org.openscience.cdk.templates
Class MoleculeFactory

java.lang.Object
  extended by org.openscience.cdk.templates.MoleculeFactory

public class MoleculeFactory
extends Object

This class contains methods for generating simple organic molecules.

Keywords:
templates
Source code:
HEAD

Constructor Summary
MoleculeFactory()
           
 
Method Summary
static IMolecule loadMolecule(String inFile)
           
static Molecule make123Triazole()
          Returns 1,2,3-triazole without explicit hydrogens.
static Molecule make124Triazole()
          Returns 1,2,4-triazole without explicit hydrogens.
static Molecule make4x3CondensedRings()
           
static IMolecule makeAdenine()
           
static Molecule makeAlkane(int chainLength)
          Generate an Alkane (chain of carbons with no hydrogens) of a given length.
static Molecule makeAlphaPinene()
           
static Molecule makeAzulene()
          Returns azulene without explicit hydrogens.
static Molecule makeBenzene()
           
static Molecule makeBicycloRings()
           
static Molecule makeBiphenyl()
          Returns biphenyl without explicit hydrogens.
static Molecule makeBranchedAliphatic()
           
static Molecule makeCyclobutadiene()
          Returns cyclobutadiene without explicit hydrogens.
static Molecule makeCyclobutane()
          Returns cyclobutane without explicit hydrogens.
static Molecule makeCyclohexane()
          Returns cyclohexane without explicit hydrogens.
static Molecule makeCyclohexene()
          Returns cyclohexene without explicit hydrogens.
static Molecule makeCyclopentane()
          Returns cyclopentane without explicit hydrogens.
static Molecule makeDiamantane()
           
static Molecule makeEthylCyclohexane()
           
static Molecule makeEthylPropylPhenantren()
           
static Molecule makeFusedRings()
           
static Molecule makeImidazole()
          Returns imidazole without explicit hydrogens.
static Molecule makeIndole()
          Returns indole without explicit hydrogens.
static Molecule makeIsothiazole()
          Returns isothiazole without explicit hydrogens.
static Molecule makeIsoxazole()
          Returns Isoxazole without explicit hydrogens.
static Molecule makeMethylDecaline()
           
static Molecule makeOxadiazole()
          Returns oxadiazole without explicit hydrogens.
static Molecule makeOxazole()
          Returns Oxazole without explicit hydrogens.
static Molecule makePhenylAmine()
           
static Molecule makePhenylEthylBenzene()
           
static Molecule makePiperidine()
           
static Molecule makePropylCycloPropane()
           
static Molecule makePyrazole()
          Returns pyrazole without explicit hydrogens.
static Molecule makePyridazine()
          Returns pyridazine without explicit hydrogens.
static Molecule makePyridine()
          Returns pyridine without explicit hydrogens.
static Molecule makePyridineOxide()
          Returns pyridine oxide without explicit hydrogens.
static Molecule makePyrimidine()
          Returns pyrimidine without explicit hydrogens.
static Molecule makePyrrole()
          Returns pyrrole without explicit hydrogens.
static Molecule makePyrroleAnion()
          Returns pyrrole anion without explicit hydrogens.
static Molecule makeQuinone()
           
static Molecule makeSingleRing()
           
static Molecule makeSpiroRings()
           
static Molecule makeSteran()
           
static Molecule makeTetrahydropyran()
           
static Molecule makeTetrazole()
          Returns tetrazole without explicit hydrogens.
static Molecule makeThiadiazole()
          Returns thiadiazole without explicit hydrogens.
static Molecule makeThiazole()
          Returns thiazole without explicit hydrogens.
static Molecule makeTriazine()
          Returns triazine without explicit hydrogens.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MoleculeFactory

public MoleculeFactory()
Method Detail

makeAlphaPinene

public static Molecule makeAlphaPinene()

makeAlkane

public static Molecule makeAlkane(int chainLength)
Generate an Alkane (chain of carbons with no hydrogens) of a given length.

This method was written by Stephen Tomkinson.

Parameters:
chainLength - The number of carbon atoms to have in the chain.
Returns:
A molecule containing a bonded chain of carbons.
Created on:
2003-08-15

makeEthylCyclohexane

public static Molecule makeEthylCyclohexane()

makeCyclohexene

public static Molecule makeCyclohexene()
Returns cyclohexene without explicit hydrogens.

InChI(s):
InChI=1/C6H10/c1-2-4-6-5-3-1/h1-2H,3-6H2

makeCyclohexane

public static Molecule makeCyclohexane()
Returns cyclohexane without explicit hydrogens.

InChI(s):
InChI=1/C6H12/c1-2-4-6-5-3-1/h1-6H2

makeCyclopentane

public static Molecule makeCyclopentane()
Returns cyclopentane without explicit hydrogens.

InChI(s):
InChI=1/C5H10/c1-2-4-5-3-1/h1-5H2

makeCyclobutane

public static Molecule makeCyclobutane()
Returns cyclobutane without explicit hydrogens.

InChI(s):
InChI=1/C4H8/c1-2-4-3-1/h1-4H2

makeCyclobutadiene

public static Molecule makeCyclobutadiene()
Returns cyclobutadiene without explicit hydrogens.

InChI(s):
InChI=1/C4H4/c1-2-4-3-1/h1-4H

makePropylCycloPropane

public static Molecule makePropylCycloPropane()

makeBiphenyl

public static Molecule makeBiphenyl()
Returns biphenyl without explicit hydrogens.

