OpenFF Sulfur Optimization Training Coverage Supplement v1.0

README.md

@@ -253,6 +253,7 @@ These are currently used to find a minimum energy conformation of a molecule.
 | `OpenFF Torsion Multiplicity Optimization Training Coverage Supplement v1.0` | [2024-06-20-OpenFF-Torsion-Multiplicity-Optimization-Training-Coverage-Supplement-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-06-20-OpenFF-Torsion-Multiplicity-Optimization-Training-Coverage-Supplement-v1.0) | Additional optimization training data for Sage 2.2.0 proper torsions and new parameters from the torsion multiplicity work | C, Cl, S, O, H, P, N, Br | |
 | `OpenFF Torsion Multiplicity Optimization Benchmarking Coverage Supplement v1.0` | [2024-06-24-OpenFF-Torsion-Multiplicity-Optimization-Benchmarking-Coverage-Supplement-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-06-24-OpenFF-Torsion-Multiplicity-Optimization-Benchmarking-Coverage-Supplement-v1.0) | Additional optimization benchmarking data for Sage 2.2.0 proper torsions and new parameters from the torsion multiplicity work | Cl, H, I, S, O, N, Br, C, P | |
 |`OpenFF Iodine Fragment Opt v1.0` | [2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0) | B3LYP-D3BJ/DZVP optimized conformers for a variety of I-containing fragment molecules | C, O, I, S, F, Br, Cl, N, H ||
+| `OpenFF Sulfur Optimization Training Coverage Supplement v1.0` | [2024-09-11-OpenFF-Sulfur-Optimization-Training-Coverage-Supplement-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-09-11-OpenFF-Sulfur-Optimization-Training-Coverage-Supplement-v1.0) | Additional optimization training data for Sage sulfur and phosphorus parameters | C, S, F, O, H, Cl, Br, P, N | |
 
 
 # TorsionDrive Datasets

submissions/2024-09-11-OpenFF-Sulfur-Optimization-Training-Coverage-Supplement-v1.0/README.md

@@ -0,0 +1,62 @@
+# OpenFF Sulfur Optimization Training Coverage Supplement v1.0
+
+## Description
+
+An optimization data set created to improve the training coverage of sulfonic
+and phosphonic acids, sulfone, sulfonate, sulfinyl, sulfoximine, sulfonamides,
+thioether, and 1,3-thiazole groups. The molecules in this data set were manually
+selected from a subset of the smallest matching structures in the ChEMBL 34
+database.
+
+## General Information
+
+* Date: 2024-09-11
+* Class: OpenFF Optimization Dataset
+* Purpose: Improve coverage in Sage
+* Name: OpenFF Sulfur Optimization Training Coverage Supplement v1.0
+* Number of unique molecules: 129
+* Number of filtered molecules: 0
+* Number of conformers: 899
+* Number of conformers per molecule (min, mean, max): 1, 6.97, 10
+* Mean molecular weight: 218.80
+* Max molecular weight: 493.37
+* Charges: [-2.0, -1.0, 0.0]
+* Dataset submitter: Brent Westbrook
+* Dataset generator: Brent Westbrook
+
+## QCSubmit Generation Pipeline
+
+* `generate-dataset.py`: This script shows how the dataset was prepared from the
+  input file `train.smi`.
+* The list of labels and SMILES pairs in `train.smi` were collected by searching
+  the ChEMBL database for all of the molecules matching the SMIRKS patterns
+  corresponding to the labels in `sulfur.dat`. The code used for all of these
+  steps can be found
+  [here](https://github.com/ntBre/curato/tree/64261e2261e5b3109223c7fbe8ef5d866937fd13).
+
+## QCSubmit Manifest
+
+* `generate-dataset.py`: Script describing dataset generation and submission
+* `input-environment.yaml`: Environment file used to create the Python environment for the script
+* `full-environment.yaml`: Fully-resolved environment used to execute the script
+* `opt.toml`: Experimental [qcaide](https://github.com/ntBre/qcaide) input file
+  for defining variables used throughout the QCA submission process
+* `dataset.json.bz2`: Compressed dataset ready for submission
+* `dataset.pdf`: Visualization of dataset molecules
+* `output.smi`: SMILES strings for dataset molecules
+
+## Metadata
+
+* Elements: {C, S, F, O, H, Cl, Br, P, N}
+* Spec: default
+	* basis: DZVP
+	* implicit_solvent: None
+	* keywords: {}
+	* maxiter: 200
+	* method: B3LYP-D3BJ
+	* program: psi4
+	* SCF properties:
+		* dipole
+		* quadrupole
+		* wiberg_lowdin_indices
+		* mayer_indices

submissions/2024-09-11-OpenFF-Sulfur-Optimization-Training-Coverage-Supplement-v1.0/full-environment.yaml

@@ -0,0 +1,304 @@
+name: qcarchive-user-submit
+channels:
+  - openeye
+  - conda-forge
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+  - zeromq=4.3.5=h59595ed_0
+  - zipp=3.17.0=pyhd8ed1ab_0
+  - zlib=1.2.13=hd590300_5
+  - zlib-ng=2.0.7=h0b41bf4_0
+  - zstandard=0.22.0=py311haa97af0_0
+  - zstd=1.5.5=hfc55251_0
+  - pip:
+      - amberutils==21.0
+      - edgembar==0.2
+      - mmpbsa-py==16.0
+      - packmol-memgen==2023.2.24
+      - pdb4amber==22.0
+      - pymsmt==22.0
+      - pytraj==2.0.6
+      - sander==22.0
+prefix: /home/brent/mambaforge/envs/qcarchive-user-submit