molecular-design-toolkit
Notebook-integrated tools for molecular simulation and visualization
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- build-env.dockerfile
- deploy-tokens.crypt
- print-environment.sh
- publish.sh
- pull-cache.sh
- pull-chemdocker.sh
- push-and-tag.sh
- push-coverage.sh
- README.md
- requirements.txt
- run-ci-tests.sh
- send-test-status.py
- test-env.dockerfile
- test-tokens.crypt
- test-version-number.sh
- runsander.py
- cleanapt
- moldesign.dockerignore
- moldesign.yml
- run_notebook.sh
- .gitignore
- DockerMake.yml
- Environments.yml
- Moldesign.yml
- PySCF.yml
- README.md
- requirements.txt
- datastructures.rst
- geometry.rst
- molecule.rst
- test.rst
- wfn.rst
- atompos.png
- atoms.png
- benz_min_traj.png
- bonds.png
- chains.png
- data.png
- ethyl_after.png
- ethyl_init.png
- ethyl_noadjust.png
- geometrybuilder.png
- howdoi_annotated.png
- howdoi_method_autocomplete.png
- howdoi_orbs.png
- howdoi_pdb1.png
- howdoi_pdb_assm.png
- howdoi_purplewater.png
- howdoi_subtle.png
- howdoi_view1.png
- molecule.png
- properties.png
- questiondoc.png
- residues.png
- shifttab_online.png
- struc_benzene.png
- tab_autocomplete.png
- wfn.png
- .gitignore
- autogen_api.sh
- biomolecule.rst
- conf.py
- creating_and_converting.rst
- dynamics.rst
- features.rst
- generate_package_api.py
- geometry.rst
- index.rst
- install.rst
- integrators.rst
- interactive.rst
- Makefile
- properties.rst
- quickstart.rst
- requirements.txt
- structure.rst
- toplevel.rst
- visualization.rst
- buckyball.ipynb
- Dexter_alkane.ipynb
- Guided tour.ipynb
- Header.ipynb
- Parallel.ipynb
- The harmonic oscillator.ipynb
- Units and gravity.ipynb
- 1bna.pdb
- 1yu8.pdb
- 3AID.pdb
- bipyridine.sdf
- buckyball.pdb
- butane.xyz
- nuc.inpcrd
- nuc.pdb
- nuc.prmtop
- octane.xyz
- solar.csv
- butadiene_orbs.png
- dna.png
- Header.png
- holliday.png
- Molecules.png
- protease.png
- Top.png
- gen_example_md.py
- gen_toc.py
- strip_nb_output.py
- .gitattributes
- .gitignore
- 3AID.cif
- Example 1. Build and simulate DNA.ipynb
- Example 2. UV-vis absorption spectra.ipynb
- Example 3. Simulating a crystal structure.ipynb
- Example 4. HIV Protease bound to an inhibitor.ipynb
- Example 5. Enthalpic barriers.ipynb
- Getting Started.ipynb
- Tutorial 1. Making a molecule.ipynb
- Tutorial 2. Biochemical basics.ipynb
- Tutorial 3. Quantum Chemistry.ipynb
- banner.png
- generate_residue_data.py
- generate_residue_templates.py
- .gitignore
- amber_ffs.yml
- apply_copyright.sh
- chemical_components.dat
- chemical_components.dir
- nist_atomic.yml
- pint_atomic_units.txt
- residue_templates.json
- input
- input.dat
- README.md
- 1hpk.pdb
- 1KBU.cif.bz2
- 1KBU.pdb.bz2
- 1pyn.pdb.gz
- 1yu8.pdb
- 2jaj.pdb.gz
- 2p8w.cif.bz2
- 3ac2.pdb.bz2
- 3aid.cif.bz2
- 3aid.pdb.gz
- 3b5x.cif.bz2
- 3p3k.pdb.gz
- 5b7a.pdb.bz2
- ACTG.cif
- ACTG.pdb
- bipyridine.mol2
- bipyridine.sdf
- bipyridine.xyz
- propane.pdb
- .gitignore
- __init__.py
- conftest.py
- debug-job
- helpers.py
- molecule_fixtures.py
- object_fixtures.py
- README.md