InChI(s):
InChI=1/C12H10/c1-3-7-11(8-4-1)12-9-5-2-6-10-12/h1-10H

makePhenylEthylBenzene

public static Molecule makePhenylEthylBenzene()

makePhenylAmine

public static Molecule makePhenylAmine()

make4x3CondensedRings

public static Molecule make4x3CondensedRings()

makeSpiroRings

public static Molecule makeSpiroRings()

makeBicycloRings

public static Molecule makeBicycloRings()

makeFusedRings

public static Molecule makeFusedRings()

makeMethylDecaline

public static Molecule makeMethylDecaline()

makeEthylPropylPhenantren

public static Molecule makeEthylPropylPhenantren()

makeSteran

public static Molecule makeSteran()

makeAzulene

public static Molecule makeAzulene()
Returns azulene without explicit hydrogens.

InChI(s):
InChI=1/C10H8/c1-2-5-9-7-4-8-10(9)6-3-1/h1-8H

makeIndole

public static Molecule makeIndole()
Returns indole without explicit hydrogens.

InChI(s):
InChI=1/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H

makePyrrole

public static Molecule makePyrrole()
Returns pyrrole without explicit hydrogens.

InChI(s):
InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H

makePyrroleAnion

public static Molecule makePyrroleAnion()
Returns pyrrole anion without explicit hydrogens.

InChI(s):
InChI=1/C4H4N/c1-2-4-5-3-1/h1-4H/q-1

makeImidazole

public static Molecule makeImidazole()
Returns imidazole without explicit hydrogens.

InChI(s):
InChI=1/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/f/h4H

makePyrazole

public static Molecule makePyrazole()
Returns pyrazole without explicit hydrogens.

InChI(s):
InChI=1/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5)/f/h4H

make124Triazole

public static Molecule make124Triazole()
Returns 1,2,4-triazole without explicit hydrogens.

InChI(s):
InChI=1/C3H4N2/c1-2-4-5-3-1/h1-3H,(H,4,5)/f/h4H

make123Triazole

public static Molecule make123Triazole()
Returns 1,2,3-triazole without explicit hydrogens.

InChI(s):
InChI=1/C2H3N3/c1-2-4-5-3-1/h1-2H,(H,3,4,5)/f/h5H

makeTetrazole

public static Molecule makeTetrazole()
Returns tetrazole without explicit hydrogens.

InChI(s):
InChI=1/CH2N4/c1-2-4-5-3-1/h1H,(H,2,3,4,5)/f/h4H

makeOxazole

public static Molecule makeOxazole()
Returns Oxazole without explicit hydrogens.

InChI(s):
InChI=1/C3H3NO/c1-2-5-3-4-1/h1-3H

makeIsoxazole

public static Molecule makeIsoxazole()
Returns Isoxazole without explicit hydrogens.

InChI(s):
InChI=1/C3H3NO/c1-2-4-5-3-1/h1-3H

makeIsothiazole

public static Molecule makeIsothiazole()
Returns isothiazole without explicit hydrogens.

InChI(s):
InChI=1/C3H3NS/c1-2-4-5-3-1/h1-3H

makeThiadiazole

public static Molecule makeThiadiazole()
Returns thiadiazole without explicit hydrogens.

InChI(s):
InChI=1/C2H2N2S/c1-3-4-2-5-1/h1-2H

makeOxadiazole

public static Molecule makeOxadiazole()
Returns oxadiazole without explicit hydrogens.

InChI(s):
InChI=1/C2H2N2O/c1-3-4-2-5-1/h1-2H

makePyridine

public static Molecule makePyridine()
Returns pyridine without explicit hydrogens.

InChI(s):
InChI=1/C3H3NO/c1-2-4-5-3-1/h1-3H

makePyridineOxide

public static Molecule makePyridineOxide()
Returns pyridine oxide without explicit hydrogens.

InChI(s):
InChI=1/C5H5NO/c7-6-4-2-1-3-5-6/h1-5H

makePyrimidine

public static Molecule makePyrimidine()
Returns pyrimidine without explicit hydrogens.

InChI(s):
InChI=1/C4H4N2/c1-2-5-4-6-3-1/h1-4H

makePyridazine

public static Molecule makePyridazine()
Returns pyridazine without explicit hydrogens.

InChI(s):
InChI=1/C4H4N2/c1-2-4-6-5-3-1/h1-4H

makeTriazine

public static Molecule makeTriazine()
Returns triazine without explicit hydrogens.

InChI(s):
InChI=1/C4H4N2/c1-2-4-6-5-3-1/h1-4H

makeThiazole

public static Molecule makeThiazole()
Returns thiazole without explicit hydrogens.

InChI(s):
InChI=1/C3H3NS/c1-2-5-3-4-1/h1-3H

makeSingleRing

public static Molecule makeSingleRing()

makeDiamantane

public static Molecule makeDiamantane()

makeBranchedAliphatic

public static Molecule makeBranchedAliphatic()

makeBenzene

public static Molecule makeBenzene()

makeQuinone

public static Molecule makeQuinone()

makePiperidine

public static Molecule makePiperidine()

makeTetrahydropyran

public static Molecule makeTetrahydropyran()

loadMolecule

public static IMolecule loadMolecule(String inFile)

makeAdenine

public static IMolecule makeAdenine()
InChI(s):
InChI=1/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)/f/h7H,6H2