├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .travis.yml ├── INSTALL.rst ├── LICENSE.rst ├── MANIFEST.in ├── README.rst ├── csb ├── __init__.py ├── apps │ ├── __init__.py │ ├── bfit.py │ ├── bfite.py │ ├── buildhmm.py │ ├── csfrag.py │ ├── embd.py │ ├── helloworld.py │ ├── hhfrag.py │ ├── hhsearch.py │ ├── precision.py │ └── promix.py ├── bio │ ├── __init__.py │ ├── fragments │ │ ├── __init__.py │ │ └── rosetta.py │ ├── hmm │ │ ├── __init__.py │ │ └── pseudocounts.py │ ├── io │ │ ├── __init__.py │ │ ├── clans.py │ │ ├── cs.py │ │ ├── dssp.py │ │ ├── fasta.py │ │ ├── hhpred.py │ │ ├── mrc.py │ │ ├── noe.py │ │ ├── procheck.py │ │ ├── psipred.py │ │ ├── svg.py │ │ ├── vasco.py │ │ ├── whatif.py │ │ └── wwpdb.py │ ├── nmr │ │ ├── __init__.py │ │ └── resources │ │ │ ├── AtomConnectivity.xml │ │ │ ├── RandomCoil.Corrections.tsv │ │ │ └── RandomCoil.Reference.tsv │ ├── sequence │ │ ├── __init__.py │ │ └── alignment.py │ ├── structure │ │ └── __init__.py │ └── utils │ │ └── __init__.py ├── build.py ├── core │ └── __init__.py ├── io │ ├── __init__.py │ ├── plots.py │ └── tsv.py ├── numeric │ ├── __init__.py │ └── integrators.py ├── statistics │ ├── __init__.py │ ├── ars.py │ ├── maxent.py │ ├── mixtures.py │ ├── pdf │ │ ├── __init__.py │ │ └── parameterized.py │ ├── rand.py │ ├── samplers │ │ ├── __init__.py │ │ └── mc │ │ │ ├── __init__.py │ │ │ ├── multichain.py │ │ │ ├── neqsteppropagator.py │ │ │ ├── propagators.py │ │ │ └── singlechain.py │ └── scalemixture.py ├── statmech │ ├── __init__.py │ ├── ensembles.py │ └── wham.py └── test │ ├── __init__.py │ ├── app.py │ ├── cases │ ├── __init__.py │ ├── bio │ │ ├── __init__.py │ │ ├── fragments │ │ │ └── __init__.py │ │ ├── hmm │ │ │ └── __init__.py │ │ ├── io │ │ │ ├── __init__.py │ │ │ ├── clans │ │ │ │ └── __init__.py │ │ │ ├── cs │ │ │ │ └── __init__.py │ │ │ ├── fasta │ │ │ │ └── __init__.py │ │ │ ├── hhpred │ │ │ │ └── __init__.py │ │ │ ├── mrc │ │ │ │ └── __init__.py │ │ │ ├── noe │ │ │ │ └── __init__.py │ │ │ ├── procheck │ │ │ │ └── __init__.py │ │ │ ├── whatif │ │ │ │ └── __init__.py │ │ │ └── wwpdb │ │ │ │ └── __init__.py │ │ ├── nmr │ │ │ └── __init__.py │ │ ├── sequence │ │ │ ├── __init__.py │ │ │ └── alignment │ │ │ │ └── __init__.py │ │ ├── structure │ │ │ └── __init__.py │ │ └── utils │ │ │ └── __init__.py │ ├── core │ │ └── __init__.py │ ├── io │ │ └── __init__.py │ ├── numeric │ │ ├── __init__.py │ │ └── integrators.py │ ├── statistics │ │ ├── __init__.py │ │ ├── ars.py │ │ ├── maxent.py │ │ ├── mixtures.py │ │ ├── pdf │ │ │ ├── __init__.py │ │ │ └── parameterized.py │ │ ├── rand.py │ │ ├── samplers │ │ │ └── __init__.py │ │ └── scalemixture.py │ └── statmech │ │ ├── __init__.py │ │ ├── ensembles.py │ │ └── wham.py │ └── data │ ├── 1C3W_10.mrc │ ├── 1d3z.legacy.pdb │ ├── 1d3z.regular.pdb │ ├── 1nz9.full.pickle │ ├── 1nz9.model1.pickle │ ├── 1nz9.pdb │ ├── 1nz9A.frags │ ├── 2JZC.sum │ ├── 2l01.v2.str │ ├── 2l01.v3.str │ ├── 3p1u.pdb │ ├── 3shm_ca.pdb │ ├── ISL5.1.isl │ ├── Sparky.peaks │ ├── Xeasy1.peaks │ ├── Xeasy2.peaks │ ├── ake-xray-ensemble-ca.pdb │ ├── csb.tsv │ ├── d1b24a2.hhm │ ├── d1ea0a1.hhr │ ├── d1nz0a_.a3m │ ├── d1nz0a_.hhm │ ├── d1nz0a_.mfasta │ ├── d1nz0a_.pdb │ ├── mapping.pdb │ ├── mapping2.pdb │ ├── mapping3.pdb │ ├── maxent.pickle │ ├── modified.pdb │ ├── modified2.pdb │ ├── out.clans │ ├── pdbout.txt │ ├── standard.tsv │ ├── struct.ali.mfasta │ ├── test.fa │ ├── test.hhm │ └── test2.hhm ├── epydoc.css ├── requirements.txt └── setup.py /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csb-toolbox/CSB/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/csb-toolbox/CSB/HEAD/.gitignore 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