molecular-design-toolkit

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Notebook-integrated tools for molecular simulation and visualization

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- ISSUE_TEMPLATE.md
- 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
- .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
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  - howdoi_pdb1.png
  - howdoi_pdb_assm.png
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  - 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
- - .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
- - .gitignore
  - amber_ffs.yml
  - apply_copyright.sh
  - chemical_components.dat
  - chemical_components.dir
  - nist_atomic.yml
  - pint_atomic_units.txt
  - residue_templates.json
- - .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
- - __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
- - __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

# Installation Guide

1. Get the code

git clone https://github.com/Autodesk/molecular-design-toolkit

Downloads the entire project code from GitHub to your computer.

cd molecular-design-toolkit

Moves into the project folder you just downloaded.

2. Official Install Script

Easy Recommended

Prerequisites

Python 3 Python is required to use pip.

pip install moldesign

Installs the package published on PyPI directly — no need to clone the source.

✅ After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.

Pulled directly from this repo's README.

3. Python

Easy

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

pip install moldesign

Installs the package published on PyPI directly — no need to clone the source.

python -m moldesign intro

Runs the Python script (or module).

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.