| biobb_pytorch/__init__.py |
(no class) |
|
4 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/LRP.py |
(no class) |
|
1 |
1 |
0 |
|
0% |
| biobb_pytorch/mdae/__init__.py |
(no class) |
|
11 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/build_model.py |
BuildModel |
|
99 |
14 |
0 |
|
86% |
| biobb_pytorch/mdae/build_model.py |
(no class) |
|
30 |
1 |
0 |
|
97% |
| biobb_pytorch/mdae/common.py |
(no class) |
|
55 |
55 |
0 |
|
0% |
| biobb_pytorch/mdae/data/__init__.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/data/dataset.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/decode_model.py |
EvaluateDecoder |
|
42 |
1 |
0 |
|
98% |
| biobb_pytorch/mdae/decode_model.py |
(no class) |
|
22 |
1 |
0 |
|
95% |
| biobb_pytorch/mdae/encode_model.py |
EvaluateEncoder |
|
42 |
1 |
0 |
|
98% |
| biobb_pytorch/mdae/encode_model.py |
(no class) |
|
23 |
1 |
0 |
|
96% |
| biobb_pytorch/mdae/evaluate_model.py |
EvaluateModel |
|
69 |
15 |
0 |
|
78% |
| biobb_pytorch/mdae/evaluate_model.py |
(no class) |
|
25 |
1 |
0 |
|
96% |
| biobb_pytorch/mdae/explainability/LRP.py |
LRP |
|
65 |
9 |
0 |
|
86% |
| biobb_pytorch/mdae/explainability/LRP.py |
(no class) |
|
26 |
1 |
0 |
|
96% |
| biobb_pytorch/mdae/explainability/__init__.py |
(no class) |
|
2 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/explainability/layerwise_relevance_prop.py |
(no class) |
|
162 |
103 |
0 |
|
36% |
| biobb_pytorch/mdae/explainability/sensitivity_analysis.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/feat2traj.py |
Feat2Traj |
|
60 |
21 |
0 |
|
65% |
| biobb_pytorch/mdae/feat2traj.py |
(no class) |
|
16 |
1 |
0 |
|
94% |
| biobb_pytorch/mdae/featurization/__init__.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/featurization/featurizer.py |
Featurizer |
|
164 |
88 |
0 |
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46% |
| biobb_pytorch/mdae/featurization/featurizer.py |
(no class) |
|
26 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/featurization/normalization.py |
Normalization |
|
50 |
12 |
0 |
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76% |
| biobb_pytorch/mdae/featurization/normalization.py |
(no class) |
|
45 |
19 |
0 |
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58% |
| biobb_pytorch/mdae/featurization/plumed_feat.py |
FeaturesGenerator |
|
81 |
81 |
0 |
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0% |
| biobb_pytorch/mdae/featurization/plumed_feat.py |
(no class) |
|
7 |
7 |
0 |
|
0% |
| biobb_pytorch/mdae/featurization/topology_selector.py |
MDTopologySelector |
|
95 |
56 |
0 |
|
41% |
| biobb_pytorch/mdae/featurization/topology_selector.py |
(no class) |
|
10 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/__init__.py |
(no class) |
|
10 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/autocorrelation.py |
AutocorrelationLoss |
|
4 |
1 |
0 |
|
75% |
| biobb_pytorch/mdae/loss/autocorrelation.py |
(no class) |
|
13 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/committor_loss.py |
CommittorLoss |
|
9 |
9 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/committor_loss.py |
SmartDerivatives |
|
43 |
43 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/committor_loss.py |
(no class) |
|
123 |
102 |
0 |
|
17% |
| biobb_pytorch/mdae/loss/eigvals.py |
ReduceEigenvaluesLoss |
|
5 |
5 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/eigvals.py |
(no class) |
|
31 |
9 |
0 |
|
71% |
| biobb_pytorch/mdae/loss/elbo.py |
ELBOGaussiansLoss |
|
1 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/elbo.py |
ELBOLoss |
|
18 |
18 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/elbo.py |
ELBOGaussianMixtureLoss |
|
15 |
12 |
0 |
|
20% |
| biobb_pytorch/mdae/loss/elbo.py |
(no class) |
|
27 |
1 |
0 |
|
96% |
| biobb_pytorch/mdae/loss/fisher.py |
FisherDiscriminantLoss |
|
7 |
1 |
0 |
|
86% |
| biobb_pytorch/mdae/loss/fisher.py |
(no class) |
|
20 |
1 |
0 |
|
95% |
| biobb_pytorch/mdae/loss/ib_loss.py |
InformationBottleneckLoss |
|
20 |
1 |
0 |
|
95% |
| biobb_pytorch/mdae/loss/ib_loss.py |
(no class) |
|
6 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/mse.py |
