Iodine frag opt (#373)

* adding dataset

* Create README.md

* correctly name notebook and update spec

* adding full env

* Update README.md

* changed to default spec

* Update README.md

* Update README.md

* Update submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/README.md

Co-authored-by: Lily Wang <[email protected]>

* Update submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/README.md

Co-authored-by: Lily Wang <[email protected]>

* Update submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/README.md

Co-authored-by: Lily Wang <[email protected]>

* Update submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/README.md

Co-authored-by: Lily Wang <[email protected]>

* updated dataset description, correctly exported full env

* submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/dataset.json.bz2: convert to Git LFS

---------

Co-authored-by: Lily Wang <[email protected]>
Co-authored-by: Lily Wang <[email protected]>

Author: amcisaac

README.md

@@ -252,6 +252,7 @@ These are currently used to find a minimum energy conformation of a molecule.
 | `OpenFF Torsion Benchmark Supplement Optimization Dataset v1.0` | [2024-04-18-OpenFF-Torsion-Benchmark-Supplement-Optimization-Dataset-v1.0](https://github.com/openforcefield/qca-dataset-submission/tree/master/submissions/2024-04-18-OpenFF-Torsion-Benchmark-Supplement-Optimization-Dataset-v1.0) | Additional optimizations for benchmarking Sage 2.2.0 proper torsions and new parameters from the torsion multiplicity work | H, C, N, O, F, P, S, Cl, Br | |
 | `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 ||
 
 
 # TorsionDrive Datasets

submissions/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/README.md

@@ -0,0 +1,60 @@
+# OpenFF Iodine Fragment Opt v1.0
+
+## Description
+
+A dataset containing fragments of molecules from the Zinc, Enamine 10240, Enamine 50240, and CHEMBL datasets, optimized at the B3LYP-D3BJ/DZVP level of theory. Molecules containing I were fragmented into small fragments. 
+Fragments containing I then had protomers enumerated.
+
+For each resulting molecule, a set of up to 5 conformers were generated by:
+  * generating a set of up to 1000 conformers with a RMS cutoff of 0.5 Å using the OpenEye backend of the OpenFF toolkit
+  * applying ELF conformer selection (max 5 conformers) using OpenEye
+
+
+## General information
+
+* Date: 2024-09-10
+* Class: OpenFF OptimizationDataset
+* Purpose: Geometry optimization for eventual ESP calculation
+* Name: OpenFF Iodine Fragment Opt v1.0
+* Number of unique molecules: 526
+* Number of conformers: 531
+* Number of conformers per molecule (min, mean, max): 1, 1.01, 5
+* Molecular weight (min, mean, max): (155.97, 242.52, 316.94)
+* Charges: [-1.0, 0.0, 1.0, 2.0]
+* Dataset submitter: Alexandra McIsaac
+* Dataset generator: Alexandra McIsaac
+
+
+## QCSubmit generation pipeline
+
+* `generate-dataset.ipynb`: This notebook shows how the dataset was prepared from the input files.
+    * Conformers were generated and selected using OpenEye
+
+
+## QCSubmit Manifest
+
+* `dataset.json.bz2`: Compressed dataset ready for submission
+* `dataset.pdf`: Visualization of dataset molecules
+* `dataset.smi`: Smiles strings for dataset molecules
+* `generate-dataset.ipynb`: Notebook describing dataset generation and submission
+* `enumerated.smi`: Input SMILES
+* `input-environment.yaml`: Environment file used to create Python environment for the notebook
+* `full-environment.yaml`: Fully-resolved environment used to execute the notebook.
+
+
+## Metadata
+
+* Elements: {C, I, Br, Cl, S, N, H, F, O}
+* unique molecules: 526
+* 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/2024-09-10-OpenFF-Iodine-Fragment-Opt-v1.0/dataset.json.bz2

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d324e5dbf3865fbe68e37c2c314ffe423b4c25c2669828bbd0243713920b8e1a
+size 134075