MoleculeAnalyzer

java.lang.Object
- edu.illinois.cs.cs125.spring2019.mp4.lib.MoleculeAnalyzer

public class MoleculeAnalyzer
extends java.lang.Object

Analyzes a given organic molecule.

Constructor Summary

Constructors
Constructor and Description

MoleculeAnalyzer(BondedAtom molecule)
Creates an MoleculeAnalyzer for analyzing a given molecule.

Constructors
Constructor and Description
`MoleculeAnalyzer(BondedAtom molecule)` Creates an MoleculeAnalyzer for analyzing a given molecule.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.util.ArrayList<BondedAtom>`	`findAllAtoms(BondedAtom current, java.util.ArrayList<BondedAtom> atoms)` Recursively adds connected atoms to the allAtoms list.
`java.util.List<BondedAtom>`	`findPath(BondedAtom start, BondedAtom end)` Find a path between two atoms in the molecule.
`java.util.List<BondedAtom>`	`findPath(BondedAtom current, BondedAtom end, java.util.List<BondedAtom> path)` Helper function to recursively find a path between two atoms in the molecule.
`java.util.List<BondedAtom>`	`getAllAtoms()` Return the list of all atoms in this molecule.
`java.util.List<java.util.List<BondedAtom>>`	`getBackbones()` Find all possible backbones in a linear molecule.
`java.lang.String`	`getFormula()` Gets a chemical formula for this molecule.
`java.lang.String`	`getIupacName()` Names the molecule according to IUPAC rules for organic compounds.
`java.util.List<BondedAtom>`	`getLinearBackbone()` Identify the linear backbone of the molecule.
`double`	`getMolecularWeight()` Determines the total molecular weight of this molecule.
`java.util.List<BondedAtom>`	`getRing()` Searches the molecule for a ring.
`java.util.List<BondedAtom>`	`getRing(BondedAtom current, java.util.List<BondedAtom> visited)` Helper function to search the molecule for a ring from a specific starting point.
`java.util.List<BondedAtom>`	`getTips()` Find all atoms that are molecule tips: carbons that are bonded to at most one other carbon.
`boolean`	`hasChargedAtoms()` Determines whether this molecule contains any charged atoms.
`java.util.List<BondedAtom>`	`rotateRing(java.util.List<BondedAtom> ring)` Rotate a backbone ring into the correct position for naming.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- 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's helper tests.
    
    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
  - getRing
```
public java.util.List<BondedAtom> getRing()
```
    Searches the molecule for a ring.
    Note that if this returns non-null (indicating that there is a ring), getIupacName will pass the list to rotateRing and use that function's output as the cyclic backbone.
    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)
```
    Helper function to 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.
    See the chemistry tutorial in the MP writeup for how to determine the best backbone.
    
    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 list.
    This is similar to 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)
```
    Helper function to 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.
    Note that if getRing returns non-null, its output will be passed to this function by getIupacName. Then this function's output will be used as the cyclic backbone for naming the molecule.
    This doesn't necessarily have a strong analogy to graphs, but it's pretty fun.
    
    Parameters:
    
    ring - the backbone ring to rotate, never null
    
    Returns:
    
    the backbone ring rotated into the correct position, never null
  - 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 rewrite it to use any formula format that you like.
    
    Returns:
    
    A chemical formula indicating all atoms the molecule contains.

Class MoleculeAnalyzer

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MoleculeAnalyzer

Method Detail

getAllAtoms

findAllAtoms

getMolecularWeight

hasChargedAtoms

getRing

getRing

getLinearBackbone

getTips

getBackbones

findPath

findPath

rotateRing

getIupacName

getFormula