def main(): decoded_file = GRAMMAR_WEIGHTS.split(".")[0] + "_decRes.txt" priors_file = GRAMMAR_WEIGHTS.split(".")[0] + "_priorsRes.txt" generation_file = GRAMMAR_WEIGHTS.split(".")[0] + "_generationRes.txt" grammar_model = molecule_vae.ZincGrammarModel(GRAMMAR_WEIGHTS) XTE = read_zinc() XTE = XTE[0:5000] # rember to comment and uncomment the line in the #moelcule_vae file decoded_result = reconstruction(grammar_model, XTE) save_decoded_results(XTE, decoded_result, decoded_file) # decoded_priors = prior(grammar_model) # save_decoded_priors(decoded_priors, priors_file) decoded_generation = generation(grammar_model) save_decoded_priors(decoded_generation, generation_file)
import sys import os import json import pickle #sys.path.insert(0, '..') import molecule_vae import numpy as np # 1. load grammar VAE grammar_weights = "pretrained/zinc_vae_grammar_L56_E100_val.hdf5" grammar_model = molecule_vae.ZincGrammarModel(grammar_weights) ################################################################## def extract_graph_properties(prop): prop = prop.split() g_tag = prop[0] g_index = int(prop[1]) return {"tag": g_tag, "index": g_index} # XYZ file reader for QM9 dataset def xyz_graph_reader(graph_file, self_loop=True): with open(graph_file, 'r') as f: # Number of atoms n_atom = int(f.readline()) # Graph properties