A B C E F G H I L M N O R S T V 

A

addSubstituent(int, OrganicMoleculeBuilder.Substituent) - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Adds a substituent to the backbone at the given position.
ALCOHOL - edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.SubstituentType
An alcohol (-OH group).
ALKANE - edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.SubstituentType
A single-bonded chain of carbons.
attach(BondedAtom) - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Builds the substituent and attaches it to the backbone.

B

BondedAtom - Class in edu.illinois.cs.cs125.mp5.lib
Represents an atom in an organic molecule and its bonds.
BondedAtom(ChemicalElement, BondedAtom[], int[]) - Constructor for class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Creates a new atom connected to the given others.
BROMINE - Static variable in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Element 35, the third halogen, bromine.
build() - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Constructs a molecule.

C

CARBON - Static variable in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Element 6, carbon.
CARBONYL - edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.SubstituentType
A carbonyl (=O group).
CHAIN_BASE_NAMES - Static variable in class edu.illinois.cs.cs125.mp5.lib.NamingConstants
Base names of carbon chains/rings based on their length.
ChemicalElement - Class in edu.illinois.cs.cs125.mp5.lib
Represents an element, that is, a type of atom.
CHLORINE - Static variable in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Element 17, the second halogen, chlorine.
createAlcohol() - Static method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Creates a neutral alcohol (OH) substituent.
createAlcohol(int) - Static method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Creates an (optionally charged) alcohol substituent.
createAlkyl(int) - Static method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Creates an alkyl substituent.
createCarbonyl() - Static method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Creates a carbonyl (double-bonded O) substituent.
createHalogen(ChemicalElement) - Static method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Creates a halogen (single-atom) substituent.
CyclicOrganicMoleculeBuilder - Class in edu.illinois.cs.cs125.mp5.lib
Provides a convenient way to construct and render cyclic organic molecules.
CyclicOrganicMoleculeBuilder(int) - Constructor for class edu.illinois.cs.cs125.mp5.lib.CyclicOrganicMoleculeBuilder
Creates a builder for a cyclic molecule containing the given number of carbons in the ring.

E

edu.illinois.cs.cs125.mp5.lib - package edu.illinois.cs.cs125.mp5.lib
 

F

findAllAtoms(BondedAtom, ArrayList<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Recursively adds connected atoms to the allAtoms list.
findPath(BondedAtom, BondedAtom) - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Find a path between two atoms in the molecule.
findPath(BondedAtom, BondedAtom, List<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Recursively find a path between two atoms in the molecule.
finishBackbone(BondedAtom, BondedAtom[], BondedAtom, BondedAtom[]) - Method in class edu.illinois.cs.cs125.mp5.lib.CyclicOrganicMoleculeBuilder
Makes the molecule cyclic by linking the first and last backbone carbons.
finishBackbone(BondedAtom, BondedAtom[], BondedAtom, BondedAtom[]) - Method in class edu.illinois.cs.cs125.mp5.lib.LinearOrganicMoleculeBuilder
Does nothing - freeValence makes sure the right number of hydrogens is added.
finishBackbone(BondedAtom, BondedAtom[], BondedAtom, BondedAtom[]) - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Completes the backbone as appropriate for the type of builder.
FLUORINE - Static variable in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Element 9, the first halogen, fluorine.
freeValence(int) - Method in class edu.illinois.cs.cs125.mp5.lib.CyclicOrganicMoleculeBuilder
Gets how many bonds a core carbon can make after inclusion in the backbone.
freeValence(int) - Method in class edu.illinois.cs.cs125.mp5.lib.LinearOrganicMoleculeBuilder
Gets how many bonds a core carbon can make after inclusion in the backbone.
freeValence(int) - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Gets how many bonds of the given carbon are not satisfied in the backbone.

