cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13883112
title: modelforge curated dataset: SPICE 1

description: Curated SPICE 1 Dataset:

1000 conformer test set restricted to elements H, C, N, O, F, Cl, S, version "nc_1000_v1_HCNOFClS":

This provides a curated hdf5 file for a subset of the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs. This subset is limited to molecules containing any of the following 7 elements: H, C, N, O, F, Cl, and S.  This  dataset contains 1000 total conformers, for 100 unique molecules (10 conformers per molecule).  Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer.  

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: 



<add commit>



Link to the script file used to generate the dataset: 



<add commit>




 

Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.13883550
title: modelforge curated dataset: SPICE 1

description: Curated SPICE 1 Dataset:

1000 conformer test set, version nc_1000_v1:

This provides a curated hdf5 file for a subset of the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs. This includes 1000 total conformers, for 100 unique molecules (10 conformers per molecule). 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:

Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer.  

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: 



<add commit>



Link to the script file used to generate the dataset: 



<add commit>




 

Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.13883617
title: modelforge curated dataset: SPICE 1

description: Curated SPICE 1 Dataset:

Full dataset restricted to elements H, C, N, O, F, Cl, S, version "full_dataset_v1_HCNOFClS":

This provides a curated hdf5 file for a subset of the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs. This subset is limited to molecules containing any of the following 7 elements: H, C, N, O, F, Cl, and S.  This  dataset contains 976,408 total conformers, for 16,565 unique molecules. 

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:

Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer.  

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


This curated dataset was generated using the modelforge software at commit c5c7153:



Link to the source code at this commit: 



<add commit>



Link to the script file used to generate the dataset: 



<add commit>




 

Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.13883667
title: modelforge curated dataset: SPICE 1

description: Curated SPICE 1 Dataset:

Full dataset, version full_dataset_v1:

This provides a curated hdf5 file for the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile  includes 1,110,165 total conformers for 19,238 unique molecules.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:

Changes: In this version, for each record `total_charge` is stored as an array of shape (N_conformers, 1), i.e., a value for each conformer; previously this was just a single value for each record as the charge state doesn't change for each conformer.  

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package.  For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


 

Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.15455029
title: modelforge curated dataset: SPICE 1

description: Modelforge Curated SPICE 1 Dataset:- Full dataset-Version: full_dataset_v1.1

This provides a curated hdf5 file for the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This datafile  includes 1,110,165 total conformers for 19,238 unique molecules.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This is compatible with modelforge HDF5 schema 2. 

For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Properties Included:



atomic_numbers 

positions       



"per_atom"

"nanometer"



dft_total_force



"per_atom"

"kilojoule_per_mole / nanometer"



mbis_charges  



"per_atom"

"elementary_charge"



mbis_dipoles   



"per_atom"

"elementary_charge * nanometer"



mbis_quadrupoles       



"per_atom"

"elementary_charge * nanometer ** 2"



mbis_octupoles 



"per_atom"

"elementary_charge * nanometer ** 3"



mayer_indices  



"per_atom"

"dimensionless"



wiberg_lowdin_indices  



"per_atom"

 "dimensionless"



total_charge   



"per_system"

"elementary_charge"



dft_total_energy       



"per_system"

"kilojoule_per_mole"



formation_energy       



"per_system"

"kilojoule_per_mole"



scf_dipole     



"per_system"

"elementary_charge * nanometer"



scf_quadrupole 



"per_system"

"elementary_charge * nanometer ** 2"



smiles 



"meta_data"




Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.15461060
title: modelforge curated dataset: SPICE 1

description: Modelforge Curated SPICE 1 Dataset:-1000 configuration test set-Version: nc_1000_v1.1

This provides a curated hdf5 file for the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 100 unique records for 1000 total configurations, with a maximum of 10 configurations per record.

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This is compatible with modelforge HDF5 schema 2. 

For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Properties Included:



atomic_numbers 

positions       



"per_atom"

"nanometer"



dft_total_force



"per_atom"

"kilojoule_per_mole / nanometer"



mbis_charges  



"per_atom"

"elementary_charge"



mbis_dipoles   



"per_atom"

"elementary_charge * nanometer"



mbis_quadrupoles       



"per_atom"

"elementary_charge * nanometer ** 2"



mbis_octupoles 



"per_atom"

"elementary_charge * nanometer ** 3"



mayer_indices  



"per_atom"

"dimensionless"



wiberg_lowdin_indices  



"per_atom"

 "dimensionless"



total_charge   



"per_system"

"elementary_charge"



dft_total_energy       



"per_system"

