code: from dataclasses import dataclass, field
  from typing import List
  
  import tensorflow as tf
  from graph_networks.utilities import * 
  import logging
  import os
  
  ATOM_FEATURE_DIM = DGIN4_ATOM_FEATURE_DIM
  EDGE_FEATURE_DIM = DGIN4_EDGE_FEATURE_DIM
  
  @dataclass
  class BasicModelConfig:
      """
      Config for model1/2/3 run file.
      General model parameters
      """
      model_name: str = 'only_logs_dmpnn4_1' # without h_w in DGIN gin part - added h_v_0 instead
                                      # whole train/eval split - no more double split within train data set
                                      # random train/test split in get_data_sd - only change overall_seed
                                      # CHANGES dgin3 10.02.2021:
                                      # *added new bondFeaturesDGIN2 and atomFeaturesDGIN2; DGIN2_ATOM_FEATURE_DIM; DGIN2_EDGE_FEATURE_DIM
                                      # *from project_path+'data/processed/lipo/pickled/train_frags3/' to project_path+'data/processed/lipo/pickled/test_frags3/'
                                      # CHANGES dgin3 16.02.2021:
                                      # *added new bondFeaturesDGIN3 and atomFeaturesDGIN3; DGIN3_ATOM_FEATURE_DIM; DGIN3_EDGE_FEATURE_DIM
                                      # *from project_path+'data/processed/lipo/pickled/train_frags_dgin3/' to project_path+'data/processed/lipo/pickled/test_frags_dgin3/'
                                      # CHANGES dgin4 16.02.2021:
                                      # *added add_species bool in model1 config - previously not there; for dgin2 featurization adds the species type after the dgin 
                                      # encoding before logD prediction
                                      # test_frags_dgin4 was added for species inclusion in model2 call()
      batch_size: int =15
      override_if_exists: bool = True
  
      overall_seed: int = 2
      
      # path to the project folder 
      project_path:str = "./" 
  
      retrain_model: bool = False
      retrain_model_name: str = ''
      retrain_model_epoch: str = ''
      retrain_model_weights_dir: str = project_path+'reports/model_weights/'+retrain_model_name+'/epoch_'+retrain_model_epoch+'/checkp_'+retrain_model_epoch
  
      train_data_dir: str = project_path+'data/processed/lipo/pickled/train_dgin4_logs/'
      test_data_dir: str = project_path+'data/processed/lipo/pickled/test_dgin4_logs/'
  
      combined_dataset: bool = False
  
      add_train_data_dir: str = project_path+'data/processed/lipo/pickled/train_dgin4_logs/'
      add_test_data_dir: str = project_path+'data/processed/lipo/pickled/test_dgin4_logs/'
  
      test_model: bool = False
      test_model_epoch: str = '887'
  
      # define the number or test runs for the CI. 
      # the mean and std of the RMSE and r^2 of the combined runs are taken as the output. 
      test_n_times: int = 1 
      # do you want to test the model with consensus mode? 
      # if yes, a defined ML model will be included in the consensus predictions during the testing. 
      consensus: bool = False 
      # include dropout during testing?
      include_dropout: bool = False
      test_model_weights_dir: str = project_path+'reports/model_weights/'+model_name+'/epoch_'+test_model_epoch+'/checkp_'+test_model_epoch
  
      # To save the prediction values for each property set to True 
      # When this flag is True - the whole test dataset is taken an test_n_times is set to zero! 
      save_predictions: bool = False 
      # define the folder where you want to save the predictions. 
      # For each property, a file is created under the property name ("./logd.txt","./logs.txt","./logp.txt","./others.txt") 
      test_prediction_output_folder: str = project_path+"reports/predictions/"+model_name+"/" 
      encode_hidden: bool = False
  
      log_dir: str = project_path+'reports/logs/'+model_name+'.log' 
      verbosity_level = logging.INFO
  
      model_type: str = 'DMPNN' # added 31.03.2021 to compare models like 'GIN' 'DMPNN' 'DGIN' 'MLP'
      
      plot_dir: str = project_path+'reports/figures/'+model_name+'/'
      tensorboard_log_dir: str = project_path+'reports/tensorboard/'+model_name+'/'
      config_log_dir: str = project_path+'reports/configs/'+model_name+'/'
      model_weights_dir: str = project_path+'reports/model_weights/'+model_name+'/'
      stats_log_dir: str = project_path+'reports/stats/'+model_name+'/'
  
