.. This file is autogenerated by dev/scripts/generate_page.py QM9 === .. grid:: 1 1 2 2 .. grid-item:: .. raw:: html :file: ../_static/visualisations/QM9.html .. grid-item:: :class: info-card 134k stable organic molecules made up of CHONF and containing up to 9 heavy atoms. Each molecule's geometry was relaxed at the PM7 semi-empirical level of theory, before being labelled with DFT. For more information, see `Quantum chemistry structures and properties of 134 kilo molecules `_. Internally, files are downloaded from `FigShare `_,. Energy labels are quoted in eV, relative to the isolated atoms of the molecule. .. code-block:: pycon >>> from load_atoms import load_dataset >>> load_dataset("QM9") QM9: structures: 133,885 atoms: 2,407,753 species: H: 51.09% C: 35.16% O: 7.81% N: 5.80% F: 0.14% properties: per atom: (partial_charges) per structure: (A, B, C, Cv, G, H, U, U0, alpha, frequencies, gap, geometry, homo, inchi, index, lumo, mu, r2, smiles, zpve) License ------- This dataset is licensed under the `CC0 `_ license. Citation -------- If you use this dataset in your work, please cite the following: .. code-block:: latex @article{Ramakrishnan-17, author={ Ramakrishnan, Raghunathan and Dral, Pavlo O and Rupp, Matthias and von Lilienfeld, O Anatole }, title = {Data for 133885 GDB-9 molecules}, year = {2017}, month = {6}, doi = {10.6084/m9.figshare.978904_D12} } @article{Ramakrishnan-14, title={ Quantum chemistry structures and properties of 134 kilo molecules }, author={ Ramakrishnan, Raghunathan and Dral, Pavlo O and Rupp, Matthias and von Lilienfeld, O Anatole }, journal={Scientific Data}, volume={1}, year={2014}, publisher={Nature Publishing Group} } @article{Ruddigkeit-12, title = { Enumeration of 166 {{Billion Organic Small Molecules}} in the {{Chemical Universe Database GDB-17}} }, author = { Ruddigkeit, Lars and {van Deursen}, Ruud and Blum, Lorenz C. and Reymond, Jean-Louis }, year = {2012}, journal = {Journal of Chemical Information and Modeling}, volume = {52}, number = {11}, pages = {2864--2875}, doi = {10.1021/ci300415d}, } Properties ---------- **Per-atom**: .. list-table:: :header-rows: 1 * - Property - Units - Type - Description * - :code:`partial_charges` - e - :class:`ndarray(N,) ` - Mulliken partial atomic charges **Per-structure**: .. list-table:: :header-rows: 1 * - Property - Units - Type - Description * - :code:`index` - - :class:`~float` - consecutive index of molecule * - :code:`A` - GHz - :class:`~float` - Rotational constant A * - :code:`B` - GHz - :class:`~float` - Rotational constant B * - :code:`C` - GHz - :class:`~float` - Rotational constant C * - :code:`mu` - Debye - :class:`~float` - Dipole moment * - :code:`alpha` - Bohr\ :math:`^3` - :class:`~float` - Isotropic polarizability * - :code:`homo` - eV - :class:`~float` - HOMO energy * - :code:`lumo` - eV - :class:`~float` - LUMO energy * - :code:`gap` - eV - :class:`~float` - HOMO-LUMO energy gap * - :code:`r2` - Bohr\ :math:`^2` - :class:`~float` - electronic spatial extent * - :code:`zpve` - eV - :class:`~float` - zero point vibrational energy * - :code:`U0` - eV - :class:`~float` - internal energy at 0 K * - :code:`U` - eV - :class:`~float` - internal energy at 298.15 K * - :code:`H` - eV - :class:`~float` - enthalpy at 298.15 K * - :code:`G` - eV - :class:`~float` - free energy at 298.15 K * - :code:`Cv` - cal mol :math:`^{-1}` K :math:`^{-1}` - :class:`~float` - heat capacity at 298.15 K * - :code:`frequencies` - cm\ :math:`^{-1}` - :class:`~list` - harmonic frequencies * - :code:`geometry` - - :class:`~bool` - final geometry check passed * - :code:`smiles` - - :class:`~str` - `SMILES `_ string * - :code:`inchi` - - :class:`~str` - `InChI `_ identifier Miscellaneous information ------------------------- ``QM9`` is imported as an :class:`~load_atoms.atoms_dataset.InMemoryAtomsDataset`: .. dropdown:: Importer script for :code:`QM9` .. literalinclude:: ../../../src/load_atoms/database/importers/qm9.py :language: python .. dropdown:: :class:`~load_atoms.database.DatabaseEntry` for :code:`QM9` .. code-block:: yaml name: QM9 year: 2014 license: CC0 category: Benchmarks description: | 134k stable organic molecules made up of CHONF and containing up to 9 heavy atoms. Each molecule's geometry was relaxed at the PM7 semi-empirical level of theory, before being labelled with DFT. For more information, see `Quantum chemistry structures and properties of 134 kilo molecules `_. Internally, files are downloaded from `FigShare `_,. Energy labels are quoted in eV, relative to the isolated atoms of the molecule. minimum_load_atoms_version: 0.2 representative_structure: 23810 citation: | @article{Ramakrishnan-17, author={ Ramakrishnan, Raghunathan and Dral, Pavlo O and Rupp, Matthias and von Lilienfeld, O Anatole }, title = {Data for 133885 GDB-9 molecules}, year = {2017}, month = {6}, doi = {10.6084/m9.figshare.978904_D12} } @article{Ramakrishnan-14, title={ Quantum chemistry structures and properties of 134 kilo molecules }, author={ Ramakrishnan, Raghunathan and Dral, Pavlo O and Rupp, Matthias and von Lilienfeld, O Anatole }, journal={Scientific Data}, volume={1}, year={2014}, publisher={Nature Publishing Group} } @article{Ruddigkeit-12, title = { Enumeration of 166 {{Billion Organic Small Molecules}} in the {{Chemical Universe Database GDB-17}} }, author = { Ruddigkeit, Lars and {van Deursen}, Ruud and Blum, Lorenz C. and Reymond, Jean-Louis }, year = {2012}, journal = {Journal of Chemical Information and Modeling}, volume = {52}, number = {11}, pages = {2864--2875}, doi = {10.1021/ci300415d}, } per_atom_properties: partial_charges: desc: Mulliken partial atomic charges units: e per_structure_properties: index: desc: consecutive index of molecule A: desc: Rotational constant A units: GHz B: desc: Rotational constant B units: GHz C: desc: Rotational constant C units: GHz mu: desc: Dipole moment units: Debye alpha: desc: Isotropic polarizability units: Bohr\ :math:`^3` homo: desc: HOMO energy units: eV lumo: desc: LUMO energy units: eV gap: desc: HOMO-LUMO energy gap units: eV r2: desc: electronic spatial extent units: Bohr\ :math:`^2` zpve: desc: zero point vibrational energy units: eV U0: desc: internal energy at 0 K units: eV U: desc: internal energy at 298.15 K units: eV H: desc: enthalpy at 298.15 K units: eV G: desc: free energy at 298.15 K units: eV Cv: desc: heat capacity at 298.15 K units: "cal mol\ :math:`^{-1}` K\ :math:`^{-1}`" frequencies: desc: harmonic frequencies units: cm\ :math:`^{-1}` geometry: desc: final geometry check passed smiles: desc: "`SMILES `_ string" inchi: desc: "`InChI `_ identifier" # TODO: remove after Dec 2024 # backwards compatability: unused as of 0.3.0 files: - url: https://figshare.com/ndownloader/files/3195389 name: dsgdb9nsd.xyz.tar.bz2 hash: 3a63848ac806 processing: - UnZip - ForEachFile: pattern: "**/*.xyz" steps: - Custom: id: read_qm9_xyz