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unit: def main()
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id: 2
unit: def get_dataset()
file: lmgvp/data_loaders.py
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id: 3
unit: def _featurize_as_graph()
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id: 4
unit: def _featurize_as_graph()
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id: 5
unit: def evaluate()
file: train.py
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id: 6
unit: def load_GO_annot()
file: lmgvp/deepfrier_utils.py
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id: 7
unit: def _forward()
file: lmgvp/modules.py
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id: 8
unit: def main()
file: data/prepare_data.py
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id: 9
unit: def _forward()
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id: 10
unit: def __init__()
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id: 11
unit: def init_residue()
file: data/xpdb.py
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id: 12
unit: def idx_align()
file: data/contact_map_utils.py
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id: 13
unit: def chain_to_coords()
file: data/prepare_GO_data.py
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id: 14
unit: def parse_args()
file: data/prepare_data.py
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id: 15
unit: def _dihedrals()
file: lmgvp/datasets.py
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id: 16
unit: def load_GO_labels()
file: lmgvp/data_loaders.py
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size: 16 LOC
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id: 17
unit: def structure_to_coords()
file: data/prepare_data.py
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id: 18
unit: def _forward()
file: lmgvp/modules.py
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id: 19
unit: def get_energy()
file: data/contact_map_utils.py
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size: 13 LOC
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number of parameters: 1

id: 20
unit: def load_state_dict_to_model()
file: lmgvp/transfer.py
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size: 13 LOC
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number of parameters: 2

id: 21
unit: def calc_contact_map()
file: contact_map/data_preparation.py
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size: 12 LOC
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number of parameters: 3

id: 22
unit: def _get_atom_line()
file: data/xpdb.py
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size: 12 LOC
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id: 23
unit: def _positional_embeddings()
file: lmgvp/datasets.py
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id: 24
unit: def _compute_loss()
file: lmgvp/modules.py
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id: 25
unit: def __init__()
file: lmgvp/modules.py
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id: 26
unit: def _preprocess()
file: lmgvp/datasets.py
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id: 27
unit: def _forward()
file: lmgvp/modules.py
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size: 11 LOC
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id: 28
unit: def add_model_specific_args()
file: lmgvp/modules.py
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size: 11 LOC
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id: 29
unit: def add_model_specific_args()
file: lmgvp/modules.py
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size: 11 LOC
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number of parameters: 1

id: 30
unit: def __init__()
file: lmgvp/modules.py
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size: 10 LOC
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id: 31
unit: def get_atom_coords()
file: data/prepare_GO_data.py
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size: 9 LOC
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number of parameters: 5

id: 32
unit: def norm_adj()
file: lmgvp/deepfrier_utils.py
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size: 9 LOC
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number of parameters: 2

id: 33
unit: def apc()
file: contact_map/data_preparation.py
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size: 8 LOC
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number of parameters: 1

id: 34
unit: def _parse_structure()
file: data/contact_map_utils.py
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size: 8 LOC
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number of parameters: 3

id: 35
unit: def is_aa_by_target_atoms()
file: data/contact_map_utils.py
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size: 8 LOC
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number of parameters: 1

id: 36
unit: def __init__()
file: lmgvp/datasets.py
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size: 8 LOC
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number of parameters: 0

id: 37
unit: def load_FASTA()
file: lmgvp/deepfrier_utils.py
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size: 8 LOC
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number of parameters: 1

id: 38
unit: def init_model()
file: train.py
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size: 7 LOC
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id: 39
unit: def extract_process_attns()
file: contact_map/data_preparation.py
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size: 7 LOC
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number of parameters: 3

id: 40
unit: def gunzip_to_ram()
file: data/contact_map_utils.py
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size: 7 LOC
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number of parameters: 1

id: 41
unit: def _rbf()
file: lmgvp/datasets.py
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number of parameters: 5

id: 42
unit: def _sidechains()
file: lmgvp/datasets.py
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size: 7 LOC
McCabe index: 1
number of parameters: 2

id: 43
unit: def __getitem__()
file: lmgvp/datasets.py
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size: 7 LOC
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number of parameters: 2

id: 44
unit: def __getitem__()
file: lmgvp/datasets.py
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size: 7 LOC
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number of parameters: 2

id: 45
unit: def preprocess_seqs()
file: lmgvp/data_loaders.py
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end line: 0
size: 7 LOC
McCabe index: 3
number of parameters: 2

id: 46
unit: def __init__()
file: lmgvp/modules.py
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size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 47
unit: def __init__()
file: lmgvp/modules.py
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size: 7 LOC
McCabe index: 1
number of parameters: 2

id: 48
unit: def __init__()
file: lmgvp/modules.py
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end line: 0
size: 7 LOC
McCabe index: 1
number of parameters: 0

id: 49
unit: def train_logistic_regression()
file: contact_map/modeling.py
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size: 6 LOC
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number of parameters: 2

id: 50
unit: def compute_scores()
file: contact_map/modeling.py
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size: 6 LOC
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number of parameters: 3

id: 51
unit: def _orientations()
file: lmgvp/datasets.py
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number of parameters: 2

id: 52
unit: def __init__()
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size: 6 LOC
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number of parameters: 5

id: 53
unit: def __getitem__()
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id: 54
unit: def _preprocess()
file: lmgvp/datasets.py
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id: 55
unit: def _preprocess()
file: lmgvp/datasets.py
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size: 6 LOC
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number of parameters: 1

id: 56
unit: def add_GO_labels()
file: lmgvp/data_loaders.py
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size: 6 LOC
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number of parameters: 3

