chem_nodes.py

import torch
from typing import Annotated, TypedDict, Literal
from langchain_community.tools import DuckDuckGoSearchRun
from langchain_core.tools import tool
from langgraph.prebuilt import ToolNode, tools_condition
from langgraph.graph import StateGraph, START, END
from langgraph.graph.message import add_messages
from langchain_core.messages import SystemMessage, trim_messages, AIMessage, HumanMessage, ToolCall

import re
import matplotlib.pyplot as plt

from rdkit import Chem
from rdkit.Chem import AllChem, QED
from rdkit.Chem import Draw
from rdkit.Chem.Draw import MolsToGridImage
from rdkit import rdBase
from rdkit.Chem import rdMolAlign
import os, re
from rdkit import RDConfig
import pubchempy as pcp
import gradio as gr
from PIL import Image

class State(TypedDict):
  '''
    The state of the agent.
  '''
  messages: Annotated[list, add_messages]
  query_smiles: str
  query_task: str
  query_name: str
  query_reference: str
  tool_choice: tuple
  which_tool: int
  props_string: str
  similars_img: str
  loop_again: str

def name_node(state: State) -> State:
  '''
    Queries Pubchem for the name of the molecule based on the smiles string.

      Args:
        smiles: the input smiles string
      Returns:
        name: the name of the molecule
        props_string: a string of the tool results
  '''
  print("name tool")
  print('===================================================')
  current_props_string = state["props_string"]

  try:
    smiles = state["query_smiles"]
    res = pcp.get_compounds(smiles, "smiles")
    name = res[0].iupac_name
    name_string = f'IUPAC molecule name: {name}\n'
    #print(smiles, name)
    syn_list = pcp.get_synonyms(res[0].cid)
    for alt_name in syn_list[0]['Synonym'][:5]:
      name_string += f'alternative or common name: {alt_name}\n'
  except:
    name = "unknown"
    name_string = 'Could not find name for molecule'

  state["query_name"] = name

  current_props_string += name_string
  state["props_string"] = current_props_string
  state["which_tool"] += 1
  return state

def smiles_node(state: State) -> State:
  '''
    Queries Pubchem for the smiles string of the molecule based on the name.
      Args:
        smiles: the molecule name
      Returns:
        smiles: the smiles string of the molecule
        props_string: a string of the tool results
  '''
  print("smiles tool")
  print('===================================================')
  current_props_string = state["props_string"]

  try:
    name = state["query_name"]
    res = pcp.get_compounds(name, "name")
    smiles = res[0].smiles
    smiles_string = f'molecule SMILES: {smiles}\n'
  except:
    smiles = "unknown"
    smiles_string = 'Could not find smiles for molecule'

  state["query_smiles"] = smiles

  current_props_string += smiles_string
  state["props_string"] = current_props_string
  state["which_tool"] += 1
  return state

def similars_node(state: State) -> State:
  '''
    Queries Pubchem for similar molecules based on the smiles string or name

      Args:
        smiles: the input smiles string, OR
        name: the molecule name
      Returns:
        props_string: a string of the tool results.
  '''
  print("similars tool")
  print('===================================================')
  current_props_string = state["props_string"]

  try:
    if state['query_smiles'] != None:
      smiles = state["query_smiles"]
      res = pcp.get_compounds(smiles, "smiles", searchtype="similarity",listkey_count=20)
    elif state['query_name'] != None:
      name = state["query_name"]
      res = pcp.get_compounds(name, "name", searchtype="similarity",listkey_count=20)
    else:
      print('Not enough information to run similars tool')
      return state

    props_string = 'Found Similar compounds: \n'
    sub_smiles = []

    i = 0
    for compound in res:
      if i == 0:
        print(compound.iupac_name)
        i+=1
      sub_smiles.append(compound.smiles)
      props_string += f'Name: {compound.iupac_name}\n'
      props_string += f'SMILES: {compound.smiles}\n'
      props_string += f'Molecular Weight: {compound.molecular_weight}\n'
      props_string += f'LogP: {compound.xlogp}\n'
      props_string += '==================='

    sub_mols = [Chem.MolFromSmiles(smile) for smile in sub_smiles]
    legend = [str(compound.smiles) for compound in res]

    img = Draw.MolsToGridImage(sub_mols, legends=legend, molsPerRow=4, subImgSize=(250, 250))
    pic = img.data

    filename = "Similars_image"
    with open(filename+".png",'wb+') as outf:
        outf.write(pic)
  except:
    props_string = 'Could not find similar molecules'
    filename = None

  current_props_string += props_string
  state["props_string"] = current_props_string
  state['similars_img'] = filename
  state["which_tool"] += 1
  return state