Hi @xuanliugit , I'm trying to run your code (at Matt Berry's request) and it appears I'm missing the file rxn_cluster_token_prompt/models/class_token_retro_std_pistachio_201002_12tokens_with-reagents_step_260000.pt

Can you please provide me with that pytorch file? That's blocking me from running ACERetro Thanks!

To reproduce

Follow ALL installation instructions in the README.
Make adjustments to hdbscan, joblib, and six to fix install dependency problems...
Run the below code.

Code:

# ./pathway_search_standalone/
import sys
import joblib
import six
sys.modules['sklearn.externals.joblib'] = joblib
sys.modules['sklearn.externals.six'] = six

from pathway_search_standalone.scripts.search_utils import hybridSearch
hybridSearch = hybridSearch()
smiles = 'CC[C@@H](CO)NCCN[C@@H](CC)CO' # Target molecule's SMILES
# Conduct a 3 min asynchronous chemoenzymatic synthesis planning
explored_rxns, explored_nodes, start_node = hybridSearch.get_chemoenzy_path_async(smiles, max_depth=10, chem_topk=10, max_num_templates=250, max_branching=15, time_lim=180)

Outputs:

INFO@pricer              : [1718667177.984s]    Loaded prices from flat file
INFO@retro_transformer   : [1718667177.985s]    Loading template prioritizer for RetroTransformer
INFO@retro_transformer   : [1718667178.237s]    Loading precursor prioritizer for RetroTransformer
INFO@pricer              : [1718667179.297s]    Cannot connect to mongodb to load prices
INFO@pricer              : [1718667179.632s]    Loaded prices from flat file
INFO@retro_transformer   : [1718667179.673s]    Loading fast filter for RetroTransformer
INFO@fast_filter         : [1718667179.674s]    Starting to load fast filter
INFO@fast_filter         : [1718667180.273s]    Done loading fast filter
INFO@retro_transformer   : [1718667180.274s]    Using default clustering for RetroTransformer
INFO@retro_transformer   : [1718667180.274s]    Loading retro-synthetic transformer
INFO@retro_transformer   : [1718667180.274s]    reading from file
INFO@template_transformer: [1718667180.274s]    Loading templates from [/home/kastan/ncsa/mmli/ACERetro/pathway_search_standalone/askcos-core/askcos/data/bkms-data/templates/bkms-and-reaxys-templates.json.gz](https://vscode-remote+ssh-002dremote-002bdankserver.vscode-resource.vscode-cdn.net/home/kastan/ncsa/mmli/ACERetro/pathway_search_standalone/askcos-core/askcos/data/bkms-data/templates/bkms-and-reaxys-templates.json.gz)
INFO@template_transformer: [1718667182.795s]    Loaded templates. Using 7984 templates

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-4-2dde280b5894> in <module>
      8 
      9 from pathway_search_standalone.scripts.search_utils import hybridSearch
---> 10 hybridSearch = hybridSearch()
     11 smiles = 'CC[C@@H](CO)NCCN[C@@H](CC)CO' # Target molecule's SMILES
     12 # Conduct a 3 min asynchronous chemoenzymatic synthesis planning

~/ncsa/mmli/ACERetro/pathway_search_standalone/scripts/search_utils.py in __init__(self, pricer, sfef, deepef, geo_iso)
     83         self.askcos_enzy.load('bkms')
     84 
---> 85         self.rxn4chem_retro_model = RXNClusterTokenPrompt(n_best=1)
     86 
     87         self.sfscore_model = SFScore()

~/ncsa/mmli/ACERetro/pathway_search_standalone/rxn_cluster_token_prompt/rxn_cluster_token_prompt/model.py in __init__(self, retro_model_path, forward_model_path, classification_model_path, n_tokens, beam_size, max_length, batch_size, n_best)
    101             max_length=self.max_length,
    102             batch_size=self.batch_size,
--> 103             gpu=-1,
    104         )
    105 

~/ncsa/mmli/ACERetro/pathway_search_standalone/rxn_cluster_token_prompt/rxn_cluster_token_prompt/onmt_utils/translator.py in from_model_path(cls, model_path, **kwargs)
     89             model_path = [model_path]
     90         opt = get_onmt_opt(translation_model=list(model_path), **kwargs)
---> 91         return cls(opt=opt)
     92 
     93     @classmethod

~/ncsa/mmli/ACERetro/pathway_search_standalone/rxn_cluster_token_prompt/rxn_cluster_token_prompt/onmt_utils/translator.py in __init__(self, opt)
     21             opt: model options.
     22         """
---> 23         self.onmt_translator = RawTranslator(opt=opt)
     24 
     25     def translate_single(self, sentence: str) -> str:

~/ncsa/mmli/ACERetro/pathway_search_standalone/rxn_cluster_token_prompt/rxn_cluster_token_prompt/onmt_utils/internal_translation_utils.py in __init__(self, opt)
     36         out_file = open(os.devnull, "w")
     37         self.internal_translator = build_translator(
---> 38             self.opt, report_score=False, out_file=out_file
     39         )
     40 

~/utils/miniconda3/envs/aceretro/lib/python3.6/site-packages/onmt/translate/translator.py in build_translator(opt, report_score, logger, out_file)
     31         else onmt.model_builder.load_test_model
     32     )
---> 33     fields, model, model_opt = load_test_model(opt)
     34 
     35     scorer = onmt.translate.GNMTGlobalScorer.from_opt(opt)

~/utils/miniconda3/envs/aceretro/lib/python3.6/site-packages/onmt/model_builder.py in load_test_model(opt, model_path)
     83         model_path = opt.models[0]
     84     checkpoint = torch.load(model_path,
---> 85                             map_location=lambda storage, loc: storage)
     86 
     87     model_opt = ArgumentParser.ckpt_model_opts(checkpoint['opt'])

~/utils/miniconda3/envs/aceretro/lib/python3.6/site-packages/torch/serialization.py in load(f, map_location, pickle_module, **pickle_load_args)
    592         pickle_load_args['encoding'] = 'utf-8'
    593 
--> 594     with _open_file_like(f, 'rb') as opened_file:
    595         if _is_zipfile(opened_file):
    596             # The zipfile reader is going to advance the current file position.

~/utils/miniconda3/envs/aceretro/lib/python3.6/site-packages/torch/serialization.py in _open_file_like(name_or_buffer, mode)
    228 def _open_file_like(name_or_buffer, mode):
    229     if _is_path(name_or_buffer):
--> 230         return _open_file(name_or_buffer, mode)
    231     else:
    232         if 'w' in mode:

~/utils/miniconda3/envs/aceretro/lib/python3.6/site-packages/torch/serialization.py in __init__(self, name, mode)
    209 class _open_file(_opener):
    210     def __init__(self, name, mode):
--> 211         super(_open_file, self).__init__(open(name, mode))
    212 
    213     def __exit__(self, *args):

FileNotFoundError: [Errno 2] No such file or directory: '/home/kastan/ncsa/mmli/ACERetro/pathway_search_standalone/rxn_cluster_token_prompt/models/class_token_retro_std_pistachio_201002_12tokens_with-reagents_step_260000.pt'

Zhao-Group / ACERetro

Missing model file: `class_token_retro_std_pistachio_201002_12tokens_with-reagents_step_260000.pt` #1

To reproduce