Code for the paper "JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design"

Related tags

Deep LearningJANUS
Overview

JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design

This repository contains code for the paper: JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design. By: AkshatKumar Nigam, Robert Pollice, Alán Aspuru-Guzik

Package Requirements:

Using The Code:

The code can be run using:

python ./JANUS.py

Within params_init.py, a user has the option to provide:

  1. A function for calculting property values (see function calc_prop).
  2. Input parameters that are to be used by JANUS (see function generate_params). Initial parameters are provided. These are picked based on prior experience by the authors of the paper.

Output Generation:

All results from running JANUS will be stored here. The following files will be created:

  1. fitness_explore.txt: Fitness values for all molecules from the exploration component of JANUS.
  2. fitness_local_search.txt: Fitness values for all molecules from the exploitation component of JANUS.
  3. generation_all_best.txt: Smiles and fitness value for the best molecule encountered in every generation (iteration).
  4. init_mols.txt: List of molecules used to initialte JANUS.
  5. population_explore.txt: SMILES for all molecules from the exploration component of JANUS.
  6. population_local_search.txt: SMILES for all molecules from the exploitation component of JANUS.

Paper Results/Reproducibility:

Our code and results for each experiment in the paper can be found here:

Questions, problems?

Make a github issue 😄 . Please be as clear and descriptive as possible. Please feel free to reach out in person: (akshat[DOT]nigam[AT]mail[DOT]utoronto[DOT]ca, rob[DOT]pollice[AT]utoronto[DOT]ca)

License

Apache License 2.0

Comments
  • freeze_support runtime error with provided example

    freeze_support runtime error with provided example

    Hello, I'm trying out JANUS and if I just run the example inside the tests as provided I get

      File "/Users/nsofroniew/opt/anaconda3/envs/chem/lib/python3.9/multiprocessing/spawn.py", line 134, in _check_not_importing_main
    raise RuntimeError('''
RuntimeError:
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.

    This can be fixed by wrapping the creation and running of the JANUS agent and inside

    if __name__ == '__main__':
    torch.multiprocessing.freeze_support()

    see for a similar fix https://github.com/pytorch/pytorch/issues/5858#issuecomment-373950687

    I'm happy to submit a PR to fix if you like - it will be very simple

    opened by sofroniewn 4
  • Enquiring on multi-objective fitness function

    Enquiring on multi-objective fitness function

    Hi, I would like to ask if there are multiple objectives which I want the fitness function to fulfil, how would I write out the function because the example on the README.md is only for one objective (logP)?

    Thank you! :D

    opened by yipy0005 3
  • error in numpy/ list multiplication inside mutate_smi_list

    error in numpy/ list multiplication inside mutate_smi_list

    Hello, I am trying to run the provided example, but get the following error

    $ python ./example.py
    Unique and valid fragments generated: 107308
    Unique and valid fragments generated: 107308
On generation 0/200
/Users/nsofroniew/opt/anaconda3/envs/chem/lib/python3.9/site-packages/janus/janus.py:457: RuntimeWarning: overflow encountered in power
  prob_ = 1.0 / (3.0 ** ((F_50_val - fitness) / (F_50_val - F_25_val)) + 1)
    (Explr) Top Fitness: 15.811199999999957
    (Explr) Top Smile: CCCCCCCCCCCCCCCCOP(=O)(O)Oc1ccc(C=Cc2ccc(OP(=O)(O)OCCCCCCCCCCCCCCCC)cc2)cc1
Traceback (most recent call last):
  File "/Users/nsofroniew/Documents/code/chem/janus/tests/./example.py", line 81, in <module>
  File "/Users/nsofroniew/opt/anaconda3/envs/chem/lib/python3.9/site-packages/janus/janus.py", line 317, in run
    mut_smi_loc = self.mutate_smi_list(smiles_local_search, "local")
  File "/Users/nsofroniew/opt/anaconda3/envs/chem/lib/python3.9/site-packages/janus/janus.py", line 137, in mutate_smi_list
    smi_list = smi_list * num_random_samples
numpy.core._exceptions._UFuncNoLoopError: ufunc 'multiply' did not contain a loop with signature matching types (dtype('<U98'), dtype('int64')) -> None

    It looks like smi_list has become a numpy array, which is unintended and it should be a list. This can be fixed by making this line https://github.com/aspuru-guzik-group/JANUS/blob/a52e5994a108063e3fc1d692752cea0ff0240120/src/janus/janus.py#L137 be

        smi_list = list(smi_list) * num_random_samples

    There could be other, more desirable fixes that avoid this problem altogether. I am happy to submit a PR if this fix is desired though.

    opened by sofroniewn 2
  • Unhandled exceptions and KeyError

    Unhandled exceptions and KeyError

    I tried running JANUS.py but got a number of exceptions. In addition, the script terminated with a KeyError.

