edu.illinois.cs.cs125.spring2019.mp4.lib

Class BondedAtom

java.lang.Object

edu.illinois.cs.cs125.spring2019.mp4.lib.BondedAtom

All Implemented Interfaces:

java.lang.Iterable<BondedAtom>

public final class BondedAtom
extends java.lang.Object
implements java.lang.Iterable<BondedAtom>

Represents an atom in an organic molecule and its bonds.

Since references to all other atoms in the molecule can be reached through the methods of this class, it also represents the overall molecule.

One atom can be connected to another through at least one bond. For example, carbon should have 4 bonds, but may be connected to only 3 other atoms if one of the connections is a double bond.

For convenience BondedAtom implements the Iterable interface allow you to iterate through all of its neighbors using the enhanced Java for-each loop.

Constructor Summary

Constructors

Constructor and Description
BondedAtom(ChemicalElement setElement, BondedAtom[] setOtherAtoms, int[] setBondCounts) Creates a new atom connected to the given others.

Method Summary

Modifier and Type	Method and Description
java.util.List<edu.illinois.cs.cs125.spring2019.mp4.lib.BondedAtom.BondInfo>	getBondInfo() Return an iterable list of bond information about all neighboring atoms.
BondedAtom	getConnectedAtom(int index) Convenience method used by the test suite.
ChemicalElement	getElement() Gets what element this atom is an instance of.
boolean	hasSubstituent(java.util.List<BondedAtom> backbone) Convenience method for determining of this atom has a substituent.
int	highPrioritySubstituentCount() Return the count of high-priority substituents attached to this atom.
boolean	isCarbon() Convenience method for determining if this atom is carbon.
boolean	isSubstituent(java.util.List<BondedAtom> backbone) Convenience method for determining if this atom is a substituent.
java.util.Iterator<BondedAtom>	iterator() Return an iterator of BondedAtoms connected to this BondedAtom.
int	lowPrioritySubstituentCount(java.util.List<BondedAtom> backbone) Return the count of low-priority substituents attached to this atom.
java.lang.String	nameEndGroup() Gets the name of the end group substituent, if any, on this carbon.
java.lang.String	nameSubstituent(BondedAtom substituent) Gets the name of a substituent starting at this carbon.
java.lang.String	toString() Returns the string representation of this atom.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

BondedAtom

public BondedAtom(ChemicalElement setElement,
                  BondedAtom[] setOtherAtoms,
                  int[] setBondCounts)

Creates a new atom connected to the given others.

Parameters:

setElement - What element this atom is.

setOtherAtoms - The distinct other atoms this atom is connected to.

setBondCounts - The bond counts in each connection.

Method Detail

getElement

public ChemicalElement getElement()

Gets what element this atom is an instance of.

Returns:

This atom's element.

iterator

public java.util.Iterator<BondedAtom> iterator()

Return an iterator of BondedAtoms connected to this BondedAtom.

This is commonly used by the molecular analysis code to explore the molecule graph.

Specified by:

iterator in interface java.lang.Iterable<BondedAtom>

Returns:

an iterator of BondedAtoms connected to this BondedAtom.

getBondInfo

public java.util.List<edu.illinois.cs.cs125.spring2019.mp4.lib.BondedAtom.BondInfo> getBondInfo()

Return an iterable list of bond information about all neighboring atoms.

Each BondInfo object includes both a reference to the neighbor and it bond count. It is frequently more convenient to use the other iterator method above that returns BondedAtoms. Only use this if you need both the BondedAtom and the bond count.

Returns:

an unmodifiable list of BondInfo objects describing our neighbor atoms.

getConnectedAtom

public BondedAtom getConnectedAtom(int index)

Convenience method used by the test suite.

Parameters:

index - index of the BondedAtom to return

Returns:

the BondedAtom at that position or null if the index is invalid

isCarbon

public boolean isCarbon()

Convenience method for determining if this atom is carbon.

Returns:

whether this atom is carbon

isSubstituent

public boolean isSubstituent(java.util.List<BondedAtom> backbone)

Convenience method for determining if this atom is a substituent.

Parameters:

backbone - the backbone of this molecule to use to identify off-backbone carbons

Returns:

whether this atom is a substituent

hasSubstituent

public boolean hasSubstituent(java.util.List<BondedAtom> backbone)

Convenience method for determining of this atom has a substituent.

This could either mean it has an attached substituent or off-backbone carbon.

Parameters:

backbone - the backbone of this molecule to use to identify off-backbone carbons

Returns:

true if this atom has a connected substituent, and false otherwise

highPrioritySubstituentCount

public int highPrioritySubstituentCount()

Return the count of high-priority substituents attached to this atom.

Returns:

the count of high-priority substituents attached to this atom

lowPrioritySubstituentCount

public int lowPrioritySubstituentCount(java.util.List<BondedAtom> backbone)

Return the count of low-priority substituents attached to this atom.

Parameters:

backbone - the backbone of this molecule to use to identify off-backbone carbons

Returns:

the count of low-priority substituents attached to this atom

nameSubstituent

public java.lang.String nameSubstituent(BondedAtom substituent)

Gets the name of a substituent starting at this carbon.

Assumes that there is no end group on the core/base carbon.

Parameters:

substituent - the first atom of the substituent

Returns:

the substituent's name, or null if none exists or this atom is not carbon

nameEndGroup

public java.lang.String nameEndGroup()

Gets the name of the end group substituent, if any, on this carbon.

Returns:

the name of any end substituent, or null if none exists or this atom is not carbon

toString

public java.lang.String toString()

Returns the string representation of this atom.

Overrides:

toString in class java.lang.Object

Returns:

This atom's element and instance ID.