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

"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

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

"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

# 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/

# 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/

- 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