Class MoleculeFactory

java.lang.Object
org.openscience.cdk.templates.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 Details

    • MoleculeFactory

      public MoleculeFactory()
      Deprecated.
  • Method Details

    • 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.
    • makeSteran

      public static IAtomContainer makeSteran()
      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.
    • loadMolecule

      public static IAtomContainer loadMolecule(String inFile)
      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