.coveragerc
CONTRIBUTING.md
DEVELOPMENT.md
LICENSE
MANIFEST.in
NOTICES
README.md
requirements.txt
setup.cfg
setup.py
versioneer.py
moldesign/HISTORY.rst
moldesign/README.md
moldesign/__init__.py
moldesign/__main__.py
moldesign/_version.py
moldesign/exceptions.py
moldesign/fileio.py
moldesign/method.py
moldesign/parameters.py
moldesign/widgets.py
moldesign.egg-info/PKG-INFO
moldesign.egg-info/SOURCES.txt
moldesign.egg-info/dependency_links.txt
moldesign.egg-info/requires.txt
moldesign.egg-info/top_level.txt
moldesign/_notebooks/.gitattributes
moldesign/_notebooks/.gitignore
moldesign/_notebooks/3AID.cif
moldesign/_notebooks/Example 1. Build and simulate DNA.ipynb
moldesign/_notebooks/Example 2. UV-vis absorption spectra.ipynb
moldesign/_notebooks/Example 3. Simulating a crystal structure.ipynb
moldesign/_notebooks/Example 4. HIV Protease bound to an inhibitor.ipynb
moldesign/_notebooks/Example 5. Enthalpic barriers.ipynb
moldesign/_notebooks/Getting Started.ipynb
moldesign/_notebooks/Tutorial 1. Making a molecule.ipynb
moldesign/_notebooks/Tutorial 2. Biochemical basics.ipynb
moldesign/_notebooks/Tutorial 3. Quantum Chemistry.ipynb
moldesign/_notebooks/.building/Dexter_alkane.ipynb
moldesign/_notebooks/.building/Guided tour.ipynb
moldesign/_notebooks/.building/Header.ipynb
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moldesign/_notebooks/.building/buckyball.ipynb
moldesign/_notebooks/data/1bna.pdb
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moldesign/_notebooks/data/solar.csv
moldesign/_notebooks/img/Header.png
moldesign/_notebooks/img/Molecules.png
moldesign/_notebooks/img/Top.png
moldesign/_notebooks/img/butadiene_orbs.png
moldesign/_notebooks/img/dna.png
moldesign/_notebooks/img/holliday.png
moldesign/_notebooks/img/protease.png
moldesign/_notebooks/nbscripts/gen_example_md.py
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moldesign/_notebooks/nbscripts/strip_nb_output.py
moldesign/_static_data/.gitignore
moldesign/_static_data/amber_ffs.yml
moldesign/_static_data/apply_copyright.sh
moldesign/_static_data/chemical_components.dat
moldesign/_static_data/chemical_components.dir
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moldesign/_static_data/pint_atomic_units.txt
moldesign/_static_data/residue_templates.json
moldesign/_static_data/img/banner.png
moldesign/_static_data/scripts/generate_residue_data.py
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moldesign/_tests/.gitignore
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moldesign/_tests/debug-job
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moldesign/compute/README.md
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moldesign/data/atomic.py
moldesign/data/biochemical.py
moldesign/data/chemical_components.py
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moldesign/external/pyquante2/one.py
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moldesign/forcefields/__init__.py
moldesign/forcefields/amber.py
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moldesign/forcefields/ffparams.py
moldesign/forcefields/forcefieldbase.py
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moldesign/geom/alignment.py
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moldesign/geom/coords.py
moldesign/geom/grads.py
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moldesign/utils/docparsers/sphinxlicense/AUTHORS
moldesign/utils/docparsers/sphinxlicense/LICENSE