net.sf.octet.util
Class RepresentationKit

java.lang.Object
  net.sf.octet.util.RepresentationKit

public class RepresentationKit

extends java.lang.Object

A collection of static methods that create pre-built representations from a RepresentationBuilder.

Author:

Richard Apodaca

Method Summary

static void	buildAromaticBenzene(RepresentationBuilder builder) Builds benzene using the specified RepresentationBuilder.
static void	buildAromaticFuran(RepresentationBuilder builder) Builds pyridine using the specified RepresentationBuilder.
static void	buildAromaticPyridine(RepresentationBuilder builder) Builds pyridine using the specified RepresentationBuilder.
static void	buildAromaticPyrrole(RepresentationBuilder builder) Builds pyrrole using the specified RepresentationBuilder.
static void	buildAromaticThiazole(RepresentationBuilder builder) Builds thiazole with a BondingSystem comprised of five atoms and six electrons.
static AtomProxy[]	buildBenzeneFragment(RepresentationBuilder builder) Returns an ordered AtomProxy array after building an aromatic benzene representation.
static void	buildBenzeneRadicalAnion(RepresentationBuilder builder) Builds a benzene radical anion using the specified RepresentationBuilder.
static void	buildBenzylRadical(RepresentationBuilder builder) Builds a benzyl radical representation.
static void	buildBicyclooctane(RepresentationBuilder builder) Directs builder to construct bicyclo[2.2.2]octane using the specified RepresentationBuilder.
static void	buildBinaphthyl(RepresentationBuilder builder) Builds a 1,1'-binaphthyl molecule with no chirality.
static void	buildBiphenyl(RepresentationBuilder builder) Directs builder to build biphenyl.
static AtomProxy[]	buildCarbonChain(RepresentationBuilder builder, int length) Returns an ordered AtomProxy array after building a chain of length carbons.
static AtomProxy[]	buildCarbonRing(RepresentationBuilder builder, int size) Returns an ordered AtomProxy array after building a carbocyclic ring of size members.
static void	buildChargeSeparatedDimethylsulfoxide(RepresentationBuilder builder) Builds dimethylsulfoxide using the specified RepresentationBuilder with a charge-separated S-O group.
static void	buildCis2Pentene(RepresentationBuilder builder) Builds cis-2-pentene using the specified RepresentationBuilder.
static void	buildCisplatin(RepresentationBuilder builder) Builds cisplatin using the specified RepresentationBuilder.
static void	buildCubane(RepresentationBuilder builder) Directs builder to build cubane.
static void	buildCyclohexane(RepresentationBuilder builder) Directs builder to build cyclohexane.
static void	buildCyclohexene(RepresentationBuilder builder) Directs builder to build cyclohexene.
static void	buildCyclopentadienylAnion(RepresentationBuilder builder) Builds a cyclopentadienyl anion using the specified RepresentationBuilder.
static void	buildDeuterochloroform(RepresentationBuilder builder) Constructs CDCl3 using the specified RepresentationBuilder.
static void	buildDeuteroKekuleBenzene(RepresentationBuilder builder) Constructs benzene-d6 using the specified RepresentationBuilder.
static void	buildDiisopropylBenzene(RepresentationBuilder builder) Directs builder to build 1,4-diisopropylbenzene.
static void	buildDoubleBondedDimethylsulfoxide(RepresentationBuilder builder) Builds dimethylsulfoxide using the specified RepresentationBuilder with a double-bonded S=0 group.
static void	buildFerrocene(RepresentationBuilder builder) Builds ferrocene using the specified RepresentationBuilder.
static void	buildHexane(RepresentationBuilder builder) Directs builder to build hexane.
static void	buildHomotropyliumCation(RepresentationBuilder builder) Builds a homotropylium cation using the specified RepresentationBuilder.
static void	buildIsopentane(RepresentationBuilder builder) Directs builder to build isopentane.
static AtomProxy[]	buildKekuleBenzene(RepresentationBuilder builder) Builds kekule benzene (1,3,5-cyclohexatriene) using the specified RepresentationBuilder.
