Package org.openscience.cdk.templates

Class MoleculeFactory

  • @Deprecated
public class MoleculeFactory
extends Object
    Deprecated.
    Old CDK class primarily for testing, for CDK Tests please use TestMoleculeFactory in cdk-data (testjar).
    This class contains methods for generating simple organic molecules.
    Source code:
    main
    Keywords:
    templates

    • Constructor Detail

      • MoleculeFactory

        public MoleculeFactory()
        Deprecated.

    • Method Detail

      • makeAlphaPinene

        public static IAtomContainer makeAlphaPinene()
        Deprecated.

      • makeAlkane

        public static IAtomContainer makeAlkane​(int chainLength)
        Deprecated.
        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()
        Deprecated.

      • makeCyclohexene

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

      • makeCyclopentane

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

      • makeCyclobutane

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

      • makeCyclobutadiene

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

      • makePropylCycloPropane

        public static IAtomContainer makePropylCycloPropane()
        Deprecated.

      • makeBiphenyl

        public static IAtomContainer makeBiphenyl()
        Deprecated.
        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()
        Deprecated.

      • makePhenylAmine

        public static IAtomContainer makePhenylAmine()
        Deprecated.

      • make4x3CondensedRings

        public static IAtomContainer make4x3CondensedRings()
        Deprecated.

      • makeSpiroRings

        public static IAtomContainer makeSpiroRings()
        Deprecated.

      • makeBicycloRings

        public static IAtomContainer makeBicycloRings()
        Deprecated.

      • makeFusedRings

        public static IAtomContainer makeFusedRings()
        Deprecated.

      • makeMethylDecaline

        public static IAtomContainer makeMethylDecaline()
        Deprecated.

      • makeEthylPropylPhenantren

        public static IAtomContainer makeEthylPropylPhenantren()
        Deprecated.

      • makeAzulene

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

      • makePyrroleAnion

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

      • makeIsoxazole

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

      • makeIsothiazole

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

      • makeThiadiazole

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

      • makeOxadiazole

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

      • makePyridine

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

      • makePyridineOxide

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

      • makePyridazine

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

      • makeTriazine

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

      • makeThiazole

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

      • makeSingleRing

        public static IAtomContainer makeSingleRing()
        Deprecated.

      • makeDiamantane

        public static IAtomContainer makeDiamantane()
        Deprecated.

      • makeBranchedAliphatic

        public static IAtomContainer makeBranchedAliphatic()
        Deprecated.

      • makeBenzene

        public static IAtomContainer makeBenzene()
        Deprecated.

      • makeQuinone

        public static IAtomContainer makeQuinone()
        Deprecated.

      • makePiperidine

        public static IAtomContainer makePiperidine()
        Deprecated.

      • makeTetrahydropyran

        public static IAtomContainer makeTetrahydropyran()
        Deprecated.

      • makeAdenine

        public static IAtomContainer makeAdenine()
        Deprecated.
        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