./.codecov.yml
.coveragerc
.style.yapf
LICENSE
devtools/conda-recipe/build.sh
docs/Makefile
docs/_static/css/theme_overrides.css
docs/api.rst
docs/build_docs.rst
docs/conf.py
docs/index.rst
docs/install.rst
docs/make.bat
docs/releasehistory.rst
docs/source/align.rst
docs/source/analysis.rst
docs/source/dummy.rst
docs/source/evaluator.rst
docs/source/modules.rst
docs/source/paprika.rst
docs/source/restraints.rst
docs/source/simulation.rst
docs/source/tleap.rst
docs/source/utils.rst
docs/tutorials/01-tutorial-cb6-but.ipynb
docs/tutorials/02-tutorial-cb6-but-pbc.ipynb
docs/tutorials/03-tutorial-k-cl.ipynb
docs/tutorials/04-tutorial-cb6-but-openmm.ipynb
docs/tutorials/05-tutorial-cb6-but-plumed.ipynb
docs/tutorials/06-tutorial-cb6-but-gromacs.ipynb
docs/tutorials/07-tutorial-cb6-but-namd.ipynb
docs/tutorials/images/anchor-atoms-diagram.py
docs/tutorials/images/anchor-atoms-diagram.svg
docs/tutorials/images/cb6-but-dum-sol-diagram.graffle/data.plist
docs/tutorials/images/cb6-but.py
docs/tutorials/images/static-restraints.graffle/data.plist
docs/workflow.rst
paprika/__init__.py
paprika/_version.py
paprika/align.py
paprika/analysis.py
paprika/data/cb6-but-apr/a000/md.nc
paprika/data/cb6-but-apr/a001/md.nc
paprika/data/cb6-but-apr/a002/md.nc
paprika/data/cb6-but-apr/a003/md.nc
paprika/data/cb6-but-apr/p000/md.nc
paprika/data/cb6-but-apr/p001/md.nc
paprika/data/cb6-but-apr/p002/md.nc
paprika/data/cb6-but-apr/p003/md.nc
paprika/data/cb6-but-apr/p004/md.nc
paprika/data/cb6-but-apr/p005/md.nc
paprika/data/cb6-but-apr/p006/md.nc
paprika/data/cb6-but-apr/p007/md.nc
paprika/data/cb6-but-apr/p008/md.nc
paprika/data/cb6-but-apr/p009/md.nc
paprika/data/cb6-but-apr/p010/md.nc
paprika/data/cb6-but-apr/p011/md.nc
paprika/data/cb6-but-apr/p012/md.nc
paprika/data/cb6-but-apr/p013/md.nc
paprika/data/cb6-but-apr/p014/md.nc
paprika/data/cb6-but-apr/p015/md.nc
paprika/data/cb6-but-apr/p016/md.nc
paprika/data/cb6-but-apr/p017/md.nc
paprika/data/cb6-but-apr/p018/md.nc
paprika/data/cb6-but-apr/vac.pdb
paprika/data/cb6-but-apr/vac.prmtop
paprika/data/cb6-but/REF_cb6-but-dum.rst7
paprika/data/cb6-but/but.frcmod
paprika/data/cb6-but/but.mol2
paprika/data/cb6-but/but.sybyl.mol2
paprika/data/cb6-but/cb6-but-dum.in
paprika/data/cb6-but/cb6-but-dum.pdb
paprika/data/cb6-but/cb6-but-minimized.pdb
paprika/data/cb6-but/cb6-but-notcentered.pdb
paprika/data/cb6-but/cb6-but.pdb
paprika/data/cb6-but/cb6.frcmod
paprika/data/cb6-but/cb6.mol2
paprika/data/cb6-but/cb6.sybyl.mol2
paprika/data/cb6-but/tleap_gb.in
paprika/data/cb6-but/tleap_gb_dum.in
paprika/data/cb6-but/tleap_solvate.in
paprika/data/cb6-but/vac.crds
paprika/data/cb6-but/vac.in
paprika/data/cb6-but/vac.pdb
paprika/data/cb6-but/vac.prmtop
paprika/data/cb6-but/vac.rst7
paprika/data/cb6-but/vac.sybyl.mol2
paprika/data/cb6-but/vac.topo
paprika/data/k-cl/atomic_ions.lib
paprika/data/k-cl/k-cl-sol.pdb
paprika/data/k-cl/k-cl-sol.prmtop
paprika/data/k-cl/k-cl-sol.rst7
paprika/data/k-cl/k-cl.pdb
paprika/data/k-cl/k-cl.prmtop
paprika/data/k-cl/k-cl.rst7
paprika/data/reference/cb6-but/REF_cb6-but-dum.rst7
paprika/data/reference/cb6-but/apr-gb/a000/md.nc