static void	buildKekuleFuran(RepresentationBuilder builder) Builds furan using the specified RepresentationBuilder.
static void	buildKekuleToluene(RepresentationBuilder builder) Directs builder to build Kekule-toluene.
static void	buildNaphthalene(RepresentationBuilder builder) Directs builder to build Kekule-naphthalene.
static AtomProxy[]	buildNaphthaleneFragment(RepresentationBuilder builder) Returns an ordered AtomProxy array after building an aromatic naphthalene representation.
static void	buildPentane(RepresentationBuilder builder) Builds n-pentane using the specified RepresentationBuilder.
static void	buildPhenoxyRadical(RepresentationBuilder builder) Builds a phenoxy radical representation.
static void	buildPhenylAnion(RepresentationBuilder builder) Builds a phenyl anion represention.
static void	buildQuinoline(RepresentationBuilder builder) Directs builder to build quinoline with aromatic bonding.
static void	buildRBinaphthyl(RepresentationBuilder builder) Builds the (R)-1,1'-binaphthyl using the specified RepresentationBuilder.
static void	buildRBinaphthylInverted(RepresentationBuilder builder) Builds the (R)-1,1'-binaphthyl using the specified RepresentationBuilder, but with an inverted conformation about the biaryl axis compared to the result obtained with buildRBinaphthyl.
static void	buildRButanonecyanohydrin(RepresentationBuilder builder) Builds (R)-2-cyano-2-butanol using the specified RepresentationBuilder.
static void	buildRDimethylallene(RepresentationBuilder builder) Builds an (R)-dimethylallene representation.
static void	buildReverseCis2Pentene(RepresentationBuilder builder) Builds cis-2-pentene using the specified RepresentationBuilder.
static void	buildReverseTrans2Pentene(RepresentationBuilder builder) Builds trans-2-pentene using the specified RepresentationBuilder.
static void	buildRIsobutanol(RepresentationBuilder builder) Builds (R)-isobutanol using the specified RepresentationBuilder.
static void	buildRR23Butanediol(RepresentationBuilder builder) Builds (R, R)-2,3-butanediol using the specified RepresentationBuilder.
static void	buildRS23ButaneDiol(RepresentationBuilder builder) Builds (2R, 3S)-butanediol, the meso form, using the specified RepresentationBuilder.
static AtomProxy[]	buildSaturatedCarbonChain(RepresentationBuilder builder, int length) Returns an ordered AtomProxy array after building a chain of length carbons.
static AtomProxy[]	buildSaturatedCarbonRing(RepresentationBuilder builder, int size) Returns an ordered AtomProxy array after building a ring of length carbons.
static void	buildSBinaphthyl(RepresentationBuilder builder) Builds (S)-1,1'-binaphthyl using the specified RepresentationBuilder.
static void	buildSButanonecyanohydrin(RepresentationBuilder builder) Builds (S)-2-cyano-2-butanol using the specified RepresentaitonBuilder.
static void	buildSDimethylallene(RepresentationBuilder builder) Builds an (S)-dimethylallene molecule.
static void	buildSerotonin(RepresentationBuilder builder) Directs builder to build serotonin with Kekule aromatic bonding.
static void	buildSingletDichlorocarbene(RepresentationBuilder builder) Builds a singlet dichlorocarbene representation.
static void	buildSIsobutanol(RepresentationBuilder builder) Builds (S)-isobutanol using the specified RepresentationBuilder.
static void	buildSS23Butanediol(RepresentationBuilder builder) Builds (S, S)-2,3-butanediol using the specified RepresentationBuilder.
static void	buildTertButylCyclohexane(RepresentationBuilder builder) Directs builder to build t-butylcyclohexane.
static void	buildTetrahedrane(RepresentationBuilder builder) Builds tetrahedrane using the specified RepresentationBuilder.
static void	buildTrans2Pentene(RepresentationBuilder builder) Builds trans-2-pentene using the specified RepresentationBuilder.
static void	buildTransplatin(RepresentationBuilder builder) Builds transplatin using the specified RepresentationBuilder
static void	buildTripletDichlorocarbene(RepresentationBuilder builder) Builds a triplet dichlorocarbene representation.

