adds the dataset card

README.md

@@ -1,87 +1,279 @@
----
-dataset_info:
-  config_name: pm7
-  features:
-  - name: title
-    dtype: string
-  - name: name
-    dtype: string
-  - name: mopac-id
-    dtype: int64
-  - name: net-charge
-    dtype: int64
-  - name: spin-multiplicity
-    dtype: int64
-  - name: openbabel-canonical-smiles
-    dtype: string
-  - name: openbabel-version
-    dtype: string
-  - name: rdkit-canonical-smiles
-    dtype: string
-  - name: rdkit-version
-    dtype: string
-  - name: oechem-canonical-smiles
-    dtype: string
-  - name: oechem-version
-    dtype: string
-  - name: mopac-keywords
-    sequence: string
-  - name: description
-    dtype: string
-  - name: atomic-indices
-    sequence: int64
-  - name: atomic-numbers
-    sequence: int64
-  - name: atomic-symbols
-    sequence: string
-  - name: coordinates
-    sequence: float64
-  - name: bonds
-    sequence: int64
-  - name: enthalpy-of-formation
-    dtype: float64
-  - name: enthalpy-of-formation-error
-    dtype: string
-  - name: enthalpy-of-formation-reference
-    dtype: 'null'
-  - name: enthalpy-of-formation-units
-    dtype: string
-  - name: ionization-energy
-    dtype: float64
-  - name: ionization-energy-error
-    dtype: string
-  - name: ionization-energy-reference
-    dtype: 'null'
-  - name: ionization-energy-units
-    dtype: string
-  - name: entropy
-    dtype: float64
-  - name: entropy-units
-    dtype: string
-  - name: constant-pressure-heat-capacity
-    dtype: float64
-  - name: constant-pressure-heat-capacity-units
-    dtype: string
-  - name: diople-moment
-    dtype: float64
-  - name: dipole-moment-reference
-    dtype: string
-  - name: dipole-moment-units
-    dtype: string
-  - name: mopac-reference-energy
-    dtype: float64
-  - name: mopac-reference-energy-units
-    dtype: string
-  splits:
-  - name: train
-    num_bytes: 6783360
-    num_examples: 4617
-  download_size: 2172928
-  dataset_size: 6783360
+--
+license:
+  - lgpl-3.0
+license_link: https://www.gnu.org/licenses/lgpl-3.0.en.html
+tags:
+  - heat-of-formation
+  - dipole-moments
+  - entropy
+  - energy
+  - pm7
+  - crystals
+  - small-molecules
+  - organometallics
+pretty_name: pm7
+size_categories:
+  - n<10K
+source_datasets:
+  - pm7
+task_categories:
+  - tabular-regression
+  - other
+task_ids:
+  - tabular-single-column-regression
 configs:
-- config_name: pm7
-  data_files:
-  - split: train
-    path: data/train-*
-  default: true
+  - config_name: pm7
+    data_files:
+      - split: train
+        path: "data/train*.parquet"
+    default: true
 ---
+# PM7 Dataset
+
+## Table of Contents
+
+- [PM7 Dataset](#pm7-dataset)
+  - [Table of Contents](#table-of-contents)
+  - [Dataset Description](#dataset-description)
+    - [Dataset Summary](#dataset-summary)
+  - [Dataset Structure](#dataset-structure)
+    - [Data Instances](#data-instances)
+    - [Data Fields](#data-fields)
+    - [Data Splits and Configurations](#data-splits-and-configurations)
+  - [How to Use the Dataset](#how-to-use-the-dataset)
+    - [Prerequisites](#prerequisites)
+    - [Accessing the Data](#accessing-the-data)
+  - [Dataset Creation](#dataset-creation)
+    - [Curation Rationale](#curation-rationale)
+      - [Initial Data Collection and Normalization](#initial-data-collection-and-normalization)
+    - [Personal and Sensitive Information](#personal-and-sensitive-information)
+  - [Considerations for Using the Data](#considerations-for-using-the-data)
+    - [Social Impact of Dataset](#social-impact-of-dataset)
+  - [Additional Information](#additional-information)
+    - [Dataset Curators](#dataset-curators)
+    - [Licensing Information](#licensing-information)
+    - [Citation Information](#citation-information)
+    - [Contributions](#contributions)
+
+## Dataset Description
+
+- **Homepage:** http://openmopac.net
+- **Repository:** https://github.com/openmopac/mopac
+- **Paper:** https://doi.org/10.1007/s00894-012-1667-x
+- **Point of Contact:** [James J. P. Stewart]([email protected])
+- **Point of Contact:** [Paul Saxe]([email protected])
+- **Point of Contact:** [Mohammad Mostafanejad]([email protected])
+- **Point of Contact:** [MolSSI-AI Hub]([email protected])
+
+### Dataset Summary
+
+PM7 is a modern semi-empirical method with broad applications in chemical space
+including organic molecules, organometallics and solid-state crystalline
+compounds. The parameterization process involved adopting a diverse set of
+experimental and high-level ab initio reference data. The current dataset,
+curated by the Molecular Sciences Software Institute, attempts to provide a
+ready-to-use version of the PM7 dataset for the computational molecular science
+and machine learning community.
