main.py

from fastapi import FastAPI
from fastapi.middleware.cors import CORSMiddleware
from typing import Dict, List, Any, Tuple
import pickle
import math
import re
import gc
from utils import split
import torch
from build_vocab import WordVocab
from pretrain_trfm import TrfmSeq2seq
from transformers import T5EncoderModel, T5Tokenizer
import numpy as np
import pydantic

app = FastAPI()

# Add CORS middleware
app.add_middleware(
	CORSMiddleware,
	allow_origins=["*"],
	allow_methods=["*"],
	allow_headers=["*"]
)

tokenizer = T5Tokenizer.from_pretrained(
			"Rostlab/prot_t5_xl_half_uniref50-enc", do_lower_case=False, torch_dtype=torch.float16)

model = T5EncoderModel.from_pretrained(
			"Rostlab/prot_t5_xl_half_uniref50-enc")

class Item(pydantic.BaseModel):
	sequence: str
	smiles: str

@app.get("/predict")
def predict(item: Item):
	endpointHandler = EndpointHandler()
	result = endpointHandler.predict({
		"inputs": {
			"sequence": item.sequence,
			"smiles": item.smiles
		}
	})

	return result

class EndpointHandler():
	def __init__(self, path=""):

		self.tokenizer = tokenizer
		self.model = model
		
		# path to the vocab_content and trfm model
		vocab_content_path = "vocab_content.txt"
		trfm_path = "trfm_12_23000.pkl"

		# load the vocab_content instead of the pickle file
		with open(vocab_content_path, "r", encoding="utf-8") as f:
			vocab_content = f.read().strip().split("\n")

		# load the vocab and trfm model
		self.vocab = WordVocab(vocab_content)
		self.trfm = TrfmSeq2seq(len(self.vocab), 256, len(self.vocab), 4)
		device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
		self.trfm.load_state_dict(torch.load(trfm_path, map_location=device))
		self.trfm.eval()

		# path to the pretrained models
		self.Km_model_path = "Km.pkl"
		self.Kcat_model_path = "Kcat.pkl"
		self.Kcat_over_Km_model_path = "Kcat_over_Km.pkl"

		# vocab indices
		self.pad_index = 0
		self.unk_index = 1
		self.eos_index = 2
		self.sos_index = 3

	def predict(self, data: Dict[str, Any]) -> List[Dict[str, Any]]:
		"""
		Function where the endpoint logic is implemented.

		Args:
				data (Dict[str, Any]): The input data for the endpoint. It only contain a single key "inputs" which is a list of dictionaries. The dictionary contains the following keys:

				- sequence (str): Amino acid sequence.
				- smiles (str): SMILES representation of the molecule.

		Returns:
				Dict[str, Any]: The output data for the endpoint. The dictionary contains the following keys:

				- Km (float): float of predicted Km value.
				- Kcat (float): float of predicted Kcat value.
				- Vmax (float): float of predicted Vmax value.
		"""

		sequence = data["inputs"]["sequence"]
		smiles = data["inputs"]["smiles"]

		seq_vec = self.Seq_to_vec(sequence)
		smiles_vec = self.smiles_to_vec(smiles)

		fused_vector = np.concatenate((smiles_vec, seq_vec), axis=1)

		pred_Km = self.predict_feature_using_model(
			fused_vector, self.Km_model_path)
		pred_Kcat = self.predict_feature_using_model(
			fused_vector, self.Kcat_model_path)
		pred_Vmax = self.predict_feature_using_model(
			fused_vector, self.Kcat_over_Km_model_path)

		result = {
			"Km": pred_Km,
			"Kcat": pred_Kcat,
			"Vmax": pred_Vmax,
		}

		return result

	def predict_feature_using_model(self, X: np.array, model_path: str) -> float:
		"""
		Function to predict the feature using the pretrained model.
		"""
		with open(model_path, "rb") as f:
			model = pickle.load(f)
		pred_feature = model.predict(X)
		pred_feature_pow = math.pow(10, pred_feature)
		return pred_feature_pow

	def smiles_to_vec(self, Smiles: str) -> np.array:
		"""
		Function to convert the smiles to a vector using the pretrained model.
		"""
		Smiles = [Smiles]

		x_split = [split(sm) for sm in Smiles]
		xid, xseg = self.get_array(x_split, self.vocab)
		X = self.trfm.encode(torch.t(xid))
		return X

	def get_inputs(self, sm: str, vocab: WordVocab) -> Tuple[List[int], List[int]]:
		"""
		Convert smiles to tensor
		"""
		seq_len = len(sm)
		sm = sm.split()
		ids = [vocab.stoi.get(token, self.unk_index) for token in sm]
		ids = [self.sos_index] + ids + [self.eos_index]
		seg = [1]*len(ids)
		padding = [self.pad_index]*(seq_len - len(ids))
		ids.extend(padding), seg.extend(padding)
		return ids, seg

	def get_array(self, smiles: list[str], vocab: WordVocab) -> Tuple[torch.tensor, torch.tensor]:
		"""
		Convert smiles to tensor
		"""
		x_id, x_seg = [], []
		for sm in smiles:
			a,b = self.get_inputs(sm, vocab)
			x_id.append(a)
			x_seg.append(b)
		return torch.tensor(x_id), torch.tensor(x_seg)

	def Seq_to_vec(self, Sequence: str) -> np.array:
		"""
		Function to convert the sequence to a vector using the pretrained model.
		"""

		Sequence = [Sequence]
		sequences_Example = []
		for i in range(len(Sequence)):
			zj = ''
			for j in range(len(Sequence[i]) - 1):
				zj += Sequence[i][j] + ' '
			zj += Sequence[i][-1]
			sequences_Example.append(zj)
		
		gc.collect()
		print(torch.cuda.is_available())
		device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
		
		self.model = self.model.to(device)
		self.model = self.model.eval()
		
		features = []
		for i in range(len(sequences_Example)):
			sequences_Example_i = sequences_Example[i]
			sequences_Example_i = [re.sub(r"[UZOB]", "X", sequences_Example_i)]
			ids = self.tokenizer.batch_encode_plus(sequences_Example_i, add_special_tokens=True, padding=True)
			input_ids = torch.tensor(ids['input_ids']).to(device)
			attention_mask = torch.tensor(ids['attention_mask']).to(device)
			with torch.no_grad():
				embedding = self.model(input_ids=input_ids, attention_mask=attention_mask)
			embedding = embedding.last_hidden_state.cpu().numpy()
			for seq_num in range(len(embedding)):
				seq_len = (attention_mask[seq_num] == 1).sum()
				seq_emd = embedding[seq_num][:seq_len - 1]
				features.append(seq_emd)

		features_normalize = np.zeros([len(features), len(features[0][0])], dtype=float)
		for i in range(len(features)):
			for k in range(len(features[0][0])):
				for j in range(len(features[i])):
					features_normalize[i][k] += features[i][j][k]
				features_normalize[i][k] /= len(features[i])
		return features_normalize