"kilojoule_per_mole"



formation_energy       



"per_system"

"kilojoule_per_mole"



scf_dipole     



"per_system"

"elementary_charge * nanometer"



scf_quadrupole 



"per_system"

"elementary_charge * nanometer ** 2"



smiles 



"meta_data"




Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.15461463
title: modelforge curated dataset: SPICE 1

description: Modelforge Curated SPICE 1 Dataset:-1000 configuration test set, limited to [H, C, N, O, F, Cl, S]-Version: nc_1000_HCNOFClS_v1.1

This provides a curated hdf5 file for the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 100 unique records for 1000 total configurations, with a maximum of 10 configurations per record. The dataset is limited to the elements that are compatible with the ANI2x NNP: [H, C, N, O, F, Cl, S].

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This is compatible with modelforge HDF5 schema 2. 

For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Properties Included:



atomic_numbers 

positions       



"per_atom"

"nanometer"



dft_total_force



"per_atom"

"kilojoule_per_mole / nanometer"



mbis_charges  



"per_atom"

"elementary_charge"



mbis_dipoles   



"per_atom"

"elementary_charge * nanometer"



mbis_quadrupoles       



"per_atom"

"elementary_charge * nanometer ** 2"



mbis_octupoles 



"per_atom"

"elementary_charge * nanometer ** 3"



mayer_indices  



"per_atom"

"dimensionless"



wiberg_lowdin_indices  



"per_atom"

 "dimensionless"



total_charge   



"per_system"

"elementary_charge"



dft_total_energy       



"per_system"

"kilojoule_per_mole"



formation_energy       



"per_system"

"kilojoule_per_mole"



scf_dipole     



"per_system"

"elementary_charge * nanometer"



scf_quadrupole 



"per_system"

"elementary_charge * nanometer ** 2"



smiles 



"meta_data"




Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.5281/zenodo.15461488
title: modelforge curated dataset: SPICE 1

description: Modelforge Curated SPICE 1 Dataset:-full dataset, limited to [H, C, N, O, F, Cl, S]-Version: full_dataset_HCNOFClS_v1.1

This provides a curated hdf5 file for the SPICE 1 dataset (release v1.1.4) designed to be compatible with modelforge, an infrastructure to implement and train NNPs.  This dataset contains 16565 unique records for 976408 total configurations. The dataset is limited to the elements that are compatible with the ANI2x NNP: [H, C, N, O, F, Cl, S].

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This is compatible with modelforge HDF5 schema 2. 

For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Properties Included:



atomic_numbers 

positions       



"per_atom"

"nanometer"



dft_total_force



"per_atom"

"kilojoule_per_mole / nanometer"



mbis_charges  



"per_atom"

"elementary_charge"



mbis_dipoles   



"per_atom"

"elementary_charge * nanometer"



mbis_quadrupoles       



"per_atom"

"elementary_charge * nanometer ** 2"



mbis_octupoles 



"per_atom"

"elementary_charge * nanometer ** 3"



mayer_indices  



"per_atom"

"dimensionless"



wiberg_lowdin_indices  



"per_atom"

 "dimensionless"



total_charge   



"per_system"

"elementary_charge"



dft_total_energy       



"per_system"

"kilojoule_per_mole"



formation_energy       



"per_system"

"kilojoule_per_mole"



scf_dipole     



"per_system"

"elementary_charge * nanometer"



scf_quadrupole 



"per_system"

"elementary_charge * nanometer ** 2"



smiles 



"meta_data"




Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE dataset contains 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.

 

Citations:

Original publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2022). SPICE 1.1.4 (1.1.4) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8222043
DOI: 10.15468/dl.g99hqk
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-869.0",
 "Geometry POLYGON((0.55307 41.88137,1.34797 41.88137,1.34797 42.57137,0.55307 42.57137,0.55307 41.88137))",
 "HasGeospatialIssue is false",
 "TaxonKey is Vipera latastei Bosca, 1878"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006495-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.58c73t
title: Occurrence Download

description: A dataset containing 5618360 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Natural History Museum (London) Collection Specimens"
 ]
}

 The dataset includes 5618360 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006484-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jxrzgc
title: Occurrence Download

description: A dataset containing 43885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is FRA.1.11.1_1",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2021-2021"
 ]
}

 The dataset includes 43885 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006496-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.39trx7
title: Occurrence Download

description: A dataset containing 447218 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Türkiye",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Month is May",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 447218 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006471-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6tahns
title: Occurrence Download

description: A dataset containing 1135751 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Mentha L."
 ]
}

 The dataset includes 1135751 records from 3554 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006488-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.