Methods inherited from class java.lang.Object

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

Method Detail

buildBenzeneRadicalAnion

public static void buildBenzeneRadicalAnion(RepresentationBuilder builder)

Builds a benzene radical anion using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildDeuterochloroform

public static void buildDeuterochloroform(RepresentationBuilder builder)

Constructs CDCl3 using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildDeuteroKekuleBenzene

public static void buildDeuteroKekuleBenzene(RepresentationBuilder builder)

Constructs benzene-d6 using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildAromaticThiazole

public static void buildAromaticThiazole(RepresentationBuilder builder)

Builds thiazole with a BondingSystem comprised of five atoms and six electrons.

Parameters:

builder - the RepresentationBuilder

buildPhenylAnion

public static void buildPhenylAnion(RepresentationBuilder builder)

Builds a phenyl anion represention. A six-electron, six-atom BondingSystem is used, and the anion resides on atom 0.

Parameters:

builder - the RepresentationBuilder

buildPhenoxyRadical

public static void buildPhenoxyRadical(RepresentationBuilder builder)

Builds a phenoxy radical representation. The unpaired electron is located on the oxygen atom.

Parameters:

builder - the RepresentationBuilder

buildBenzylRadical

public static void buildBenzylRadical(RepresentationBuilder builder)

Builds a benzyl radical representation. The unpaired electron is located on the benzylic carbon.

Parameters:

builder - the RepresentationBuilder

buildSingletDichlorocarbene

public static void buildSingletDichlorocarbene(RepresentationBuilder builder)

Builds a singlet dichlorocarbene representation. Two paired electrons will be placed into one orbital on carbon, and another carbon orbital will be empty.

Parameters:

builder - the RepresentationBuilder

buildTripletDichlorocarbene

public static void buildTripletDichlorocarbene(RepresentationBuilder builder)

Builds a triplet dichlorocarbene representation. Two electrons with the same spin will occupy one orbital each on carbon.

Parameters:

builder - the RepresentationBuilder

buildRDimethylallene

public static void buildRDimethylallene(RepresentationBuilder builder)

Builds an (R)-dimethylallene representation.

Parameters:

builder - the RepresentationBuilder

buildSDimethylallene

public static void buildSDimethylallene(RepresentationBuilder builder)

Builds an (S)-dimethylallene molecule.

Parameters:

builder - the RepresentationBuilder

buildBinaphthyl

public static void buildBinaphthyl(RepresentationBuilder builder)

Builds a 1,1'-binaphthyl molecule with no chirality.

Parameters:

builder - the RepresentationBuilder

buildRBinaphthyl

public static void buildRBinaphthyl(RepresentationBuilder builder)

Builds the (R)-1,1'-binaphthyl using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildRBinaphthylInverted

public static void buildRBinaphthylInverted(RepresentationBuilder builder)

Builds the (R)-1,1'-binaphthyl using the specified RepresentationBuilder, but with an inverted conformation about the biaryl axis compared to the result obtained with buildRBinaphthyl.

Parameters:

builder - the RepresentationBuilder

buildSBinaphthyl

public static void buildSBinaphthyl(RepresentationBuilder builder)

Builds (S)-1,1'-binaphthyl using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildCis2Pentene

public static void buildCis2Pentene(RepresentationBuilder builder)

Builds cis-2-pentene using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildTrans2Pentene

public static void buildTrans2Pentene(RepresentationBuilder builder)

Builds trans-2-pentene using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildReverseTrans2Pentene

public static void buildReverseTrans2Pentene(RepresentationBuilder builder)

Builds trans-2-pentene using the specified RepresentationBuilder. The polarity of the GammaSequence is reversed compared to the result of buildTrans2Pentene.

Parameters:

builder - the RepresentationBuilder

buildReverseCis2Pentene

public static void buildReverseCis2Pentene(RepresentationBuilder builder)

Builds cis-2-pentene using the specified RepresentationBuilder. The polarity of the GammaSequence is the opposite of that from buildCis2Pentene.