paprika/data/reference/cb6-but/apr-gb/a001/md.nc
paprika/data/reference/cb6-but/apr-gb/a002/md.nc
paprika/data/reference/cb6-but/apr-gb/a003/md.nc
paprika/data/reference/cb6-but/apr-gb/p000/md.nc
paprika/data/reference/cb6-but/apr-gb/p001/md.nc
paprika/data/reference/cb6-but/apr-gb/p002/md.nc
paprika/data/reference/cb6-but/apr-gb/p003/md.nc
paprika/data/reference/cb6-but/apr-gb/p004/md.nc
paprika/data/reference/cb6-but/apr-gb/p005/md.nc
paprika/data/reference/cb6-but/apr-gb/p006/md.nc
paprika/data/reference/cb6-but/apr-gb/p007/md.nc
paprika/data/reference/cb6-but/apr-gb/p008/md.nc
paprika/data/reference/cb6-but/apr-gb/p009/md.nc
paprika/data/reference/cb6-but/apr-gb/p010/md.nc
paprika/data/reference/cb6-but/apr-gb/p011/md.nc
paprika/data/reference/cb6-but/apr-gb/p012/md.nc
paprika/data/reference/cb6-but/apr-gb/p013/md.nc
paprika/data/reference/cb6-but/apr-gb/p014/md.nc
paprika/data/reference/cb6-but/apr-gb/p015/md.nc
paprika/data/reference/cb6-but/apr-gb/p016/md.nc
paprika/data/reference/cb6-but/apr-gb/p017/md.nc
paprika/data/reference/cb6-but/apr-gb/p018/md.nc
paprika/data/reference/cb6-but/apr-gb/vac.pdb
paprika/data/reference/cb6-but/apr-gb/vac.prmtop
paprika/data/reference/cb6-but/but.frcmod
paprika/data/reference/cb6-but/but.mol2
paprika/data/reference/cb6-but/but.sybyl.mol2
paprika/data/reference/cb6-but/cb6-but-dum.in
paprika/data/reference/cb6-but/cb6-but-minimized.pdb
paprika/data/reference/cb6-but/cb6-but-notcentered.pdb
paprika/data/reference/cb6-but/cb6-but.pdb
paprika/data/reference/cb6-but/cb6.frcmod
paprika/data/reference/cb6-but/cb6.mol2
paprika/data/reference/cb6-but/cb6.sybyl.mol2
paprika/data/reference/cb6-but/tleap_gb.in
paprika/data/reference/cb6-but/tleap_gb_dum.in
paprika/data/reference/cb6-but/tleap_solvate.in
paprika/data/reference/cb6-but/vac.crds
paprika/data/reference/cb6-but/vac.in
paprika/data/reference/cb6-but/vac.pdb
paprika/data/reference/cb6-but/vac.prmtop
paprika/data/reference/cb6-but/vac.rst7
paprika/data/reference/cb6-but/vac.sybyl.mol2
paprika/data/reference/cb6-but/vac.topo
paprika/dummy.py
paprika/evaluator/__init__.py
paprika/evaluator/amber.py
paprika/evaluator/analyze.py
paprika/evaluator/setup.py
paprika/evaluator/utils.py
paprika/io.py
paprika/log.py
paprika/restraints/__init__.py
paprika/restraints/amber.py
paprika/restraints/colvars.py
paprika/restraints/openmm.py
paprika/restraints/plumed.py
paprika/restraints/read_yaml.py
paprika/restraints/restraints.py
paprika/restraints/utils.py
paprika/simulate/__init__.py
paprika/simulate/amber.py
paprika/simulate/gromacs.py
paprika/simulate/namd.py
paprika/simulate/simulation.py
paprika/tests/__init__.py
paprika/tests/addons.py
paprika/tests/test_align.py
paprika/tests/test_analysis.py
paprika/tests/test_dummy.py
paprika/tests/test_evaluator.py
paprika/tests/test_io.py
paprika/tests/test_paprika.py
paprika/tests/test_restraints.py
paprika/tests/test_simulate.py
paprika/tests/test_tleap.py
paprika/tests/test_utils.py
paprika/tleap.py
paprika/utils.py
setup.cfg
setup.py
versioneer.py
<<<<<< network
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<<<<<< EOF