README.md

# Files

辅助文件：

* `pistachio_rxn_name_def_map.json`
  * "2.1.2": "Carboxylic acid + amine condensation"

重要文件：

* coley_rxn_type_lib.json

  * ```bash
    "REACTION_TYPE": List[
    	"A>B>C [optional |f:x.x|]" 
    ]
    # A: reactants
    # B: reagents
    # C: product
    ```

* coley_rxn_type_lib_wo_agent_smiles.json

  * w/o reagents, only "A>>C"

* Coley_reaction_example.json

  * ```bash
    ID[int]: {
    	"name_rxn": "2.1.2",
    	"name_rxn_def": "Carboxylic acid + amine condensation",
    	"smiles": A>B>C
    }
    ```

  * Sub-set of `pistachio_rxn_type_lib.json` (only included in coley paper)

* `mech_total.json`

  * ```bash
    "REACTION_TYPE": List[
    	"pickle_path":  "/cto_labs/AIDD/DATA/React/Mechanism/pistachio/single/CO2H-tBu deprotection/type_1/513.pickle",
    	"atom_map_rxn": {
    		"reactants": List[SMILES-AtomMap],
    		"products": List[SMILES-AtomMap],
    		"byproducts": List[SMILES-AtomMap],
    	},
    	"unmapped_rxn": {
    		"reactants": List[SMILES],
    		"products": List[SMILES],
    		"byproducts": List[SMILES],
    	}
    	...
    ]
    ...
    ```

    * `mech_example.json`: each rxn-type contains 1 example

重要Dir

* `single/`

  each folder is a leaf-type reaction

  * ```bash
    # 89 types
    - Alcohol + amine condensation/
    	- type_0
    		- xxx.pickle # mechanism step graph
    		- xxx.txt # mechanism steps
    	- ...
    ...
    ```

* `test5/` (similar to `test50/`)

  random sample 5 instances for each leaf-type of reaction from `coley_rxn_type_lib.json`

  * `taxonomy/`

    ```bash
    # 5 major rxn types (define by Bing Feng + Claude)
    Carbon-Carbon Bond Formation/
    	- unmapped_rxn.txt
    Carbon-Heteroatom Bond Formation/
    	- unmapped_rxn.txt
    Deprotection Reactions/
    	- unmapped_rxn.txt
    Functional Group Interconversion/
    	- unmapped_rxn.txt
    Other Reactions/
    	- unmapped_rxn.txt
    ```

  * `template/`

    ```bash
    - indices.json # each rxn type extracted 5 ids, correspond to id in coley_rxn_type_lib.json. To keep traceable.
    - templates.json
    	"REACTION_TYPE": List[
            {
                "reactants_smiles_am": "CC(C)(C)[O:1][CH:2]=[O:3]", # reactants smiles based "reactants_smarts", maybe not valid, w/ atomMap
                "products_smiles_am": "[O:1][CH:2]=[O:3]", # similar to "reactants_smiles_am"
                "reactants_smiles": "CC(C)(C)OC=O", # reactants_smiles_am w/o atomMap
                "product_smiles": "OC=O", # products_smiles_am w/o atomAmp
                "reactants_smarts": "C-C(-C)(-C)-[O;H0;D2;+0:1]-[C:2]=[O;D1;H0:3]", # extracted using coley rdChiral template extracion function
                "products_smarts": "[O;D1;H0:3]=[C:2]-[OH;D1;+0:1]",
                "reagents_smiles_am": "COc1ccccc1.O=C(O)C(F)(F)F", # w/ atomMap
                "rxn_am": "[CH2:1]=[CH:2][C@:3]1([S:4][C@@H:5]2[C@@H:6]([C:7]([N:8]2[CH:9]1[C:10](=[O:11])[O:12]C(C)(C)C)=[O:13])[NH:14][C:15](=[O:16])[C@H:17]([NH2:18])[c:19]1[cH:20][cH:21][cH:22][cH:23][cH:24]1)[CH3:25]>>[CH2:1]=[CH:2][C@:3]1([S:4][C@@H:5]2[C@@H:6]([C:7]([N:8]2[CH:9]1[C:10](=[O:11])[OH:12])=[O:13])[NH:14][C:15](=[O:16])[C@H:17]([NH2:18])[c:19]1[cH:20][cH:21][cH:22][cH:23][cH:24]1)[CH3:25]", # rxn w/ atomMap
                "rxn_unmapped": "C=C[C@@]1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccccc3)C(=O)N2C1C(=O)OC(C)(C)C>>C=C[C@@]1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccccc3)C(=O)N2C1C(=O)O" # w/o atomMap
            },
            ...
        ]
    ```

* `taxonomy/`

  * 五大类每一类的`train.json` and `test.json`

    | Major Types                      | # Types | # Train | # Test |
    | -------------------------------- | ------- | ------- | ------ |
    | Carbon-Carbon Bond Formation     | 25      | 94,543  | 1250   |
    | Carbon-Heteroatom Bond Formation | 28      | 567,574 | 1400   |
    | Deprotection Reactions           | 10      | 243,266 | 500    |
    | Functional Group Interconversion | 19      | 189,296 | 950    |
    | Other Reactions                  | 3       | 21,917  | 150    |

    > Total # Types = 85
    > Total # Train = 1,116,596
    > Total # Test = 4,250

  * json List[Dict], 信息来源`mech_total.json`