Parameters:

builder - the RepresentationBuilder

buildCisplatin

public static void buildCisplatin(RepresentationBuilder builder)

Builds cisplatin using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildTransplatin

public static void buildTransplatin(RepresentationBuilder builder)

Builds transplatin using the specified RepresentationBuilder

Parameters:

builder - the RepresentationBuilder

buildRR23Butanediol

public static void buildRR23Butanediol(RepresentationBuilder builder)

Builds (R, R)-2,3-butanediol using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildSS23Butanediol

public static void buildSS23Butanediol(RepresentationBuilder builder)

Builds (S, S)-2,3-butanediol using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildRS23ButaneDiol

public static void buildRS23ButaneDiol(RepresentationBuilder builder)

Builds (2R, 3S)-butanediol, the meso form, using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildRIsobutanol

public static void buildRIsobutanol(RepresentationBuilder builder)

Builds (R)-isobutanol using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildSIsobutanol

public static void buildSIsobutanol(RepresentationBuilder builder)

Builds (S)-isobutanol using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildRButanonecyanohydrin

public static void buildRButanonecyanohydrin(RepresentationBuilder builder)

Builds (R)-2-cyano-2-butanol using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildSButanonecyanohydrin

public static void buildSButanonecyanohydrin(RepresentationBuilder builder)

Builds (S)-2-cyano-2-butanol using the specified RepresentaitonBuilder.

Parameters:

builder - the RepresentationBuilder

buildFerrocene

public static void buildFerrocene(RepresentationBuilder builder)

Builds ferrocene using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildQuinoline

public static void buildQuinoline(RepresentationBuilder builder)

Directs builder to build quinoline with aromatic bonding.

Parameters:

builder - the RepresentationBuilder

buildSerotonin

public static void buildSerotonin(RepresentationBuilder builder)

Directs builder to build serotonin with Kekule aromatic bonding.

Parameters:

builder - the RepresentationBuilder

buildHexane

public static void buildHexane(RepresentationBuilder builder)

Directs builder to build hexane.

Parameters:

builder - the RepresentationBuilder

buildIsopentane

public static void buildIsopentane(RepresentationBuilder builder)

Directs builder to build isopentane.

Parameters:

builder - the RepresentationBuilder

buildTertButylCyclohexane

public static void buildTertButylCyclohexane(RepresentationBuilder builder)

Directs builder to build t-butylcyclohexane.

Parameters:

builder - the RepresentationBuilder

buildCyclohexane

public static void buildCyclohexane(RepresentationBuilder builder)

Directs builder to build cyclohexane.

Parameters:

builder - the RepresentationBuilder

buildBicyclooctane

public static void buildBicyclooctane(RepresentationBuilder builder)

Directs builder to construct bicyclo[2.2.2]octane using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder to be used

buildDiisopropylBenzene

public static void buildDiisopropylBenzene(RepresentationBuilder builder)

Directs builder to build 1,4-diisopropylbenzene.

Parameters:

builder - the RepresentationBuilder

buildCubane

public static void buildCubane(RepresentationBuilder builder)

Directs builder to build cubane.

Parameters:

builder - the RepresentationBuilder

buildNaphthalene

public static void buildNaphthalene(RepresentationBuilder builder)

Directs builder to build Kekule-naphthalene.

Parameters:

builder - the RepresentationBuilder

buildCyclohexene

public static void buildCyclohexene(RepresentationBuilder builder)

Directs builder to build cyclohexene.

Parameters:

builder - the RepresentationBuilder

buildDoubleBondedDimethylsulfoxide

public static void buildDoubleBondedDimethylsulfoxide(RepresentationBuilder builder)

Builds dimethylsulfoxide using the specified RepresentationBuilder with a double-bonded S=0 group.

Parameters:

builder - the RepresentationBuilder

buildChargeSeparatedDimethylsulfoxide

public static void buildChargeSeparatedDimethylsulfoxide(RepresentationBuilder builder)

Builds dimethylsulfoxide using the specified RepresentationBuilder with a charge-separated S-O group.

Parameters:

builder - the RepresentationBuilder

buildAromaticBenzene

public static void buildAromaticBenzene(RepresentationBuilder builder)

Builds benzene using the specified RepresentationBuilder. The pi system is configured as a six-atom, six-electron BondingSystem.

Parameters:

builder - the RepresentationBuilder

buildKekuleBenzene

public static AtomProxy[] buildKekuleBenzene(RepresentationBuilder builder)

Builds kekule benzene (1,3,5-cyclohexatriene) using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildBiphenyl

public static void buildBiphenyl(RepresentationBuilder builder)

Directs builder to build biphenyl.

Parameters:

builder - the RepresentationBuilder

buildKekuleToluene

public static void buildKekuleToluene(RepresentationBuilder builder)

Directs builder to build Kekule-toluene.

