├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── examples ├── MSA_RF00167.fa ├── pydca_demo.ipynb ├── pydca_demo.py └── ref_RF00167.fa ├── how_to_docker.md ├── install.sh ├── pydca ├── __init__.py ├── config_dca │ ├── __init__.py │ └── config_log.py ├── contact_visualizer │ ├── __init__.py │ └── contact_visualizer.py ├── dca_utilities │ ├── __init__.py │ └── dca_utilities.py ├── extras │ └── a2m2aln.pl ├── fasta_reader │ ├── __init__.py │ └── fasta_reader.py ├── main.py ├── meanfield_dca │ ├── __init__.py │ ├── meanfield_dca.py │ └── msa_numerics.py ├── mfdca_main.py ├── msa_trimmer │ ├── __init__.py │ └── msa_trimmer.py ├── plmdca │ ├── __init__.py │ ├── include │ │ └── plmdca.h │ ├── lbfgs │ │ ├── include │ │ │ ├── arithmetic_ansi.h │ │ │ ├── arithmetic_sse_double.h │ │ │ ├── arithmetic_sse_float.h │ │ │ └── lbfgs.h │ │ └── lib │ │ │ └── lbfgs.cpp │ ├── msa_numerics.py │ ├── plmdca.py │ ├── plmdcaBackend.cpp │ └── plmdca_numerics.cpp ├── plmdca_main.py └── sequence_backmapper │ ├── __init__.py │ ├── scoring_matrix.py │ └── sequence_backmapper.py ├── requirements.txt ├── setup.py └── tests ├── __init__.py ├── fasta_reader_test.py ├── input_files_path.py ├── meanfield_dca_test.py ├── sequence_backmapper_test.py └── tests_input ├── MSA_RF00059_trimmed_gap_treshold_50.fa ├── PF02826.faa ├── ref_seq_PF02826.faa ├── ref_seq_RF00059.faa ├── ref_seq_RF00059_test1.faa ├── ref_seq_RF00059_test2.faa ├── ref_seq_RF00059_test3.faa └── ref_seq_RF00059_test4.faa /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KIT-MBS/pydca/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KIT-MBS/pydca/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: 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