- test_alignments.py
- test_ambertools_xface.py
- test_atom_bond_computed_properties.py
- test_atom_containers.py
- test_atoms.py
- test_biopython_xface.py
- test_cli.py
- test_config.py
- test_constraints.py
- test_copies.py
- test_dna_primary_structure.py
- test_gaussian_math.py
- test_geometry.py
- test_imports.py
- test_io.py
- test_mathutils.py
- test_minimizers.py
- test_molecules.py
- test_objects.py
- test_openbabel_xface.py
- test_openmm_xface.py
- test_pdb_processing.py
- test_pdbfixer_xface.py
- test_protein_primary_structure.py
- test_qm_xfaces.py
- test_qmmm.py
- test_symmetry.py
- test_tools.py
- test_trajectory.py
- test_units.py
- test_wfn.py
- __init__.py
- CHEMDOCKER_TAG
- compute.py
- configuration.py
- packages.py
- README.md
- remote_procedure_calls.py
- __init__.py
- atomic.py
- biochemical.py
- chemical_components.py
- data.py
- ff.py
- PYTHON
- __init__.py
- LICENSE
- one.py
- utils.py
- __init__.py
- pathlib.py
- README.md
- transformations.py
- __init__.py
- amber.py
- errors.py
- ffparams.py
- forcefieldbase.py
- __init__.py
- alignment.py
- constraints.py
- coords.py
- grads.py
- monitor.py
- README.md
- setcoord.py
- shake.py
- symmetry.py
- __init__.py
- helpers.py
- logs.py
- pdb.py
- qmmm.py
- README.md
- __init__.py
- base.py
- openmm.py
- README.md
- verlet.py
- __init__.py
- ambertools.py
- biopython_interface.py
- nbo_interface.py
- openbabel.py
- openmm.py
- opsin_interface.py
- parmed_interface.py
- pdbfixer_interface.py
- pyscf_interface.py
- README.md
- symmol_interface.py
- tleap_interface.py
- __init__.py
- eigen.py
- grids.py
- spherical_harmonics.py
- vectormath.py
- __init__.py
- base.py
- descent.py
- README.md
- scipy.py
- smart.py
- __init__.py
- amber.py
- base.py
- jsonmodel.py
- models.py
- nwchem.py
- openbabel.py
- openmm.py
- pyscf.py
- qmmm.py
- README.md
- toys.py
- __init__.py
- atomcollections.py
- atoms.py
- biounits.py
- bond_graph.py
- bonds.py
- chain.py
- coord_arrays.py
- molecule.py
- primary_structure.py
- properties.py
- README.md
- residue.py
- trajectory.py
- __init__.py
- atomic_basis_fn.py
- basis.py
- cartesian.py
- gaussians.py
- orbitals.py
- primitives.py
- spherical.py
- wfn.py
- __init__.py
- build.py
- README.md
- topology.py
- __init__.py
- constants.py
- quantity.py
- tools.py
- unitsystem.py
- AUTHORS
- LICENSE
- __init__.py
- google.py
- __init__.py
- _deadfunctions.py.txt
- apply_copyright.sh
- callsigs.py
- classes.py
- databases.py
- descriptors.py
- exportutils.py
- json_extension.py
- numerical.py
- README.md
- utils.py
- __init__.py
- __main__.py
- _version.py
- exceptions.py
- fileio.py
- HISTORY.md
- method.py
- parameters.py
- README.md
- widgets.py
- .coveragerc
- .coveralls.yml
- .dockerignore
- .gitattributes
- .gitignore
- codeship-services.yml
- codeship-steps.yml
- CONTRIBUTING.md
- DEVELOPMENT.md
- environment.yml
- LICENSE
- MANIFEST.in
- nb-output-filter.sh
- NOTICES
- pytest.ini
- README.md
- requirements.txt
- setup.cfg
- setup.py
- versioneer.py
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