Package org.openscience.cdk.templates

Class TestMoleculeFactory

java.lang.Object
org.openscience.cdk.templates.TestMoleculeFactory
public class TestMoleculeFactory extends Object
This class contains methods for generating simple organic molecules and is copy of MoleculeFactory for use in tests.

  • Constructor Details

    • TestMoleculeFactory

      public TestMoleculeFactory()

  • Method Details

    • makeAlphaPinene

      public static IAtomContainer makeAlphaPinene()

    • makeAlkane

      public static IAtomContainer 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 IAtomContainer makeEthylCyclohexane()

    • makeCyclohexene

      public static IAtomContainer 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 IAtomContainer makeCyclohexane()
      Returns cyclohexane without explicit hydrogens.
      InChI(s):
      InChI=1/C6H12/c1-2-4-6-5-3-1/h1-6H2

    • makeCyclopentane

      public static IAtomContainer makeCyclopentane()
      Returns cyclopentane without explicit hydrogens.
      InChI(s):
      InChI=1/C5H10/c1-2-4-5-3-1/h1-5H2

    • makeCyclobutane

      public static IAtomContainer makeCyclobutane()
      Returns cyclobutane without explicit hydrogens.
      InChI(s):
      InChI=1/C4H8/c1-2-4-3-1/h1-4H2

    • makeCyclobutadiene

      public static IAtomContainer makeCyclobutadiene()
      Returns cyclobutadiene without explicit hydrogens.
      InChI(s):
      InChI=1/C4H4/c1-2-4-3-1/h1-4H

    • makePropylCycloPropane

      public static IAtomContainer makePropylCycloPropane()

    • makeBiphenyl

      public static IAtomContainer 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 IAtomContainer makePhenylEthylBenzene()

    • makePhenylAmine

      public static IAtomContainer makePhenylAmine()

    • make4x3CondensedRings

      public static IAtomContainer make4x3CondensedRings()

    • makeSpiroRings

      public static IAtomContainer makeSpiroRings()

    • makeBicycloRings

      public static IAtomContainer makeBicycloRings()

    • makeFusedRings

      public static IAtomContainer makeFusedRings()

    • makeMethylDecaline

      public static IAtomContainer makeMethylDecaline()

    • makeEthylPropylPhenantren

      public static IAtomContainer makeEthylPropylPhenantren()

    • makeSteran

      public static IAtomContainer makeSteran()

    • makeAzulene

      public static IAtomContainer 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 IAtomContainer 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 IAtomContainer makePyrrole()
      Returns pyrrole without explicit hydrogens.
      InChI(s):
      InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H

    • makePyrroleAnion

      public static IAtomContainer 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 IAtomContainer 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 IAtomContainer 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 IAtomContainer 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 IAtomContainer 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 IAtomContainer 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 IAtomContainer makeOxazole()
      Returns Oxazole without explicit hydrogens.
      InChI(s):
      InChI=1/C3H3NO/c1-2-5-3-4-1/h1-3H

    • makeIsoxazole

      public static IAtomContainer makeIsoxazole()
      Returns Isoxazole without explicit hydrogens.
      InChI(s):
      InChI=1/C3H3NO/c1-2-4-5-3-1/h1-3H

    • makeIsothiazole

      public static IAtomContainer makeIsothiazole()
      Returns isothiazole without explicit hydrogens.
      InChI(s):
      InChI=1/C3H3NS/c1-2-4-5-3-1/h1-3H

    • makeThiadiazole

      public static IAtomContainer makeThiadiazole()
      Returns thiadiazole without explicit hydrogens.
      InChI(s):
      InChI=1/C2H2N2S/c1-3-4-2-5-1/h1-2H

    • makeOxadiazole

      public static IAtomContainer makeOxadiazole()
      Returns oxadiazole without explicit hydrogens.
      InChI(s):
      InChI=1/C2H2N2O/c1-3-4-2-5-1/h1-2H

    • makePyridine

      public static IAtomContainer makePyridine()
      Returns pyridine without explicit hydrogens.
      InChI(s):
      InChI=1/C3H3NO/c1-2-4-5-3-1/h1-3H

    • makePyridineOxide

      public static IAtomContainer 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 IAtomContainer makePyrimidine()
      Returns pyrimidine without explicit hydrogens.
      InChI(s):
      InChI=1/C4H4N2/c1-2-5-4-6-3-1/h1-4H

    • makePyridazine

      public static IAtomContainer makePyridazine()
      Returns pyridazine without explicit hydrogens.
      InChI(s):
      InChI=1/C4H4N2/c1-2-4-6-5-3-1/h1-4H

    • makeTriazine

      public static IAtomContainer makeTriazine()
      Returns triazine without explicit hydrogens.
      InChI(s):
      InChI=1/C4H4N2/c1-2-4-6-5-3-1/h1-4H

    • makeThiazole

      public static IAtomContainer makeThiazole()
      Returns thiazole without explicit hydrogens.
      InChI(s):
      InChI=1/C3H3NS/c1-2-5-3-4-1/h1-3H

    • makeSingleRing

      public static IAtomContainer makeSingleRing()

    • makeDiamantane

      public static IAtomContainer makeDiamantane()

    • makeBranchedAliphatic

      public static IAtomContainer makeBranchedAliphatic()

    • makeBenzene

      public static IAtomContainer makeBenzene()

    • makeQuinone

      public static IAtomContainer makeQuinone()

    • makePiperidine

      public static IAtomContainer makePiperidine()

    • makeTetrahydropyran

      public static IAtomContainer makeTetrahydropyran()

    • makeAdenine

      public static IAtomContainer 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

    • makeNaphthalene

      public static IAtomContainer makeNaphthalene()
      InChI=1/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H

    • makeAnthracene

      public static IAtomContainer makeAnthracene()
      InChI(s):
      InChI=1/C14H10/c1-2-6-12-10-14-8-4-3-7-13(14)9-11(12)5-1/h1-10H

    • makeCyclophaneLike

      public static IAtomContainer makeCyclophaneLike()
      octacyclo[17.2.2.2¹,⁴.2⁴,⁷.2⁷,¹⁰.2¹⁰,¹³.2¹³,¹⁶.2¹⁶,¹⁹]pentatriacontane
      InChI(s):
      InChI=1/C35H56/c1-2-30-6-3-29(1)4-7-31(8-5-29)13-15-33(16-14-31)21-23-35(24-22-33)27-25-34(26-28-35)19-17-32(11-9-30,12-10-30)18-20-34/h1-28H2

    • makeGappedCyclophaneLike

      public static IAtomContainer makeGappedCyclophaneLike()
      octacyclo[24.2.2.2²,⁵.2⁶,⁹.2¹⁰,¹³.2¹⁴,¹⁷.2¹⁸,²¹.2²²,²⁵]dotetracontane
      InChI(s):
      InChI=1/C42H70/c1-2-30-4-3-29(1)31-5-7-33(8-6-31)35-13-15-37(16-14-35)39-21-23-41(24-22-39)42-27-25-40(26-28-42)38-19-17-36(18-20-38)34-11-9-32(30)10-12-34/h29-42H,1-28H2