LICENSE.md
README.md
setup.py
biobuild/__init__.py
biobuild.egg-info/PKG-INFO
biobuild.egg-info/SOURCES.txt
biobuild.egg-info/dependency_links.txt
biobuild.egg-info/requires.txt
biobuild.egg-info/top_level.txt
biobuild/core/Linkage.py
biobuild/core/Molecule.py
biobuild/core/__init__.py
biobuild/core/base_classes.py
biobuild/core/entity.py
biobuild/core/linkage.py
biobuild/core/molecule.py
biobuild/graphs/AtomGraph.py
biobuild/graphs/BaseGraph.py
biobuild/graphs/ResidueGraph.py
biobuild/graphs/__init__.py
biobuild/optimizers/DistanceRotatron.py
biobuild/optimizers/ForceFieldRotatron.py
biobuild/optimizers/OverlapRotatron.py
biobuild/optimizers/OverlapRotatron_allGMM.py
biobuild/optimizers/OverlapRotatron_orig.py
biobuild/optimizers/Rotatron.py
biobuild/optimizers/__init__.py
biobuild/optimizers/algorithms.py
biobuild/optimizers/utils.py
biobuild/resources/__init__.py
biobuild/resources/charmm.py
biobuild/resources/components_amino_acids.json
biobuild/resources/components_amino_acids.pkl
biobuild/resources/components_base.json
biobuild/resources/components_base.pkl
biobuild/resources/components_lipids.json
biobuild/resources/components_lipids.pkl
biobuild/resources/components_nucleotides.json
biobuild/resources/components_nucleotides.pkl
biobuild/resources/components_small.json
biobuild/resources/components_small.pkl
biobuild/resources/components_sugars.json
biobuild/resources/components_sugars.pkl
biobuild/resources/defaults.py
biobuild/resources/pdbe_compounds.py
biobuild/resources/pdbe_template.cif
biobuild/resources/pubchem.py
biobuild/resources/topology.json
biobuild/resources/topology.pkl
biobuild/structural/__init__.py
biobuild/structural/base.py
biobuild/structural/connector.py
biobuild/structural/infer.py
biobuild/structural/neighbors.py
biobuild/structural/patch.py
biobuild/structural/smiles.py
biobuild/structural/stitch.py
biobuild/utils/__init__.py
biobuild/utils/abstract.py
biobuild/utils/auxiliary.py
biobuild/utils/cif.py
biobuild/utils/constants.py
biobuild/utils/convert.py
biobuild/utils/defaults.py
biobuild/utils/ic.py
biobuild/utils/info.py
biobuild/utils/json.py
biobuild/utils/pdb.py
biobuild/utils/sdmol.py
biobuild/utils/visual.py
tests/test_charmm.py
tests/test_convert.py
tests/test_graphs.py
tests/test_molecule.py
tests/test_optimizers.py
tests/test_pdbe_compounds.py
tests/test_structural.py
tests/test_toplevel.py