Package edu.illinois.cs.cs125.mp5.lib

Class MoleculeAnalyzer

  • public class MoleculeAnalyzer
extends java.lang.Object
    Analyzes a given organic molecule.

    • Constructor Detail

      • MoleculeAnalyzer

        public MoleculeAnalyzer​(BondedAtom molecule)
        Creates an MoleculeAnalyzer for analyzing a given molecule.
        Parameters:
        molecule - an atom belonging to the molecule that will be analyzed.

    • Method Detail

      • getAllAtoms

        public java.util.List<BondedAtom> getAllAtoms()
        Return the list of all atoms in this molecule.

        This is a convenience method used by the test suite.

        Returns:
        a list of all atoms in this molecule.

      • findAllAtoms

        public java.util.ArrayList<BondedAtom> findAllAtoms​(BondedAtom current,
                                                    java.util.ArrayList<BondedAtom> atoms)
        Recursively adds connected atoms to the allAtoms list.

        This is recursive graph traversal.

        Parameters:
        current - the atom we're currently examining
        atoms - list of all atoms we've found so far
        Returns:
        all atoms found in the molecule
        See Also:
        Graph Traversal

      • getMolecularWeight

        public double getMolecularWeight()
        Determines the total molecular weight of this molecule.

        Computes molecular weight by summing the weights of all the atoms that comprise the molecule.

        Returns:
        the molecular weight of the molecule in grams per mole

      • hasChargedAtoms

        public boolean hasChargedAtoms()
        Determines whether this molecule contains any charged atoms.

        Charged atoms have a different total number of bonds than their valence. For example, an oxygen atom with three bonds is charged.

        Note that this should be easy to complete once you have found all atoms in the molecule and added them to the allAtoms list.

        Returns:
        true if there is at least one charged atom in the molecule, false otherwise

      • isRing

        public boolean isRing()
        Returns whether the molecule is a ring.

        Used by the test suite for debugging.

        Returns:
        true if the molecule is a ring and false otherwise

      • getRing

        public java.util.List<BondedAtom> getRing()
        Searches the molecule for a ring.

        This is cycle detection.

        Returns:
        a list containing the atoms in the ring if a ring exists, null otherwise
        See Also:
        Cycle Detection

      • getRing

        public java.util.List<BondedAtom> getRing​(BondedAtom current,
                                          java.util.List<BondedAtom> visited)
        Search the molecule for a ring from a specific starting point.

        This is cycle detection.

        Parameters:
        current - the current atom we are examining.
        visited - a list of previously-visited atom. The previous atom is the last in the list.
        Returns:
        a list containing the atoms in the ring if a ring exists, null otherwise
        See Also:
        Cycle Detection

      • getLinearBackbone

        public java.util.List<BondedAtom> getLinearBackbone()
        Identify the linear backbone of the molecule.
        Returns:
        the list of atoms constituting the linear backbone of this atom

      • getTips

        public java.util.List<BondedAtom> getTips()
        Find all atoms that are molecule tips: carbons that are bonded to at most one other carbon.

        Note that tips can only be bonded to one other carbon but may also be bonded to other atoms.

        Note that this should be easy to complete once you have found all atoms in the molecule and added them to the allAtoms Set.

        This is searching for leaf vertices in a graph.

        Returns:
        a list of all BondedAtoms that are tips of this molecule, which may be empty if it is a simple ring.
        See Also:
        Leaf Vertex

      • getBackbones

        public java.util.List<java.util.List<BondedAtom>> getBackbones()
        Find all possible backbones in a linear molecule.

        To do this, first find all tip carbons, and then find all paths between them. So this function uses both getTips and findPath.

        Returns:
        a list of all possible backbones, each itself a list of atoms

      • findPath

        public java.util.List<BondedAtom> findPath​(BondedAtom start,
                                           BondedAtom end)
        Find a path between two atoms in the molecule.

        This function will only produce a meaningful result on non-cyclic molecules where there is only one path between any two molecules.

        This is graph pathfinding, simplified by being run on a non-cyclic graph.

        Parameters:
        start - the atom to start from
        end - the atom to end at
        Returns:
        the path from the start atom to the end atom
        See Also:
        Graph Pathfinding

      • findPath

        public java.util.List<BondedAtom> findPath​(BondedAtom current,
                                           BondedAtom end,
                                           java.util.List<BondedAtom> path)
        Recursively find a path between two atoms in the molecule.

        This function will only produce a meaningful result on non-cyclic molecules where there is only one path between any two molecules.

        This is graph pathfinding, simplified by being run on a non-cyclic graph.

        Parameters:
        current - the current atom we are examining
        end - the atom to end at
        path - the atoms we've already visited on our way to the current atom
        Returns:
        the path from the current atom to the end atom
        See Also:
        Graph Pathfinding

      • rotateRing

        public java.util.List<BondedAtom> rotateRing​(java.util.List<BondedAtom> ring)
        Rotate a backbone ring into the correct position for naming.

        This doesn't necessarily have a strong analogy to graphs, but it's pretty fun.

        Parameters:
        ring - the backbone ring to rotate
        Returns:
        the backbone ring rotated into the correct position

      • getIupacName

        public java.lang.String getIupacName()
        Names the molecule according to IUPAC rules for organic compounds.

        See the MP page for information on naming. This function will not work until you complete the functions above: getRing, getLinearBackbone, and rotateRing.

        Returns:
        The systematic IUPAC name of the molecule.

      • getFormula

        public java.lang.String getFormula()
        Gets a chemical formula for this molecule. This function is optional and not tested by the test suite; it is only used by the app. You may use any formula format that you like.
        Returns:
        A chemical formula indicating the allAtoms the molecule contains.