├── .gitignore ├── LICENSE ├── README.MD ├── docs ├── Makefile ├── conf.py ├── contents │ └── test.rst └── index.rst ├── evolutron ├── __init__.py ├── engine │ ├── __init__.py │ └── krs.py ├── extra_callbacks.py ├── extra_layers.py ├── extra_metrics.py ├── extra_objectives.py ├── motifs │ ├── __init__.py │ └── extraction.py ├── structural │ ├── GetInterfaces.py │ └── __init__.py ├── templates │ ├── Embedders.py │ ├── __init__.py │ └── callback_templates.py └── tools │ ├── SecS_from_PDBs.py │ ├── __init__.py │ ├── data_tools.py │ ├── io_tools.py │ ├── seq_tools.py │ ├── structure_tools.py │ ├── utils.py │ └── visual.py ├── notebooks ├── cnn_design.py ├── compare_comet.py ├── contact_sensitivity.py ├── dna_tf_analysis.ipynb ├── fix_filesaving.ipynb ├── fix_motif_visualization.ipynb ├── lengths.npz ├── m6a_analysis.py ├── motif_distribution.ipynb ├── motif_distribution.py ├── test ├── test_deconv.ipynb ├── test_dedense.ipynb ├── test_depool.ipynb ├── test_save_load.ipynb └── visualize_output.py └── tests ├── __init__.py ├── test_metrics ├── __init__.py └── test_extra_metrics.py ├── test_networks └── __init__.py └── test_tools ├── __init__.py ├── samples ├── no_codes.fasta ├── sample.tsv ├── smallSecS.sec └── type2p_codes.fasta ├── test_data_tools.py ├── test_io_tools.py └── test_seq_tools.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/LICENSE -------------------------------------------------------------------------------- /README.MD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/README.MD -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/contents/test.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/docs/contents/test.rst -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/docs/index.rst -------------------------------------------------------------------------------- /evolutron/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/__init__.py -------------------------------------------------------------------------------- /evolutron/engine/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/engine/__init__.py -------------------------------------------------------------------------------- /evolutron/engine/krs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/engine/krs.py -------------------------------------------------------------------------------- /evolutron/extra_callbacks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/extra_callbacks.py -------------------------------------------------------------------------------- /evolutron/extra_layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/extra_layers.py -------------------------------------------------------------------------------- /evolutron/extra_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/extra_metrics.py -------------------------------------------------------------------------------- /evolutron/extra_objectives.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/extra_objectives.py -------------------------------------------------------------------------------- /evolutron/motifs/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/motifs/__init__.py -------------------------------------------------------------------------------- /evolutron/motifs/extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/motifs/extraction.py -------------------------------------------------------------------------------- /evolutron/structural/GetInterfaces.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/structural/GetInterfaces.py -------------------------------------------------------------------------------- /evolutron/structural/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /evolutron/templates/Embedders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/templates/Embedders.py -------------------------------------------------------------------------------- /evolutron/templates/__init__.py: -------------------------------------------------------------------------------- 1 | # coding=utf-8 2 | -------------------------------------------------------------------------------- /evolutron/templates/callback_templates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/templates/callback_templates.py -------------------------------------------------------------------------------- /evolutron/tools/SecS_from_PDBs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/SecS_from_PDBs.py -------------------------------------------------------------------------------- /evolutron/tools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/__init__.py -------------------------------------------------------------------------------- /evolutron/tools/data_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/data_tools.py -------------------------------------------------------------------------------- /evolutron/tools/io_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/io_tools.py -------------------------------------------------------------------------------- /evolutron/tools/seq_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/seq_tools.py -------------------------------------------------------------------------------- /evolutron/tools/structure_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/structure_tools.py -------------------------------------------------------------------------------- /evolutron/tools/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/utils.py -------------------------------------------------------------------------------- /evolutron/tools/visual.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/evolutron/tools/visual.py -------------------------------------------------------------------------------- /notebooks/cnn_design.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/cnn_design.py -------------------------------------------------------------------------------- /notebooks/compare_comet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/compare_comet.py -------------------------------------------------------------------------------- /notebooks/contact_sensitivity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/contact_sensitivity.py -------------------------------------------------------------------------------- /notebooks/dna_tf_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/dna_tf_analysis.ipynb -------------------------------------------------------------------------------- /notebooks/fix_filesaving.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/fix_filesaving.ipynb -------------------------------------------------------------------------------- /notebooks/fix_motif_visualization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/fix_motif_visualization.ipynb -------------------------------------------------------------------------------- /notebooks/lengths.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/lengths.npz -------------------------------------------------------------------------------- /notebooks/m6a_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/m6a_analysis.py -------------------------------------------------------------------------------- /notebooks/motif_distribution.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/motif_distribution.ipynb -------------------------------------------------------------------------------- /notebooks/motif_distribution.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/motif_distribution.py -------------------------------------------------------------------------------- /notebooks/test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/test -------------------------------------------------------------------------------- /notebooks/test_deconv.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/test_deconv.ipynb -------------------------------------------------------------------------------- /notebooks/test_dedense.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/test_dedense.ipynb -------------------------------------------------------------------------------- /notebooks/test_depool.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/test_depool.ipynb -------------------------------------------------------------------------------- /notebooks/test_save_load.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/test_save_load.ipynb -------------------------------------------------------------------------------- /notebooks/visualize_output.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/notebooks/visualize_output.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_metrics/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_metrics/test_extra_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_metrics/test_extra_metrics.py -------------------------------------------------------------------------------- /tests/test_networks/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_tools/samples/no_codes.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/samples/no_codes.fasta -------------------------------------------------------------------------------- /tests/test_tools/samples/sample.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/samples/sample.tsv -------------------------------------------------------------------------------- /tests/test_tools/samples/smallSecS.sec: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/samples/smallSecS.sec -------------------------------------------------------------------------------- /tests/test_tools/samples/type2p_codes.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/samples/type2p_codes.fasta -------------------------------------------------------------------------------- /tests/test_tools/test_data_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/test_data_tools.py -------------------------------------------------------------------------------- /tests/test_tools/test_io_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/test_io_tools.py -------------------------------------------------------------------------------- /tests/test_tools/test_seq_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mitmedialab/Evolutron/HEAD/tests/test_tools/test_seq_tools.py --------------------------------------------------------------------------------