  @dataclass
  class DGINConfig:
      """
      Config for direcpted-mpnn class.
      """
      dropout_aggregate_dmpnn: bool = False
      layernorm_aggregate_dmpnn: bool = True
      dropout_passing_dmpnn: bool = False
      layernorm_passing_dmpnn: bool = True
  
      dropout_aggregate_gin: bool = False
      layernorm_aggregate_gin: bool = True
      dropout_passing_gin: bool = False
      layernorm_passing_gin: bool = True
  
      gin_aggregate_bias: bool = False
      dmpnn_passing_bias: bool = False
      init_bias: bool = False
  
      massge_iteration_dmpnn: int = 4
      message_iterations_gin: int = 4
      dropout_rate: float = 0.15
      input_size: int = (ATOM_FEATURE_DIM+EDGE_FEATURE_DIM) # combination of node feature len (33) and edge feature len (12)
      passing_hidden_size: int = 56 # this can be changed
      input_size_gin: int = (ATOM_FEATURE_DIM) # changed 31.03.2021
  
      return_hv: bool = True # model3 parameter
  
  @dataclass
  class Model1Config:
      """
      Config model1 class - no subclass configs are defined here.
      """
      validation_split: float = 0.90
      learning_rate: float = 0.004
      clip_rate: float = 0.6
      optimizer = tf.keras.optimizers.Adam(learning_rate)
      lipo_loss_mse = tf.keras.losses.mse
      lipo_loss_mae = tf.keras.losses.mae
      logP_loss_mse = tf.keras.losses.mse
      logS_loss_mse = tf.keras.losses.mse
      other_loss_mse = tf.keras.losses.mse 
      mw_loss_mse = tf.keras.losses.mse
      metric = tf.keras.losses.mae
      epochs: int = 1600
      # define the number of epochs for each test run.  
      save_after_epoch: int = 3 
      # dropout rate for the general model - mainly the MLP for the different log predictions 
      dropout_rate: float = 0.15 # the overall dropout rate of the readout functions 
      # the seed to shuffle the training/validation dataset; For the same dataset, even when 
      # combined_dataset is True, it is the same training/valiation instances 
      train_data_seed: int = 0 
      dropout_rate: float = 0.15 # the overall dropout rate of the readout functions
      train_data_seed: int = 0
  
      hidden_readout_1: int = 32
      hidden_readout_2: int = 14
      activation_func_readout = tf.nn.relu
      
      include_logD: bool = False
      include_logS: bool = True
      include_logP: bool = False
  
      include_other: bool = False 
      include_mw: bool = False
      include_rot_bond: bool = False
      include_HBA: bool = False
      include_HBD: bool = False
  
      # define the starting threshold for the RMSE of the model. When the comnbined RMSE 
      # is below this threshold, the model weights are being safed and a new threshold 
      # is set. It only serves as a starting threshold so that not too many models 
      # are being safed. Depends on how many log endpoints are being taken into 
      # consideration - as three endpoints have a higher combined RMSE as only one 
      # endpoint. 
      best_evaluation_threshold: float = 2.45 #was introduced on the 25.03.2021/ 
  
      # define the individual thresholds. If one model is better, the corresponding 
      # model weights are being saved. 
      best_evaluation_threshold_logd: float = 1.85 
      best_evaluation_threshold_logp: float = 1.65 
      best_evaluation_threshold_logs: float = 2.15 
      best_evaluation_threshold_other: float = 2.15 
                                              # 2.45 for all_logs
                                              # 0.70 logP
                                              # 0.75 logD
                                              # 1.00 logS
                                              # 1.75 logSD
                                              # 1.70 logSP
                                              # 1.45 logDP
  
      include_fragment_conv: bool = False # was introduced on the 4.12.2020
  
      use_rmse: bool = True # uses RMSE instead of MSE for only lipo_loss
      shuffle_inside: bool = True # reshuffles the train/valid test seach in each epoch (generalizes)
  
      add_species: bool = False # 16.02 introduction; previously not there; for dgin3 adds the species type after the dgin encoding before logD prediction
  
  @dataclass
  class FrACConfig:
      """
      Config fragment aggregation class - no subclass configs are defined here.
      """
      input_size_gin: int = 28
      layernorm_aggregate: bool = True
      reduce_mean: bool = True # when false -> reduce_sum
  
  @dataclass 
  class MLConfig: 
      """ 
      Configs for the ML algorithm 
      """ 
      # which algorithm do you want to use for the consensus? 
      # possibilities are: "SVM", "RF", "KNN" or "LR" - all are regression models! 
          # SVM: Support Vector Machine; RF: Random Forest, KNN: K-Nearest Neigbors; LR: Linear Regression;
      algorithm: str = "SVM" 
      # which fingerprint to use - possibilities are: "ECFP" or "MACCS" 
      fp_types: str = "ECFP" 
      # If 'ECFP' fingerprint is used, define the number of bits - maximum is 2048! 
      n_bits: int = 2048 
      # If "ECFP" fingerprint is used, define the radius 
      radius: int = 4 
      # define if descriptors should be included into the non-GNN molecular representation 
      include_descriptors: bool = True 
      # define if the descriptors should be standardizedby scaling and centering (Sklearn) 
      standardize: bool = True 
  
  @dataclass
  class Config():
      """
      Overall config class for model2 and run file.
      Includes all submodels config
      """
      basic_model_config: BasicModelConfig
      model1_config: Model1Config
      d_gin_config: DGINConfig
      frag_acc_config: FrACConfig
  
      ml_config: MLConfig 
      model: str = 'model11'
apis: tensorflow.keras.optimizers.Adam