    Initial population obtained!
Forming Fragments!
    Fragment creation: 0/10000
    Fragment creation: 1000/10000
    Fragment creation: 2000/10000
    Fragment creation: 3000/10000
    Fragment creation: 4000/10000
    Fragment creation: 5000/10000
    Fragment creation: 6000/10000
    Fragment creation: 7000/10000
    Fragment creation: 8000/10000
    Fragment creation: 9000/10000
Process Process-5:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch3_1]'
	SELFIES: [S][C][=N][N][=C][Branch1][Ring1][C][C][C][Branch1][#Branch1][O][C][Branch1][C][C][=O][C][Branch1][C][C][Branch1][C][C][C][N][N][N][Branch3_1][C][C][=C][=C][Branch1][C][N][C][=C][Ring1][#Branch1][C][#Branch1][N]
Process Process-7:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 124, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Expl=Ring3]'
	SELFIES: [C][Expl=Ring3][=C][Branch2][Ring1][=Branch1][C][=C][C][=C][Branch1][#C][C][=C][Ring1][=Branch1][C][=C][C][=C][C][=C][Ring1][=Branch1][Ring1][=C][F][C][Branch1][C][C][C][C][C][N][Branch1][=Branch2][S][Branch1][C][C][=Branch1][C][=O][=O][C][C][Ring1][#Branch2][C][N][Branch1][Branch1][C][C][C][C][C][C][C][C]
Process Process-4:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch1_3]'
	SELFIES: [C][C][=C][Branch1][=Branch1][C][C][=Ring1][=Branch1][Branch1_3][C][C][=C][C][=C][Branch1][C][C][=C][C][=C][Branch1][C][N][C][=N][Ring1][#Branch1][#Branch2][C][N][C][O][C][C][Ring1][=Branch1][C][Branch1][C][O][=C][C][=C][Ring1][=C][O][Ring1][P]
Process Process-6:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch3_2]'
	SELFIES: [C][C][=Branch1][#C][=C][C][=C][C][=Ring1][=Branch1][C][Branch1][C][F][Branch1][C][F][F][C][C][Branch1][C][C][=N][N][C][=Branch1][C][C][C][N][C][C][C][Branch1][C][N][C][C][Ring1][#Branch1][C][O][=C][C][Branch1][O][C][Branch3_2][C][N][C][C][O][C][C][Ring1][=Branch1][=O]
Process Process-8:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch2_1]'
	SELFIES: [C][=Branch1][C][=O][Branch1][C][O][C][N][C][=Branch1][C][=O][C][Branch2][Ring1][=Branch1][N][C][=Branch1][C][=O][C][Branch1][N][C][=C][C][=C][C][Branch2_1][Ring2][=N][Ring1][=Branch1][N][=N][O][C][Ring2][Ring1][C][S][C][C][=Ring2][Ring1][=Branch1][S][C][S][N][=C][Branch1][Ring2][N][=Ring1][Branch1][S][C][C][N]
Process Process-11:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch2_3]'
	SELFIES: [C][C][=C][C][Branch1][=C][C][N][Branch1][C][C][N][C][=Branch1][C][=O][C][S][C][C][C][Ring1][#Branch1][=C][C][=Ring1][O][C][=C][C][=C][C][=C][Ring1][=Branch1][O][C][=C][Branch2_3][Branch1]
Process Process-10:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch3_3]'
	SELFIES: [F][C][=C][C][=C][Branch2][Ring2][O][C][N][C][Branch2][Ring2][Ring2][C][Branch1][#C][C][C][=C][Branch1][=Branch2][C][=C][C][=C][C][=Branch1][C][=O][N][Branch1][C][C][Branch3_3][C][Branch1][C][F][C][=Ring1][#Branch1][F][=N][C][C][Ring1][C][N][C][C][N][C][C][Ring1][=Branch1][=C][=N][C][=Branch1][Branch1][=N][C][=Ring1][=Branch1][N][Branch1][C][C][C][=O][C][=C][Ring2][Ring1][=N]
Process Process-9:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 116, in _derive_mol_from_symbols
    init_state=binit_state, root_atom=prev_atom, rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch3_3]'
	SELFIES: [C][C][Branch1][#Branch2][C][=C][C][=Branch1][Ring2][=C][=Branch1][F][=N][C][=C][Branch2][Ring2][Branch1][N][Branch1][Branch2][C][=N][C][Ring1][=Branch1][=Ring1][=C][N][=C][C][=C][C][=C][Branch1][P][C][=Branch1][Ring2][=C][Ring1][=Branch1][C][Branch3_3][C][N][=C][C][=C][C][=Ring1][=Branch1][O][C][O]
