Package org.openscience.cdk.templates

Class 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 Detail

      • TestMoleculeFactory

        public TestMoleculeFactory()

    • Method Detail

      • 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()

      • make4x3CondensedRings

        public static IAtomContainer make4x3CondensedRings()

      • makeMethylDecaline

        public static IAtomContainer makeMethylDecaline()

      • makeEthylPropylPhenantren

        public static IAtomContainer makeEthylPropylPhenantren()

      • 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

      • makeBranchedAliphatic

        public static IAtomContainer makeBranchedAliphatic()

      • 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