Functions — github.com/aqlaboratory/rgn2

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Functions355 in github.com/aqlaboratory/rgn2

⨍ Functions 355◇ Types & classes 27

Method_finish

Instructs the model to shutdown.

rgn/geomnet_model.py:553

Function_higher_recurrence

Higher-order recurrence that creates multiple layers, possibly with interleaving dihedrals and dssps

rgn/rnn.py:11

Method_is_done

Returns True if training is finished, False otherwise.

rgn/geomnet_model.py:543

Function_parse_function

(example_proto)

aminobert/training_data_processing_utils.py:42

Method_predict

Predict 3D structures.

rgn/geomnet_model.py:379

Method_save

Checkpoints current model.

rgn/geomnet_model.py:536

Method_start

Initializes model from scratch or loads state from disk. Must be run once (and only once) before model is used.

rgn/geomnet_model.py:446

Method_train

Performs one iteration of training and, if applicable, advances the curriculum.

rgn/geomnet_model.py:349

Functionaminobert_postprocess

(data_dir, dataset_name, prepend_m)

data_processing/aminobert_postprocessing.py:171

Functionaminobert_predict_sequence

(seq, header, prepend_m, checkpoint, data_dir)

aminobert/prediction.py:121

Functionangularize_different_angles

Restricts real-valued tensors to the intervals [-pi,pi] and [0,pi] by feeding them through a cosine

rgn/geom_ops.py:39

Methodapply_gradients

See base class.

aminobert/optimization.py:131

Functionattend

(states_single)

rgn/geomnet_model.py:1040

(i, frame, coords_ta)

rgn/geom_ops.py:406

Functionbuild_tfrecord_data_iterator

(max_seq_length, max_predictions_per_seq, batch_size=128)

aminobert/training_data_processing_utils.py:40

Functionbytes_feature_list

Returns a list of bytes_list from a string / byte.

data_processing/aminobert_postprocessing.py:133

Functionchunk_permute

(tseq, num_fragments, rng)

aminobert/training_data_processing_utils.py:215

Functionconvert_examples_to_features

Convert a set of `InputExample`s to a list of `InputFeatures`.

aminobert/run_classifier.py:779

Methodconvert_ids_to_tokens

(self, ids)

aminobert/tokenization.py:228

Functionconvert_to_unicode

Converts `text` to Unicode (if it's not already), assuming utf-8 input.

aminobert/tokenization.py:29

Functioncreate_masked_lm_predictions

Creates the predictions for the masked LM objective.

aminobert/training_data_processing_utils.py:288

Functioncreate_optimizer

Creates an optimizer training op.

aminobert/optimization.py:27

Functioncreate_unsupervised_training_data

( input_files, output_files, k, random_seed, min_seq_length,

aminobert/training_data_processing.py:61

Functiondevice_function

(op)

rgn/geomnet_model.py:582

Functionfloat_feature_list

Returns a list of float_list from a float / double.

data_processing/aminobert_postprocessing.py:129

Functionfull_increment_func

()

rgn/geomnet_model.py:1486

Functiongelu

Gaussian Error Linear Unit. This is a smoother version of the RELU. Original paper: https://arxiv.org/abs/1606.08415 Args: input_t

aminobert/modeling.py:269

Methodget_all_encoder_layers

(self)

aminobert/modeling.py:250

Functionget_assignment_map_from_checkpoint

Compute the union of the current variables and checkpoint variables.

aminobert/modeling.py:322

Methodget_dev_examples

See base class.

aminobert/run_classifier.py:232

Methodget_dev_examples

See base class.

aminobert/run_classifier.py:263

Methodget_dev_examples

See base class.

aminobert/run_classifier.py:305

Methodget_dev_examples

See base class.

aminobert/run_classifier.py:345

Methodget_embedding_output

Gets output of the embedding lookup (i.e., input to the transformer). Returns: float Tensor of shape [batch_size, seq_length,

aminobert/modeling.py:253

Methodget_labels

See base class.

aminobert/run_classifier.py:250

Methodget_labels

See base class.

aminobert/run_classifier.py:274

Methodget_labels

See base class.

aminobert/run_classifier.py:315

Methodget_labels

See base class.

aminobert/run_classifier.py:355

Methodget_test_examples

See base class.

aminobert/run_classifier.py:269

Methodget_test_examples

See base class.

aminobert/run_classifier.py:310

Methodget_test_examples

See base class.

aminobert/run_classifier.py:350

Methodget_train_examples

See base class.

aminobert/run_classifier.py:213

Methodget_train_examples

See base class.

aminobert/run_classifier.py:258

Methodget_train_examples

See base class.

aminobert/run_classifier.py:300

Methodget_train_examples

See base class.

aminobert/run_classifier.py:340

Functioninput_fn

The actual input function.