MSELoss |
|
1 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/mse.py |
(no class) |
|
17 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/physics_loss.py |
PhysicsLoss |
|
28 |
28 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/physics_loss.py |
(no class) |
|
8 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/tda_loss.py |
TDALoss |
|
11 |
11 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/tda_loss.py |
(no class) |
|
34 |
26 |
0 |
|
24% |
| biobb_pytorch/mdae/loss/utils/__init__.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
ModifiedForceField |
|
50 |
50 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
OpenmmPluginScore |
|
96 |
96 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
OpenmmTorchEnergyMinimizer |
|
16 |
16 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
OpenMMPluginScoreSoftForceField |
|
18 |
18 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
openmm_energy_function |
|
16 |
16 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
openmm_clamped_energy_function |
|
17 |
17 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
openmm_energy |
|
13 |
13 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
openmm_energy_setup |
|
6 |
6 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
MolDataFrame |
|
31 |
31 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/openmm_thread.py |
(no class) |
|
52 |
52 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/torch_protein_energy.py |
TorchProteinEnergy |
|
191 |
191 |
0 |
|
0% |
| biobb_pytorch/mdae/loss/utils/torch_protein_energy.py |
(no class) |
|
18 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/loss/utils/torch_protein_energy_utils.py |
(no class) |
|
756 |
737 |
0 |
|
3% |
| biobb_pytorch/mdae/make_plumed.py |
GeneratePlumed |
|
194 |
67 |
0 |
|
65% |
| biobb_pytorch/mdae/make_plumed.py |
(no class) |
|
23 |
1 |
0 |
|
96% |
| biobb_pytorch/mdae/mdfeaturizer.py |
MDFeaturePipeline |
|
82 |
9 |
0 |
|
89% |
| biobb_pytorch/mdae/mdfeaturizer.py |
(no class) |
|
24 |
1 |
0 |
|
96% |
| biobb_pytorch/mdae/models/__init__.py |
(no class) |
|
6 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/ae.py |
AutoEncoder |
|
51 |
10 |
0 |
|
80% |
| biobb_pytorch/mdae/models/ae.py |
(no class) |
|
17 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/gmvae.py |
GaussianMixtureVariationalAutoEncoder |
|
153 |
128 |
0 |
|
16% |
| biobb_pytorch/mdae/models/gmvae.py |
(no class) |
|
21 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/gnnae.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/molearn.py |
GraphLayer |
|
9 |
9 |
0 |
|
0% |
| biobb_pytorch/mdae/models/molearn.py |
Encoder |
|
29 |
29 |
0 |
|
0% |
| biobb_pytorch/mdae/models/molearn.py |
FoldingLayer |
|
14 |
14 |
0 |
|
0% |
| biobb_pytorch/mdae/models/molearn.py |
Decoder_Layer |
|
14 |
14 |
0 |
|
0% |
| biobb_pytorch/mdae/models/molearn.py |
Decoder |
|
14 |
14 |
0 |
|
0% |
| biobb_pytorch/mdae/models/molearn.py |
CNNAutoEncoder |
|
50 |
50 |
0 |
|
0% |
| biobb_pytorch/mdae/models/molearn.py |
(no class) |
|
49 |
14 |
0 |
|
71% |
| biobb_pytorch/mdae/models/nn/__init__.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/nn/feedforward.py |
FeedForward |
|
23 |
5 |
0 |
|
78% |
| biobb_pytorch/mdae/models/nn/feedforward.py |
(no class) |
|
8 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/nn/utils.py |
Shifted_Softplus |
|
3 |
3 |
0 |
|
0% |
| biobb_pytorch/mdae/models/nn/utils.py |
Custom_Sigmoid |
|
3 |
3 |
0 |
|
0% |
| biobb_pytorch/mdae/models/nn/utils.py |
(no class) |
|
46 |
26 |
0 |
|
43% |
| biobb_pytorch/mdae/models/spib.py |
SPIB |
|
144 |
106 |
0 |
|
26% |
| biobb_pytorch/mdae/models/spib.py |
(no class) |
|
31 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/models/vae.py |
VariationalAutoEncoder |
|
60 |
32 |
0 |
|
47% |
| biobb_pytorch/mdae/models/vae.py |
(no class) |
|
17 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/plots.py |
(no class) |
|
105 |
7 |
0 |
|
93% |
| biobb_pytorch/mdae/train_model.py |
TrainModel |
|
86 |
19 |
0 |
|
78% |
| biobb_pytorch/mdae/train_model.py |
(no class) |
