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`template_domain_names` missing in features.pkl on multimer mode.

Open eunos-1128 opened this issue 2 years ago • 0 comments

I tried to check out features.pkl generated by running AlphaFold to find which templates are used.

When --model_preset=monomer is used I could find template_domain_names as a key name of the dictionary unpickled, but not upon --model_preset=multimer.

import pickle

with open("../features.pkl", "rb") as f:
    features = pickle.load(f)
    print('template_domain_name' in features)  # => False

features.keys()

# => `template_domain_names` not found
# dict_keys(['aatype', 'residue_index', 'seq_length', 'msa', 'num_alignments', 'template_aatype', 'template_all_atom_mask',  'template_all_atom_positions', 'asym_id', 'sym_id', 'entity_id', 'deletion_matrix', 'deletion_mean', 'all_atom_mask', 'all_atom_positions', 'assembly_num_chains', 'entity_mask', 'num_templates', 'cluster_bias_mask', 'bert_mask', 'seq_mask', 'msa_mask'])

When running with multimer mode, templates are not used for prediction models? (I could see things like template names in docker log file, though.)

Otherwise, running on multimer mode generates no data related to templates used for prediction while it makes use of templates' information?

eunos-1128 avatar Nov 10 '22 01:11 eunos-1128