On generation 0/200
    (Explr) Top Fitness: 1.0
    (Explr) Top Smile: C=C1N=CC=C(N=CNc2ccc(N)cc2)N=C(C)[SH]1C
Process Process-27:
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
    self.run()
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/multiprocessing/process.py", line 99, in run
    self._target(*self._args, **self._kwargs)
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 205, in calc_parr_prop
    props_collect[property_name][smile] = get_prop_material(smile, alphabet=alphabet, num_random_samples=num_random_samples, num_mutations=num_mutations)  # TODO: TESTING
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in get_prop_material
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/software/JANUS/mutate_parr.py", line 129, in 
    mutated_smiles = [decoder(x) for x in mutated_sf]
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 59, in decoder
    rings=rings
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 147, in _derive_mol_from_symbols
    _raise_decoder_error(selfies, symbol)
  File "/home/ubuntu/anaconda3/envs/reinvent.v3.2/lib/python3.7/site-packages/selfies/decoder.py", line 179, in _raise_decoder_error
    raise DecoderError(err_msg)
selfies.exceptions.DecoderError: invalid symbol '[Branch3_2]'
	SELFIES: [C][O][=C][N][C][N][C][=Branch1][C][=O][N][Branch1][=Branch1][N+1][=Branch1][C][=O][O-1][C][Ring1][=Branch2][N][Ring1][N][O][C][=C][C][C][N][C][N][C][N][C][=C][C][=C][Branch1][C][F][C][Branch1][C][F][=C][Ring1][Branch2][=N][C][Branch1][C][C][Branch3_2][Branch1][=Branch1][C][Branch1][C][C][=O][S][Ring1][=Branch2][=C][C][=Ring1][#Branch1][N][C][N][C][C][=C][C][=C][C][=C][Ring1][=Branch1][C][N][=C][Branch1][=C][SH1][Branch1][C][C][C][=C][C][=C][C][=C][Ring1][=Branch1][=Branch1][C][=C][N][=C][C][=Ring1][#Branch2][C]
Traceback (most recent call last):
  File "./JANUS.py", line 308, in 
    mut_smi_dict_local  = mut_smi_dict_local[population[top_idx]]
KeyError: 'C=C1N=CC=C(N=CNc2ccc(N)cc2)N=C(C)[SH]1C'
    opened by PatWalters 2
  • multiprocessing in windows

    multiprocessing in windows

    Hi. I was run the code, but I met errors in all codes that used multiprocessing. As I know these errors came from the difference of OS.

    Since I use Windows, I wonder how to correct the code for Windows.

    Thanks.

    opened by gunwook12 1

  • "aux" folder name should be changed to make the repository compatible with Windows.

    It looks like "aux" is a reserved word in Windows and directory of this name cannot be used. This is causing error, when I try to clone the repository.

    opened by sptiwari 1
  • Question: How sensitive is the model to molecule initialization?

    Question: How sensitive is the model to molecule initialization?

    Hello, great work! I'm excited to try this out for a chemical design project I'm working on. One question that I had after reading the pre-print— how sensitive is the model to molecule initialization?

    I read that you can start JANUS with random molecules or provide it with defined molecules. Did you perform any tests on what happens if the best molecule's scaffold was ablated from the initial bank of molecules? And how much, if at all, does rational initialization improve over random molecular initialization? Does this relate back to being trapped in local minima, and would the choice of initialization help explore more chemical space?

    Thank you!

    question 
    opened by jrhorne 1
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