|
34 |
1 |
0 |
|
97% |
| biobb_pytorch/mdae/utils/__init__.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/mdae/utils/log_utils.py |
(no class) |
|
11 |
4 |
0 |
|
64% |
| biobb_pytorch/mdae/utils/model_utils.py |
(no class) |
|
9 |
0 |
0 |
|
100% |
| biobb_pytorch/test/__init__.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_all_models.py |
TestAllModels |
|
102 |
4 |
0 |
|
96% |
| biobb_pytorch/test/unitests/test_mdae/test_all_models.py |
(no class) |
|
21 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_build_model.py |
TestBuildModel |
|
29 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_build_model.py |
TestBuildModel.test_assert_valid_kwargs.DummyClass |
|
1 |
1 |
0 |
|
0% |
| biobb_pytorch/test/unitests/test_mdae/test_build_model.py |
(no class) |
|
15 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_common.py |
(no class) |
|
0 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_decode_model.py |
TestDecodeModel |
|
10 |
3 |
0 |
|
70% |
| biobb_pytorch/test/unitests/test_mdae/test_decode_model.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_encode_model.py |
TestEncodeModel |
|
10 |
3 |
0 |
|
70% |
| biobb_pytorch/test/unitests/test_mdae/test_encode_model.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_evaluate_model.py |
TestEvaluateModel |
|
11 |
4 |
0 |
|
64% |
| biobb_pytorch/test/unitests/test_mdae/test_evaluate_model.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_feat2traj.py |
TestFeat2Traj |
|
13 |
2 |
0 |
|
85% |
| biobb_pytorch/test/unitests/test_mdae/test_feat2traj.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestMSELoss |
|
24 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestELBOLosses |
|
42 |
1 |
0 |
|
98% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestInformationBottleneckLoss |
|
30 |
2 |
0 |
|
93% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestReduceEigenvaluesLoss |
|
14 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestAutocorrelationLoss |
|
12 |
2 |
0 |
|
83% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestFisherDiscriminantLoss |
|
13 |
2 |
0 |
|
85% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestTDALoss |
|
12 |
2 |
0 |
|
83% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestPhysicsLoss |
|
5 |
1 |
0 |
|
80% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestCommittorLoss |
|
1 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestLossFunctionIntegration |
|
36 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
TestLossFunctionEdgeCases |
|
17 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_loss_functions.py |
(no class) |
|
46 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_lrp.py |
TestLRP |
|
11 |
3 |
0 |
|
73% |
| biobb_pytorch/test/unitests/test_mdae/test_lrp.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_make_plumed.py |
TestMakePlumed |
|
12 |
1 |
0 |
|
92% |
| biobb_pytorch/test/unitests/test_mdae/test_make_plumed.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_mdfeaturizer.py |
Testmdfeaturizer |
|
16 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_mdfeaturizer.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_plots.py |
TestPlots |
|
113 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_plots.py |
(no class) |
|
22 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_sensitivity_analysis.py |
TestSensitivityAnalysis |
|
32 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_sensitivity_analysis.py |
(no class) |
|
7 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_specialized_models.py |
TestGMVAE |
|
21 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_specialized_models.py |
TestSPIB |
|
37 |
2 |
0 |
|
95% |
| biobb_pytorch/test/unitests/test_mdae/test_specialized_models.py |
TestCNNAutoEncoder |
|
6 |
6 |
0 |
|
0% |
| biobb_pytorch/test/unitests/test_mdae/test_specialized_models.py |
(no class) |
|
21 |
0 |
0 |
|
100% |
| biobb_pytorch/test/unitests/test_mdae/test_train_model.py |
TestTrainModel |
|
15 |
3 |
0 |
|
80% |
| biobb_pytorch/test/unitests/test_mdae/test_train_model.py |
(no class) |
|
8 |
0 |
0 |
|
100% |