make_model_pickle.py

# MIT License
#
# Copyright (c) 2018 Silvia Amabilino
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# SOFTWARE.


import pickle
import glob
import numpy as np
from aglaia.wrappers import OSPMRMP

estimator = OSPMRMP(batch_size = 100, representation = "sorted_coulomb_matrix")
filenames = glob.glob("qm7/*.xyz")[:1000]
energies = np.loadtxt('qm7/hof_qm7.txt', usecols=[1])[:1000]
estimator.generate_compounds(filenames)
estimator.set_properties(energies)
#real_estimator = OSPMRMP(batch_size = 100, representation = "sorted_coulomb_matrix", compounds = estimator.compounds,
#        properties = energies)
#estimator.set_properties(energies)
#print(estimator.properties.size, estimator.compounds.size)

pickle.dump(estimator, open('model.pickle', 'wb'))
with open('idx.csv', 'w') as f:
    for i in range(energies.size):
        f.write('%s\n' % i)

    
#np.save('idx.npy', np.arange(0,energies.size)[:,None])