+
+## Dataset Structure
+
+### Data Instances
+
+An example of a data instance is as follows:
+
+```json
+{'title': 'MOPAC_54/PM7_reference',
+ 'name': '1,1,1-Trifluoroethane',
+ 'mopac-id': 54,
+ 'net-charge': 0,
+ 'spin-multiplicity': 1,
+ 'openbabel-canonical-smiles': 'CC(F)(F)F',
+ 'openbabel-version': '3.1.0',
+ 'rdkit-canonical-smiles': 'CC(F)(F)F',
+ 'rdkit-version': '2024.03.5',
+ 'oechem-canonical-smiles': 'CC(F)(F)F',
+ 'oechem-version': '20240905',
+ 'mopac-keywords': ['SYMMETRY', 'PM7'],
+ 'description': '1,1,1-Trifluoroethane\nI=13.8 IR=LLNBS82 D=2.32 H=-178.9 HR=NIST DR=MCC1963 S=66.9 CP=18.69',
+ 'atomic-indices': [1, 2, 3, 4, 5, 6, 7, 8],
+ 'atomic-numbers': [6, 6, 9, 9, 9, 1, 1, 1],
+ 'atomic-symbols': ['C', 'C', 'F', 'F', 'F', 'H', 'H', 'H'],
+ 'coordinates': [0.0,
+  0.0,
+  0.0,
+  ...,
+  -0.41029998660087585,
+  -0.8860999941825867,
+  0.5116000175476074],
+ 'bonds': [1, 7, 1, 1, 2, 1, 1, 6, 1, 1, 8, 1, 2, 5, 1, 2, 4, 1, 2, 3, 1],
+ 'enthalpy-of-formation': -748.5176,
+ 'enthalpy-of-formation-error': None,
+ 'enthalpy-of-formation-reference': None,
+ 'enthalpy-of-formation-units': 'kJ/mol',
+ 'ionization-energy': 13.8,
+ 'ionization-energy-error': None,
+ 'ionization-energy-reference': None,
+ 'ionization-energy-units': 'eV',
+ 'entropy': 279.9096,
+ 'entropy-units': 'J/mol/K',
+ 'constant-pressure-heat-capacity': 78.19896000000001,
+ 'constant-pressure-heat-capacity-units': 'J/mol/K',
+ 'diople-moment': 2.32,
+ 'dipole-moment-reference': 'MCC1963',
+ 'dipole-moment-units': 'D',
+ 'mopac-reference-energy': -731.158184,
+ 'mopac-reference-energy-units': 'kJ/mol'}
+```
+
+### Data Fields
+
+| Field                                 | Description                                                     |
+| ------------------------------------- | --------------------------------------------------------------- |
+| title                                 | Title line in the MOPAC input/SDF file                          |
+| name                                  | Name of the molecule                                            |
+| mopac-id                              | MOPAC ID of the molecule                                        |
+| net-charge                            | Net charge of the molecule                                      |
+| spin-multiplicity                     | Spin multiplicity of the molecule                               |
+| openbabel-canonical-smiles            | Canonical SMILES string generated by OpenBabel                  |
+| openbabel-version                     | Version of OpenBabel used to generate the canonical SMILES      |
+| rdkit-canonical-smiles                | Canonical SMILES string generated by RDKit                      |
+| rdkit-version                         | Version of RDKit used to generate the canonical SMILES          |
+| oechem-canonical-smiles               | Canonical SMILES string generated by OpenEye OEChem             |
+| oechem-version                        | Version of OpenEye OEChem used to generate the canonical SMILES |
+| mopac-keywords                        | Keywords used in the MOPAC input file                           |
+| description                           | Description of the molecule                                     |
+| atomic-indices                        | Atomic indices of the atoms in the molecule                     |
+| atomic-numbers                        | Atomic numbers of the atoms in the molecule                     |
+| atomic-symbols                        | Atomic symbols of the atoms in the molecule                     |
+| coordinates                           | Atomic coordinates of the atoms in the molecule                 |
+| bonds                                 | Bond information of the molecule                                |
+| enthalpy-of-formation                 | Enthalpy of formation of the molecule                           |
+| enthalpy-of-formation-error           | Error in the enthalpy of formation                              |
+| enthalpy-of-formation-reference       | Reference for the enthalpy of formation                         |
+| enthalpy-of-formation-units           | Units of the enthalpy of formation                              |
+| ionization-energy                     | Ionization energy of the molecule                               |
+| ionization-energy-error               | Error in the ionization energy                                  |
+| ionization-energy-reference           | Reference for the ionization energy                             |
