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.
Belongs to CDK module:
test-data

  • 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