irumeria/smiles-mapper

chemical analyse tools for converting SMILES to map structure, or converting the map structure to SMILES

SMILES Mapper

Description

• convert SMILES to map structure, or convert the map structure to SMILES

• What is SMILES

Usage

 # in the parent folder of src
 python ./src/main.py

• First, the examples.csv in folder "assets" will be read.
• Then, output.json from decoder will be generated, containing the data of map structure like this:

// in output.json
  "7": [  // The 7th smiles in example.csv
      {
          "atom": "C",
          "index": 0, // THe first atom in smiles 
          "neighbors": [ // list of its neighbors
              {
                  "index": 1, 
                  "bond": 1, // bond number of the atom and its neighbors
                  "atom": "Mn"
              }
          ]
      },
      {
          "atom": "Mn",
          "index": 1,
          "neighbors": [
              {
                  "index": 0,
                  "bond": 1,
                  "atom": "C"
              },
              {
                  "index": 2,
                  "bond": 1,
                  "atom": "C"
              }
          ]
      },
      ...

• Finally, result.json will be generated. This is the output of the encoder, which takes output.json as its input.

  // in result.json
{
    "1": "CCCCC(CC)OCC",
    "2": "CCOCc1ccccc1CC",
    "3": "CCOCc1cccc(c1)CC",
    "4": "CCOCCCNc1cc(C)ccc1N",
    "5": "c2ccc1c(c2)cccc1",
    "6": "C[13C]OCC[Fe]CC(SCC[Mn]C)CS[OH3+]",
    "7": "C[Mn]CC(C(C=S)[Fe]CCC=O)SC",
    "8": "c4cc1CCc2c3c1c(c4)CCc3ccc2"
}

Encoder config

# in main.py

# default: 0 and the last index of the map will be taken as the endpoints of main chain
map_to_smiles(nodeMap)

# search the main chain in the map Automatically, equivalent representation may be generated
map_to_smiles(nodeMap,autoSearch=True)

Improvement

• The signals \ and @ are not already supported

Announcement

• DO NOT use this code in your paper, it is for learning and still under testing