├── .gitignore ├── AtomObjectBuilder.py ├── AutoMapper.py ├── AutoMapper_Manual.pdf ├── Example_Workflow ├── instructions.txt ├── phenolic_resin.png ├── post_reaction.data ├── pre_reaction.data ├── run.bond ├── system.in.init └── system.in.settings ├── LICENSE.md ├── LammpsSearchFuncs.py ├── LammpsToMolecule.py ├── LammpsTreatmentFuncs.py ├── LammpsUnifiedCleaner.py ├── MapProcessor.py ├── MapTesting.py ├── PathSearch.py ├── QueueFuncs.py ├── README.md ├── Test_Cases ├── Cleaner │ └── Methane_Ethane │ │ ├── cleanedpost-system.data │ │ ├── cleanedpre-system.data │ │ ├── cleanedsystem.in.settings │ │ ├── post-system.data │ │ ├── pre-system.data │ │ └── system.in.settings ├── DGEBA_DETDA │ ├── cleanedpost_rx1.data │ ├── cleanedpre-reaction.data │ └── post_rx1_molecule.data ├── Map_Tests │ ├── Caprolactam │ │ ├── automap.data │ │ ├── caprolactam.png │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Create_Atoms │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── DGEBA_DETDA │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── dgeba_detda.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Edge_Atom_Symmetry │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── edge_atom_symmetry.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Ethyl_Ethanoate │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── ethyl_ethanoate.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Generic_PU │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── generic_pu.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Methane_Ethane │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── methane_ethane.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Phenol_Alkylation │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── phenol_o-alkylation.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Phenolic_Resin │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── phenolic_resin.png │ │ ├── post-molecule.data │ │ └── pre-molecule.data │ ├── Queue_Tester │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── post-molecule.data │ │ ├── pre-molecule.data │ │ └── queue_tester.png │ ├── Symmetric_Diol │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── post-molecule.data │ │ ├── pre-molecule.data │ │ └── symmetric_diol.png │ └── Third_Neighbour_Symmetry │ │ ├── automap.data │ │ ├── cleanedpost_reaction.data │ │ ├── cleanedpre_reaction.data │ │ ├── post-molecule.data │ │ ├── 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