Parameters:

builder - the RepresentationBuilder

buildCyclopentadienylAnion

public static void buildCyclopentadienylAnion(RepresentationBuilder builder)

Builds a cyclopentadienyl anion using the specified RepresentationBuilder. The negative charge resides within a five-atom, six-electron BondingSystem

Parameters:

builder - the RepresentationBuilder to be used

buildHomotropyliumCation

public static void buildHomotropyliumCation(RepresentationBuilder builder)

Builds a homotropylium cation using the specified RepresentationBuilder. The positive charge resides in a seven-atom, six-electron BondingSystem.

Parameters:

builder - the RepresentationBuilder to be used

buildAromaticPyridine

public static void buildAromaticPyridine(RepresentationBuilder builder)

Builds pyridine using the specified RepresentationBuilder. The pi system is configured as a six-atom, six-electron BondingSystem.

Parameters:

builder - the RepresentationBuilder to be used

buildAromaticFuran

public static void buildAromaticFuran(RepresentationBuilder builder)

Builds pyridine using the specified RepresentationBuilder. The pi system is configured as a five-atom, six-electron BondingSystem.

Parameters:

builder - the RepresentationBuilder

buildKekuleFuran

public static void buildKekuleFuran(RepresentationBuilder builder)

Builds furan using the specified RepresentationBuilder. The pi system is configured as two double bonds.

Parameters:

builder - the RepresentationBuilder

buildPentane

public static void buildPentane(RepresentationBuilder builder)

Builds n-pentane using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildAromaticPyrrole

public static void buildAromaticPyrrole(RepresentationBuilder builder)

Builds pyrrole using the specified RepresentationBuilder. The pi system is configured as a five-atom, six-electron BondingSystem.

Parameters:

builder - the RepresentationBuilder

buildTetrahedrane

public static void buildTetrahedrane(RepresentationBuilder builder)

Builds tetrahedrane using the specified RepresentationBuilder.

Parameters:

builder - the RepresentationBuilder

buildBenzeneFragment

public static AtomProxy[] buildBenzeneFragment(RepresentationBuilder builder)

Returns an ordered AtomProxy array after building an aromatic benzene representation. All carbons will have one associated hydrogen.

Parameters:

builder - the RepresentationBuilder

Returns:

an ordered array containing six AtomProxies

buildNaphthaleneFragment

public static AtomProxy[] buildNaphthaleneFragment(RepresentationBuilder builder)

Returns an ordered AtomProxy array after building an aromatic naphthalene representation. Non-bridgehead atoms will have one associated hydrogen atom.

Parameters:

builder - the RepresentationBuilder

Returns:

an ordered array containing ten AtomProxies

buildCarbonRing

public static AtomProxy[] buildCarbonRing(RepresentationBuilder builder,
                                          int size)

Returns an ordered AtomProxy array after building a carbocyclic ring of size members. Each carbon will have no associated hydrogen atoms.

Parameters:

builder - the RepresentationBuilder

Returns:

an ordered array containing size AtomProxies

Throws:

java.lang.IllegalArgumentException - if size is less than three

buildCarbonChain

public static AtomProxy[] buildCarbonChain(RepresentationBuilder builder,
                                           int length)

Returns an ordered AtomProxy array after building a chain of length carbons. Each carbon will have no associated hydrogen atoms.

Parameters:

builder - the RepresentationBuilder

length - the length of the chain

Returns:

an ordered array containing length AtomProxies

Throws:

java.lang.IllegalArgumentException - if length is less than one

buildSaturatedCarbonChain

public static AtomProxy[] buildSaturatedCarbonChain(RepresentationBuilder builder,
                                                    int length)

Returns an ordered AtomProxy array after building a chain of length carbons. Internal carbons will have two associated hydrogen atoms and external carbons will have thrww associated hydrogen atoms.

Parameters:

builder - the RepresentationBuilder

length - the number of carbons in the chain

Returns:

an ordered array containing length AtomProxies

buildSaturatedCarbonRing

public static AtomProxy[] buildSaturatedCarbonRing(RepresentationBuilder builder,
                                                   int size)

Returns an ordered AtomProxy array after building a ring of length carbons. All carbons will have two associated hydrogen atoms.

Parameters:

builder - the RepresentationBuilder

size - the number of carbons in the ring

Returns:

an ordered array containing length AtomProxies