Commit 087542f

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Delete 'output' folder in RMG-database

- This is not very useful and is a duplicate of RMG-Java's database, but not actually up to date. - The importOldDatabase.py script now can point to a user-specified directory, so we should not be keeping this output folder around.

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output
- RMG_database_sulfur
  - ForbiddenStructures.txt
  - kinetics_groups
    - 1+2_Cycloaddition
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,2_Insertion
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,2_shiftS
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,3_Insertion_CO2
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,3_Insertion_ROR
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 2+2_cycloaddition_CCO
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 2+2_cycloaddition_CO
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 2+2_cycloaddition_Cd
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Birad_recombination2
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Birad_recombination
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Cyclic_Ether_Formation
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Diels_alder_addition
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Disproportionation_O2d
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Disproportionation
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - HO2_Elimination_from_PeroxyRadical
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - H_Abstraction
      - CVS
        Entries
        Repository
        Root
      - Oude files.zip
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Intra_R_Add_Endocyclic
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Intra_R_Add_Exocyclic
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Oa_R_Recombination
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Addition_COm
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Addition_MultipleBond
      - CBS-QB3 Library.txt
      - CVS
        Entries
        Repository
        Root
      - Oude files.zip
      - Pure rateLibrary.txt
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Recombination
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - SubstitutionS
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - families.txt
    - intra_H_migration
      - CVS
        Entries
        Repository
        Root
      - comments.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_OH_migration
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionCS_cyclization
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionCS_isomerization
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionS_cyclization
      - CVS
        Entries
        Repository
        Root
      - Oude kopie van dict.txt
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionS_isomerization
      - CVS
        Entries
        Repository
        Root
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
  - kinetics_libraries
    - DMDS
    - thiofene
  - thermo_groups
  - virtualAtoms
    - basic
      - virtualAtoms.orig
      - virtualAtoms.txt
    - more
      - virtualAtoms.txt
- RMG_database
  - ForbiddenStructures.txt
  - frequencies_groups
  - kinetics_groups
    - 1+2_Cycloaddition
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,2-Birad_to_alkene
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,2_Insertion
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,2_shiftS
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,3_Insertion_CO2
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,3_Insertion_ROR
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,3_Insertion_RSR
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,4_Cyclic_birad_scission
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 1,4_Linear_birad_scission
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 2+2_cycloaddition_CCO
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 2+2_cycloaddition_CO
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - 2+2_cycloaddition_Cd
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Birad_recombination
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Cyclic_Ether_Formation
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Diels_alder_addition
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Disproportionation
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - HO2_Elimination_from_PeroxyRadical
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - H_Abstraction
      - comments.rst
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Intra_Diels_alder
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Intra_Disproportionation
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt.orig
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Intra_R_Add_Endocyclic
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Intra_R_Add_Exocyclic
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Korcek_step1
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Korcek_step2
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Oa_R_Recombination
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Addition_COm
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Addition_CSm
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Addition_MultipleBond
      - comments.rst
      - dictionary.txt.orig
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - R_Recombination
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - SubstitutionS
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - Substitution_O
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - families.txt
    - intra_H_migration
      - comments.rst
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_OH_migration
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionCS_cyclization
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionCS_isomerization
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionS_cyclization
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - intra_substitutionS_isomerization
      - dictionary.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
    - ketoenol
      - dictionary.txt
      - forbiddenGroups.txt
      - rateLibrary.txt
      - reactionAdjList.txt
      - tree.txt
  - kinetics_libraries
    - Dooley
      - C1
        pdepreactions.txt
        reactions.txt
        remove_unused_species.py
        species.txt
      - README.txt
      - methylformate_2
        pdepreactions.txt
        reactions.txt
        species.txt
        species_molfiles
        CH2O2H.mol
        CH2OCHO.mol
        CH2OCOOOH.mol
        CH3CH2OCHO.mol
        CH3CO2CH3.mol
        CH3O2.mol
        CH3O2H.mol
        CH3OCHO.mol
        CH3OCO.mol
        CH3OCOO.mol
        CH3OCOO2H.mol
        CH3OCOOO.mol
        CHOOCO.mol
        HCOOH.mol
        HO2CH2OCHO.mol
        HOOCH2OCO.mol
        HOOCH2OCOOO.mol
        OCH2O2H.mol
        OCH2OCHO.mol
        OCHO.mol
        OCHOCOOOH.mol
        OOCH2OCHO.mol
        OOCH2OCOOOH.mol
        cyOCH2OCO.mol
      - methylformate_all_ARHEbathgas
        README.txt
        pdepreactions.txt
        reactions.txt
        species.txt
      - methylformate_all_N2bathgas
        README.txt
        pdepreactions.txt
        reactions.txt
        species.txt
      - methylformate
        pdepreactions.txt
        reactions.txt
        species.txt
    - GRI-HCO
    - GRI-Mech3.0
    - Glarborg
    - Methylformate
    - OxygenSingTrip
    - TEOS
    - combustion_core
  - thermo_groups
  - thermo_libraries
    - CBS_QB3_1dHR
      - Dictionary.txt
      - Library.txt
    - DFT_QCI_thermo
      - Dictionary.txt
      - Library.txt
    - GRI-Mech3.0
    - KlippensteinH2O2
      - Dictionary.txt
      - Library.txt
    - SolventLibrary
      - Library.txt
    - SulfurLibrary
      - Dictionary.txt
      - Library.txt
    - primaryAbrahamLibrary
      - Dictionary.txt
      - Library.txt
    - primaryThermoLibrary
  - transport_groups
  - transport_libraries
    - GRI-Mech3.0
      - Dictionary.txt
      - Library.txt
    - primaryTransportLibrary
      - Dictionary.txt
      - Library.txt
- liquid_oxidation/kinetics_groups
  - H_Abstraction
  - alkoxy_beta-scission
  - beta-scission_C_radical
  - disproportionation_A
  - disproportionation_B
  - families.txt
  - hydroperoxide_bond_fission
  - hydroperoxide_decomposition
  - oxygen_addition
  - primary_initiation
  - recombination

`‎output/RMG_database/ForbiddenStructures.txt‎`

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