aminobert/run_finetuning_and_prediction.py:73

Functioninput_fn

The actual input function.

aminobert/run_pretraining.py:563

Functioninput_fn

The actual input function.

aminobert/run_classifier.py:542

Functioninput_fn

The actual input function.

aminobert/training.py:262

Functioninput_fn_builder

Creates an `input_fn` closure to be passed to TPUEstimator.

aminobert/run_classifier.py:724

Methodinput_size

(self)

rgn/rnn_cell_extended.py:65

Functioninstance_to_padded_features

(instance, tokenizer, max_seq_length, max_predictions_per_seq, return_feature_plain_dict=False)

aminobert/training_data_processing_utils.py:93

aminobert/run_pretraining.py:642

Functionmain

(_)

aminobert/run_classifier.py:796

Functionmake_sequence_chimeric

(tseq, chimeric_fragment_generator, tokenizer, rng, fragment_size=[5,20])

aminobert/training_data_processing_utils.py:244

Functionmerge_two_dicts

Efficiently merges two dicts, giving precedence to second dict.

rgn/utils.py:28

Functionmetric_fn

(predictions, labels)

aminobert/run_finetuning_and_prediction.py:410

Functionmetric_fn

(log_probs_cp, labels_cp, weights_cp, example_loss_cp, log_probs_ch, labels_ch, weights_ch, example_loss_c

aminobert/run_pretraining.py:131

Functionmetric_fn

(per_example_loss, label_ids, logits, is_real_example)

aminobert/run_classifier.py:694

Functionmetric_fn

Computes the loss and accuracy of the model.

aminobert/training.py:115

Functionmodel_fn

The `model_fn` for TPUEstimator.

aminobert/run_finetuning_and_prediction.py:328

Functionmodel_fn

The `model_fn` for TPUEstimator.

aminobert/run_pretraining.py:193

Functionmodel_fn

The `model_fn` for TPUEstimator.

aminobert/run_classifier.py:631

Functionmodel_fn

The `model_fn` for TPUEstimator.

aminobert/training.py:31

Methodoutput_size

(self)

rgn/rnn_cell_extended.py:69

Functionprintable_text

Returns text encoded in a way suitable for print or `tf.logging`.

aminobert/tokenization.py:182

Functionreduce_l1_norm

Computes the (possibly weighted) L1 norm of a tensor along the dimensions given in reduction_indices. Args: input_tensor: [..., NUM_DIME

rgn/geom_ops.py:113

Functionrun_refine

(seq_path, ter_path, output_dir=None, timeout=None, seq_id=None)

ter2pdb/ter2pdb.py:106

MethodsetUp

(self)

rgn/tests.py:1973

Functionsimple_static_rotation_translation_to_coordinate

Takes rotation and translation from torsion_and_curvature_to_rotation_translation and sequentially converts them into the coordinates of a 3D structu

rgn/geom_ops.py:324

Methodstate_size

(self)

rgn/rnn_cell_extended.py:73

MethodtestAllPrunedTrainingSamplesConsumed

(self)

rgn/tests.py:2177

MethodtestAlphabetTemperature

MethodtestAngularOutput

MethodtestBidirectionality

MethodtestConstantLengthCurriculum

(self)

rgn/tests.py:1669

MethodtestConstantLossCurriculum

(self)

rgn/tests.py:242

MethodtestDiagnosticTracking

MethodtestEvaluationSubgroupsFirstOrderBatchIndependentLoss

(self)

rgn/tests.py:1889

MethodtestEvaluationSubgroupsFirstOrderLoss

(self)

rgn/tests.py:1551

MethodtestEvaluationSubgroupsFirstOrderLossWithFourInvocations

(self)

rgn/tests.py:2596

MethodtestEvaluationSubgroupsSecondOrderBatchIndependentLoss

(self)

rgn/tests.py:1929

MethodtestEvaluationSubgroupsSecondOrderLoss

(self)

rgn/tests.py:1590

MethodtestEvaluationSubgroupsSecondOrderLossWithFourInvocations

(self)

rgn/tests.py:2651

MethodtestEvaluationSubgroupsZerothOrderLoss

(self)

rgn/tests.py:1513

MethodtestEvaluationSubgroupsZerothOrderLossWithFourInvocations

(self)

rgn/tests.py:2542

MethodtestFirstOrderLoss

(self)

rgn/tests.py:446

MethodtestFixedRateLengthCurriculum

(self)

rgn/tests.py:1709

MethodtestFixedRateLossCurriculum

(self)

rgn/tests.py:267

MethodtestFourFragmentReconstruction

(self)

rgn/tests.py:1643

MethodtestFourLayersResidualsEverySecondLayerStartFirstLayer

(self)

rgn/tests.py:1061

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