id: 57
unit: def _forward()
file: lmgvp/modules.py
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size: 6 LOC
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number of parameters: 3

id: 58
unit: def _step()
file: lmgvp/modules.py
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number of parameters: 4

id: 59
unit: def _step()
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id: 60
unit: def _step()
file: lmgvp/modules.py
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number of parameters: 4

id: 61
unit: def _step()
file: lmgvp/modules.py
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size: 6 LOC
McCabe index: 1
number of parameters: 4

id: 62
unit: def calc_adj_matrix()
file: data/contact_map_utils.py
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size: 5 LOC
McCabe index: 2
number of parameters: 2

id: 63
unit: def parse_structure()
file: data/contact_map_utils.py
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size: 5 LOC
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number of parameters: 4

id: 64
unit: def load_gvp_data()
file: lmgvp/data_loaders.py
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size: 5 LOC
McCabe index: 1
number of parameters: 1

id: 65
unit: def _bert_forward()
file: lmgvp/modules.py
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size: 5 LOC
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number of parameters: 0

id: 66
unit: def _step()
file: lmgvp/modules.py
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size: 5 LOC
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number of parameters: 4

id: 67
unit: def __init__()
file: lmgvp/modules.py
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size: 5 LOC
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number of parameters: 0

id: 68
unit: def three_to_one_standard()
file: data/contact_map_utils.py
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size: 4 LOC
McCabe index: 2
number of parameters: 1

id: 69
unit: def parse_pdb_gz_to_json_record()
file: data/prepare_data.py
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size: 4 LOC
McCabe index: 1
number of parameters: 4

id: 70
unit: def __init__()
file: data/xpdb.py
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size: 4 LOC
McCabe index: 1
number of parameters: 2

id: 71
unit: def _normalize()
file: lmgvp/datasets.py
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size: 4 LOC
McCabe index: 1
number of parameters: 2

id: 72
unit: def __getitem__()
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size: 4 LOC
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number of parameters: 2

id: 73
unit: def __init__()
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size: 4 LOC
McCabe index: 1
number of parameters: 3

id: 74
unit: def __init__()
file: lmgvp/datasets.py
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size: 4 LOC
McCabe index: 1
number of parameters: 3

id: 75
unit: def prep_seq()
file: lmgvp/utils.py
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size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 76
unit: def add_model_specific_args()
file: lmgvp/modules.py
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size: 4 LOC
McCabe index: 1
number of parameters: 1

id: 77
unit: def forward()
file: lmgvp/modules.py
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number of parameters: 2

id: 78
unit: def forward()
file: lmgvp/modules.py
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number of parameters: 2

id: 79
unit: def forward()
file: lmgvp/modules.py
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number of parameters: 3

id: 80
unit: def forward()
file: lmgvp/modules.py
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size: 4 LOC
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number of parameters: 2

id: 81
unit: def load_logistic_regression()
file: contact_map/modeling.py
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size: 3 LOC
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number of parameters: 1

id: 82
unit: def _preprocess()
file: lmgvp/datasets.py
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size: 3 LOC
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number of parameters: 1

id: 83
unit: def configure_optimizers()
file: lmgvp/modules.py
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number of parameters: 1

id: 84
unit: def forward()
file: lmgvp/modules.py
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id: 85
unit: def save_logistic_regression()
file: contact_map/modeling.py
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size: 2 LOC
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number of parameters: 2

id: 86
unit: def calc_self_attn()
file: contact_map/data_preparation.py
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size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 87
unit: def symmetrize()
file: contact_map/data_preparation.py
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size: 2 LOC
McCabe index: 1
number of parameters: 1

id: 88
unit: def calc_dataset_attn_and_contact()
file: contact_map/data_preparation.py
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end line: 0
size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 89
unit: def get_atom_coords()
file: data/prepare_data.py
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end line: 0
size: 2 LOC
McCabe index: 2
number of parameters: 5

id: 90
unit: def parse_structure_file_to_json_record()
file: data/prepare_GO_data.py
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size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 91
unit: def __len__()
file: lmgvp/datasets.py
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size: 2 LOC
McCabe index: 1
number of parameters: 1

id: 92
unit: def _featurize_as_graph()
file: lmgvp/datasets.py
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size: 2 LOC
McCabe index: 1
number of parameters: 2

id: 93
unit: def __init__()
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size: 2 LOC
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number of parameters: 3

id: 94
unit: def __len__()
file: lmgvp/datasets.py
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size: 2 LOC
McCabe index: 1
number of parameters: 1

id: 95
unit: def _micro_aupr()
file: lmgvp/deepfrier_utils.py
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size: 2 LOC
McCabe index: 1
number of parameters: 2

id: 96
unit: def compute_f1_score_at_threshold()
file: lmgvp/deepfrier_utils.py
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size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 97
unit: def evaluate_multilabel()
file: lmgvp/deepfrier_utils.py
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size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 98
unit: def _freeze_bert()
file: lmgvp/modules.py
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size: 2 LOC
McCabe index: 1
number of parameters: 0

id: 99
unit: def add_model_specific_args()
file: lmgvp/modules.py
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size: 2 LOC
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number of parameters: 1

id: 100
unit: def _step()
file: lmgvp/modules.py
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size: 2 LOC
McCabe index: 1
number of parameters: 4

id: 101
unit: def training_step()
file: lmgvp/modules.py
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size: 2 LOC
McCabe index: 1
number of parameters: 3

id: 102
unit: def validation_step()
file: lmgvp/modules.py
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size: 2 LOC
McCabe index: 1
number of parameters: 3