+| ionization-energy-units               | Units of the ionization energy                                  |
+| entropy                               | Entropy of the molecule                                         |
+| entropy-units                         | Units of the entropy                                            |
+| constant-pressure-heat-capacity       | Constant pressure heat capacity of the molecule                 |
+| constant-pressure-heat-capacity-units | Units of the constant pressure heat capacity                    |
+| diople-moment                         | Dipole moment of the molecule                                   |
+| dipole-moment-reference               | Reference for the dipole moment                                 |
+| dipole-moment-units                   | Units of the dipole moment                                      |
+| mopac-reference-energy                | Reference energy of the molecule                                |
+| mopac-reference-energy-units          | Units of the reference energy                                   |
+
+### Data Splits and Configurations
+
+The dataset has only one `train` split. Currently, the PM7 dataset has one
+configuration/subset:
+
+- `pm7` (default)
+
+## How to Use the Dataset
+
+### Prerequisites
+
+We recommend isolating your work in a virtualenv or conda environment.
+You can create a new conda environment, `pm7`,
+
+```bash
+  conda create -n pm7 python=3.12
+```
+
+and activate it using the following command
+
+```bash
+  conda activate pm7
+```
+
+Once the conda environment is activated, you can
+install the dependencies in it as shown below
+
+```bash
+  pip install huggingface_hub
+```
+
+### Accessing the Data
+
+Once the required packages are installed, you can run the following code
+to access the data
+
+```python
+  # import the modules
+  from datasets import load_dataset
+  # load the dataset with streaming
+  hub_ds = load_dataset(path="molssiai-hub/pm7",
+                        name="pm7",
+                        split="train",
+                        cache_dir="./tmp")
+  # fetch a random batch of 32 samples from the dataset
+  ds = hub_ds.shuffle(seed=1234).select(range(32))
+```
+
+The argument `name` by default is set to `pm7`. The `split` must be set to
+`train` as it is the only split in our dataset. The `cache_dir` allows us to
+store the Hugging Face datasets' and models' artifacts in a non-default
+directory (by default, it is set to `~/.cache/huggingface`). The `shuffle`
+method shuffles the dataset with a seed of 1234, and the `select` method selects
+the first 32 samples from the shuffled dataset.
+
+## Dataset Creation
+
+### Curation Rationale
+
+The present version of PM7 dataset has been extracted from the
+[pm7.sdf.gz](https://huggingface.co/datasets/molssiai-hub/pm7/blob/main/pm7.sdf.gz)
+file, transformed into a dictionary and stored in the `.json` format.
+
+#### Initial Data Collection and Normalization
+
+Other than the changes detailed in Sec. [Curation Rationale](#curation-rationale),
+no data modification has been performed on the PM7 dataset.
+
+### Personal and Sensitive Information
+
+The PM7 dataset does not involve any personal or sensitive information.
+
+## Considerations for Using the Data
+
+### Social Impact of Dataset
+
+The PM7 dataset paves the way for applications in (in)organic chemistry,
+solid-state physics and materials science, among others.
+
+## Additional Information
+
+### Dataset Curators
+
+- **James J. P. Stewart**, Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, CO, 80921, USA
+- **Paul Saxe**, The Molecular Sciences Software Institute (MolSSI), Blacksburg, VA, 24060, USA
+- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI), Blacksburg, VA, 24060, USA
+
+### Licensing Information
+
+[GNU lesser general public license version 3.0](https://www.gnu.org/licenses/lgpl-3.0.en.htm)
+
+### Citation Information
+
+```tex
+@article{Stewart:2013:1,
+   author = {Stewart, James J. P.},
+   doi = {10.1007/S00894-012-1667-X},
+   journal = {Journal of Molecular Modeling},
+   pages = {1-32},
+   publisher = {Springer},
+   title = {Optimization of parameters for semiempirical methods VI: More modifications to the NDDO approximations and re-optimization of parameters},
+   volume = {19},
+   url = {https://link.springer.com/article/10.1007/s00894-012-1667-x},
+   year = {2013}
+}
+```
+
+### Contributions
+
+- **James J. P. Stewart**, Stewart Computational Chemistry
+- **Paul Saxe**, The Molecular Sciences Software Institute (MolSSI)
+- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)