G

getAlkylLength() - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Gets how long this alkyl substituent is.
getAllAtoms() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Return the list of all atoms in this molecule.
getBackbones() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Find all possible backbones in a linear molecule.
getBondInfo() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Return an iterable list of bond information about all neighboring atoms.
getConnectedAtom(int) - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Convenience method used by the test suite.
getCoreCarbons() - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Gets the number of carbons in the base chain/cycle of this molecule.
getElement() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Gets what element this atom is an instance of.
getFormula() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Gets a chemical formula for this molecule.
getHalogen() - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Gets what halogen element this substituent is.
getIupacName() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Names the molecule according to IUPAC rules for organic compounds.
getLinearBackbone() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Identify the linear backbone of the molecule.
getMolecularWeight() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Determines the total molecular weight of this molecule.
getRing() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Searches the molecule for a ring.
getRing(BondedAtom, List<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Search the molecule for a ring from a specific starting point.
getSubstituents(int) - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Gets all present substituents at the given position.
getSymbol() - Method in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Gets the element's symbol on the periodic table.
getTips() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Find all atoms that are molecule tips: carbons that are bonded to at most one other carbon.
getType() - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
Gets what kind of substituent this is.
getValence() - Method in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Gets the element's valence, that is, how many bonds an atom of this element should have.
getValenceConsumed() - Method in class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
How many bonds this substituent consumes on the backbone carbon it's attached to.
getWeight() - Method in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Gets the element's average atomic mass.

H

HALIDES - Static variable in class edu.illinois.cs.cs125.mp5.lib.NamingConstants
Names of halogen substituents.
HALOGEN - edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.SubstituentType
A halogen.
hasChargedAtoms() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Determines whether this molecule contains any charged atoms.
hasSubstituent(List<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Convenience method for determining of this atom has a substituent.
highPrioritySubstituentCount() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Return the count of high-priority substituents attached to this atom.
HYDROGEN - Static variable in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Element 1, hydrogen.

I

isCarbon() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Convenience method for determining if this atom is carbon.
isRing() - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Returns whether the molecule is a ring.
isSubstituent(List<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Convenience method for determining if this atom is a substituent.
iterator() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Return an iterator of BondedAtoms connected to this BondedAtom.

L

LinearOrganicMoleculeBuilder - Class in edu.illinois.cs.cs125.mp5.lib
Provides a convenient way to build and render linear/branched organic molecules.
LinearOrganicMoleculeBuilder(int) - Constructor for class edu.illinois.cs.cs125.mp5.lib.LinearOrganicMoleculeBuilder
Creates a builder for a linear/branched molecule.
lowPrioritySubstituentCount(List<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Return the count of high-priority substituents attached to this atom.

M

MoleculeAnalyzer - Class in edu.illinois.cs.cs125.mp5.lib
Analyzes a given organic molecule.
MoleculeAnalyzer(BondedAtom) - Constructor for class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Creates an MoleculeAnalyzer for analyzing a given molecule.
MULTIPLICITY_NAMES - Static variable in class edu.illinois.cs.cs125.mp5.lib.NamingConstants
Prefixes for naming when there are multiple instances of the same substituent.

N

nameEndGroup() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Gets the name of the end group substituent, if any, on this carbon.
nameSubstituent(BondedAtom) - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Gets the name of a substituent starting at this carbon.
NamingConstants - Class in edu.illinois.cs.cs125.mp5.lib
Class to hold various naming constants used by MoleculeAnalyzer.
NamingConstants() - Constructor for class edu.illinois.cs.cs125.mp5.lib.NamingConstants
 

O

OrganicMoleculeBuilder - Class in edu.illinois.cs.cs125.mp5.lib
Provides a convenient way to construct OrganicMolecule objects.
OrganicMoleculeBuilder(int) - Constructor for class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder
Creates an organic molecule builder.
OrganicMoleculeBuilder.Substituent - Class in edu.illinois.cs.cs125.mp5.lib
Helps represent, build, and attach substituents to the backbone.
OrganicMoleculeBuilder.SubstituentType - Enum in edu.illinois.cs.cs125.mp5.lib
Possible types of substituents.
OXYGEN - Static variable in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Element 8, oxygen.

R

rotateRing(List<BondedAtom>) - Method in class edu.illinois.cs.cs125.mp5.lib.MoleculeAnalyzer
Rotate a backbone ring into the correct position for naming.

S

Substituent() - Constructor for class edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.Substituent
 

T

toString() - Method in class edu.illinois.cs.cs125.mp5.lib.BondedAtom
Returns the string representation of this atom.
toString() - Method in class edu.illinois.cs.cs125.mp5.lib.ChemicalElement
Gets a string representation of the element object.

V

valueOf(String) - Static method in enum edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.SubstituentType
Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.illinois.cs.cs125.mp5.lib.OrganicMoleculeBuilder.SubstituentType
Returns an array containing the constants of this enum type, in the order they are declared.
VOWELS - Static variable in class edu.illinois.cs.cs125.mp5.lib.NamingConstants
All letters that are considered vowels for purposes of molecule naming.
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