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Mlpepper iodines
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...ssions/2024-10-11-MLPepper-RECAP-Optimized-Fragments-Add-Iodines-v1.0/README.md
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| # MLPepper-RECAP-Optimized-Fragments-Add-Iodines-v1.0 | ||
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| ## Description | ||
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| A single point dataset created by combining the [50k ESP from Simon](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2022-01-16-OpenFF-ESP-Fragment-Conformers-v1.0) and | ||
| [Br substituted set from Lily](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2023-11-30-OpenFF-multi-Br-ESP-Fragment-Conformers-v1.1-single-point), filtering by Cl and Br and replacing them successively with iodines, as well as some additional iodines from [Lexie and Lily's set](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0). | ||
| Each fragment had 5 conformations generated which were optimised locally using an AIMNET2 model trained to `wb97m-d3`. | ||
| This adds an extension of iodines molecules to the [original mlpepper dataset](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-07-26-MLPepper-RECAP-Optimized-Fragments-v1.0). | ||
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| The aim of the dataset is to provide polarised and gas phase electrostatic properties which can be used to generate ML models | ||
| for partial charge prediction. Unlike past datasets the wavefunction will not be saved to recompute the ESP instead we recommend building the ESP | ||
| from the MBIS atomic multipoles which save substantial amount of space. | ||
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| An off equilibrium data set will also be generated to enable conformation dependent prediction of charges. | ||
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| ## General Information | ||
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| * Date: 2024-10-11 | ||
| * Class: OpenFF SinglePoint Dataset | ||
| * Purpose: Electrostatic properties for ML prediction models | ||
| * Name: MLPepper RECAP Optimized Fragments v1.0 Add Iodines | ||
| * Number of unique molecules: 5733 | ||
| * Number of filtered molecules: 0 | ||
| * Number of conformers: 6131 | ||
| * Number of conformers per molecule (min, mean, max): 1, 1.07, 3 | ||
| * Mean molecular weight: 278.86 | ||
| * Max molecular weight: 701.59 | ||
| * Charges: [-4.0, -2.0, -1.0, 0.0, 1.0, 2.0, 3.0] | ||
| * Dataset submitter: Josh Horton/ Charlie Adams | ||
| * Dataset generator: Josh Horton/ Charlie Adams | ||
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| ## QCSubmit generation pipeline | ||
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| - `create_optimisation.py`: Was used to create the iodine Cl and Br replacements from the original MLPepper, and | ||
| then optimisation dataset. | ||
| - `create_singlepoints.py`: Was used to create the singlepoints dataset for the optimised iodine sets. | ||
| - `create_dataset.py`: Finally this script combines the resulting datasets into a single point dataset ready for submission. | ||
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| ## QCSubmit Manifest | ||
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| ### Input Files | ||
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| - `create_optimisation.py`: Script used to make the optimisation dataset for local optimisation. | ||
| - `create_singlepoints.py`: Script to create the singlepoints dataset from the optimised geometries. | ||
| - `create_dataset.py`: Script to create the singlepoint dataset from the optimization set, removing any connectivity issues. | ||
| - `basic_env.yml`: input file to create environment this dataset was built with. | ||
| - `conda_export.yml`: file created from conda export. | ||
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| ### Output Files | ||
| - `dataset.json.bz2`: The basic dataset ready for submission. | ||
| - `dataset.pdf`: A pdf file containing molecule 2D structures. | ||
| - `dataset.smi`: SMILES for every molecule in the submission. | ||
| - `dataset_mlpepper.smi`: SMILES of the original dataset to generate the Iodines | ||
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| ### Metadata | ||
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| * Number of conformers: 6131 | ||
| * Number of conformers per molecule (min, mean, max): 1, 1.07, 3 | ||
| * Mean molecular weight: 278.86 | ||
| * Max molecular weight: 701.59 | ||
| * Charges: [-4.0, -2.0, -1.0, 0.0, 1.0, 2.0, 3.0] | ||
| * Elements: {B, Si, I, C, N, Br, O, S, Cl, H, F, P} | ||
| * Spec: wb97x-d/def2-tzvpp | ||
| * basis: def2-tzvpp | ||
| * implicit_solvent: None | ||
| * keywords: {'dft_spherical_points': 590, 'dft_radial_points': 99} | ||
| * maxiter: 200 | ||
| * method: wb97x-d | ||
| * program: psi4 | ||
| * SCF properties: | ||
| * dipole | ||
| * quadrupole | ||
| * lowdin_charges | ||
| * mulliken_charges | ||
| * mbis_charges | ||
| * mayer_indices | ||
| * wiberg_lowdin_indices | ||
| * dipole_polarizabilities | ||
| * Spec: wb97x-d/def2-tzvpp/ddx-water | ||
| * basis: def2-tzvpp | ||
| * implicit_solvent: {'ddx_model': 'pcm', 'ddx_radii_scaling': 1.1, 'ddx_radii_set': 'uff', 'ddx_solvent_epsilon': 78.4, 'ddx_solvent': 'water'} | ||
| * keywords: {'dft_spherical_points': 590, 'dft_radial_points': 99} | ||
| * maxiter: 200 | ||
| * method: wb97x-d | ||
| * program: psi4 | ||
| * SCF properties: | ||
| * dipole | ||
| * quadrupole | ||
| * lowdin_charges | ||
| * mulliken_charges | ||
| * mbis_charges | ||
| * mayer_indices | ||
| * wiberg_lowdin_indices | ||
| * dipole_polarizabilities |
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submissions/2024-10-11-MLPepper-RECAP-Optimized-Fragments-Add-Iodines-v1.0/basic_env.yml
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| name: qc-submit | ||
| channels: | ||
| - conda-forge | ||
| - defaults | ||
| dependencies: | ||
| - python=3.11 | ||
| - pip | ||
| - qcportal=0.53 | ||
| - openff-qcsubmit=0.50.3 | ||
| - openff-toolkit | ||
| - ca-certificates | ||
| - certifi | ||
| - openssl | ||
| - nglview | ||
| prefix: /mnt/nfs/home/nca121/mambaforge/envs/qc-submit |
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