVertexId = this.parentVertexId;
    clone.children = ArrayHelper.clone(this.children);
    clone.spanningTreeChildren = ArrayHelper.clone(this.spanningTreeChildren);
    clone.edges = ArrayHelper.clone(this.edges);
    clone.positioned = this.positioned;
    clone.angle = this.angle;
    clone.forcePositioned = this.forcePositioned;
    return clone;
  }

  /**
   * Returns true if this vertex and the supplied vertex both have the same id, else returns false.
   *
   * @param {Vertex} vertex The vertex to check.
   * @returns {Boolean} A boolean indicating whether or not the two vertices have the same id.
   */
  equals(vertex) {
    return this.id === vertex.id;
  }

  /**
   * Returns the angle of this vertexes positional vector. If a reference vector is supplied in relations to this vector, else in relations to the coordinate system.
   *
   * @param {Vector2} [referenceVector=null] - The reference vector.
   * @param {Boolean} [returnAsDegrees=false] - If true, returns angle in degrees, else in radians.
   * @returns {Number} The angle of this vertex.
   */
  getAngle(referenceVector = null, returnAsDegrees = false) {
    let u = null;

    if (!referenceVector) {
      u = Vector2.subtract(this.position, this.previousPosition);
    } else {
      u = Vector2.subtract(this.position, referenceVector);
    }

    if (returnAsDegrees) {
      return MathHelper.toDeg(u.angle());
    }

    return u.angle();
  }

  /**
   * Returns the suggested text direction when text is added at the position of this vertex.
   *
   * @param {Vertex[]} vertices The array of vertices for the current molecule.
   * @returns {String} The suggested direction of the text.
   */
  getTextDirection(vertices) {
    let neighbours = this.getDrawnNeighbours(vertices);
    let angles = Array();

    for (let i = 0; i < neighbours.length; i++) {
      angles.push(this.getAngle(vertices[neighbours[i]].position));
    }

    let textAngle = MathHelper.meanAngle(angles);

    // Round to 0, 90, 180 or 270 degree
    let halfPi = Math.PI / 2.0;
    textAngle = Math.round(Math.round(textAngle / halfPi) * halfPi);

    if (textAngle === 2) {
      return 'down';
    } else if (textAngle === -2) {
      return 'up';
    } else if (textAngle === 0 || textAngle === -0) {
      return 'right'; // is checking for -0 necessary?
    } else if (textAngle === 3 || textAngle === -3) {
      return 'left';
    } else {
      return 'down'; // default to down
    }
  }

  /**
   * Returns an array of ids of neighbouring vertices.
   *
   * @param {Number} [vertexId=null] If a value is supplied, the vertex with this id is excluded from the returned indices.
   * @returns {Number[]} An array containing the ids of neighbouring vertices.
   */
  getNeighbours(vertexId = null) {
    if (vertexId === null) {
      return this.neighbours.slice();
    }

    let arr = Array();

    for (let i = 0; i < this.neighbours.length; i++) {
      if (this.neighbours[i] !== vertexId) {
        arr.push(this.neighbours[i]);
      }
    }

    return arr;
  }

  /**
   * Returns an array of ids of neighbouring vertices that will be drawn (vertex.value.isDrawn === true).
   * 
   * @param {Vertex[]} vertices An array containing the vertices associated with the current molecule.
   * @returns {Number[]} An array containing the ids of neighbouring vertices that will be drawn.
   */
  getDrawnNeighbours(vertices) {
    let arr = Array();

    for (let i = 0; i < this.neighbours.length; i++) {
      if (vertices[this.neighbours[i]].value.isDrawn) {
        arr.push(this.neighbours[i]);
      }
    }

    return arr;
  }

  /**
   * Returns the number of neighbours of this vertex.
   *
   * @returns {Number} The number of neighbours.
   */
  getNeighbourCount() {
    return this.neighbourCount;
  }

  /**
   * Returns a list of ids of vertices neighbouring this one in the original spanning tree, excluding the ringbond connections.
   *
   * @param {Number} [vertexId=null] If supplied, the vertex with this id is excluded from the array returned.
   * @returns {Number[]} An array containing the ids of the neighbouring vertices.
   */
  getSpanningTreeNeighbours(vertexId = null) {
    let neighbours = Array();

    for (let i = 0; i < this.spanningTreeChildren.length; i++) {
      if (vertexId === undefined || vertexId != this.spanningTreeChildren[i]) {
        neighbours.push(this.spanningTreeChildren[i]);
      }
    }

    if (this.parentVertexId != null) {
      if (vertexId === undefined || vertexId != this.parentVertexId) {
        neighbours.push(this.parentVertexId);
      }
    }

    return neighbours;
  }

  /**
   * Gets the next vertex in the ring in opposide direction to the supplied vertex id.
   *
   * @param {Vertex[]} vertices The array of vertices for the current molecule.
   * @param {Number} ringId The id of the ring containing this vertex.
   * @param {Number} previousVertexId The id of the previous vertex. The next vertex will be opposite from the vertex with this id as seen from this vertex.
   * @returns {Number} The id of the next vertex in the ring.
   */
  getNextInRing(vertices, ringId, previousVertexId) {
    let neighbours = this.getNeighbours();

    for (let i = 0; i < neighbours.length; i++) {
      if (ArrayHelper.contains(vertices[neighbours[i]].value.rings, {
          value: ringId
        }) &&
        neighbours[i] != previousVertexId) {
        return neighbours[i];
      }
    }

    return null;
  }
}

module.exports = Vertex;