openforcefield · lilyminium · Sep 14, 2024 · Sep 11, 2024 · Sep 13, 2024 · Sep 14, 2024
@@ -252,7 +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 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
 These are currently used perform a complete rotation of one or more selected bonds, where optimizations are performed over a discrete set of angles.

@@ -0,0 +1,61 @@
+# 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 selected
+from 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
@@ -0,0 +1,304 @@
+name: qcarchive-user-submit
+channels:
+  - openeye
+  - conda-forge
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - ambertools=23.3=py311h9fea076_6
+  - annotated-types=0.6.0=pyhd8ed1ab_0
+  - anyio=4.2.0=pyhd8ed1ab_0
+  - apsw=3.46.0.0=py311h3ea06b8_0
+  - argcomplete=3.2.2=pyhd8ed1ab_0
+  - argon2-cffi=23.1.0=pyhd8ed1ab_0
+  - argon2-cffi-bindings=21.2.0=py311h459d7ec_4
+  - arpack=3.8.0=nompi_h0baa96a_101
+  - arrow=1.3.0=pyhd8ed1ab_0
+  - asttokens=2.4.1=pyhd8ed1ab_0
+  - astunparse=1.6.3=pyhd8ed1ab_0
+  - async-lru=2.0.4=pyhd8ed1ab_0
+  - attrs=23.2.0=pyh71513ae_0
+  - babel=2.14.0=pyhd8ed1ab_0
+  - basis_set_exchange=0.9.1=pyhd8ed1ab_0
+  - beautifulsoup4=4.12.3=pyha770c72_0
+  - bleach=6.1.0=pyhd8ed1ab_0
+  - blosc=1.21.5=h0f2a231_0
+  - brotli=1.1.0=hd590300_1
+  - brotli-bin=1.1.0=hd590300_1
+  - brotli-python=1.1.0=py311hb755f60_1
+  - bson=0.5.9=py_0
+  - bzip2=1.0.8=hd590300_5
+  - c-ares=1.26.0=hd590300_0
+  - c-blosc2=2.13.1=hb4ffafa_0
+  - ca-certificates=2024.6.2=hbcca054_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cachetools=5.3.2=pyhd8ed1ab_0
+  - cairo=1.18.0=h3faef2a_0
+  - certifi=2024.6.2=pyhd8ed1ab_0
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+  - charset-normalizer=3.3.2=pyhd8ed1ab_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - comm=0.2.1=pyhd8ed1ab_0
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+  - cycler=0.12.1=pyhd8ed1ab_0
+  - debugpy=1.8.0=py311hb755f60_1
+  - decorator=5.1.1=pyhd8ed1ab_0
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+  - entrypoints=0.4=pyhd8ed1ab_0
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+  - executing=2.0.1=pyhd8ed1ab_0
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+  - font-ttf-ubuntu=0.83=h77eed37_1
+  - fontconfig=2.14.2=h14ed4e7_0
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+  - fonttools=4.47.2=py311h459d7ec_0
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+  - gettext=0.21.1=h27087fc_0
+  - greenlet=3.0.3=py311hb755f60_0
+  - hdf4=4.2.15=h2a13503_7
+  - hdf5=1.14.3=nompi_h4f84152_100
+  - icu=73.2=h59595ed_0
+  - idna=3.6=pyhd8ed1ab_0
+  - importlib-metadata=7.0.1=pyha770c72_0
+  - importlib_metadata=7.0.1=hd8ed1ab_0
+  - importlib_resources=6.1.1=pyhd8ed1ab_0
+  - iniconfig=2.0.0=pyhd8ed1ab_0
+  - ipykernel=6.29.0=pyhd33586a_0
+  - ipython=8.20.0=pyh707e725_0
+  - ipywidgets=8.1.1=pyhd8ed1ab_0
+  - isoduration=20.11.0=pyhd8ed1ab_0
+  - jedi=0.19.1=pyhd8ed1ab_0
+  - jinja2=3.1.3=pyhd8ed1ab_0
+  - joblib=1.3.2=pyhd8ed1ab_0
+  - json5=0.9.14=pyhd8ed1ab_0
+  - jsonpointer=2.4=py311h38be061_3
+  - jsonschema=4.21.1=pyhd8ed1ab_0
+  - jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
+  - jsonschema-with-format-nongpl=4.21.1=pyhd8ed1ab_0
+  - jupyter-lsp=2.2.2=pyhd8ed1ab_0
+  - jupyter_client=8.6.0=pyhd8ed1ab_0
+  - jupyter_core=5.7.1=py311h38be061_0
+  - jupyter_events=0.9.0=pyhd8ed1ab_0
+  - jupyter_server=2.12.5=pyhd8ed1ab_0
+  - jupyter_server_terminals=0.5.2=pyhd8ed1ab_0
+  - jupyterlab=4.0.12=pyhd8ed1ab_0
+  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_0
+  - jupyterlab_server=2.25.2=pyhd8ed1ab_0
+  - jupyterlab_widgets=3.0.9=pyhd8ed1ab_0
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.4.5=py311h9547e67_1
+  - krb5=1.21.2=h659d440_0
+  - lcms2=2.16=hb7c19ff_0
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - lerc=4.0.0=h27087fc_0
+  - libaec=1.1.2=h59595ed_1
+  - libblas=3.9.0=21_linux64_openblas
+  - libboost=1.82.0=h6fcfa73_6
+  - libboost-python=1.82.0=py311h92ebd52_6
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+  - libbrotlidec=1.1.0=hd590300_1
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+  - libcblas=3.9.0=21_linux64_openblas
+  - libcurl=8.5.0=hca28451_0
+  - libdeflate=1.19=hd590300_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=hd590300_2
+  - libexpat=2.5.0=hcb278e6_1
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-ng=13.2.0=h807b86a_4
+  - libgfortran-ng=13.2.0=h69a702a_4
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+  - libglib=2.78.3=h783c2da_0
+  - libgomp=13.2.0=h807b86a_4
+  - libiconv=1.17=hd590300_2
+  - libjpeg-turbo=3.0.0=hd590300_1
+  - liblapack=3.9.0=21_linux64_openblas
+  - libnetcdf=4.9.2=nompi_h9612171_113
+  - libnghttp2=1.58.0=h47da74e_1
+  - libnsl=2.0.1=hd590300_0
+  - libopenblas=0.3.26=pthreads_h413a1c8_0
+  - libpng=1.6.39=h753d276_0
+  - libsodium=1.0.18=h36c2ea0_1
+  - libsqlite=3.46.0=hde9e2c9_0
+  - libssh2=1.11.0=h0841786_0
+  - libstdcxx-ng=13.2.0=h7e041cc_4
+  - libtiff=4.6.0=ha9c0a0a_2
+  - libuuid=2.38.1=h0b41bf4_0
+  - libwebp-base=1.3.2=hd590300_0
+  - libxcb=1.15=h0b41bf4_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libxml2=2.12.4=h232c23b_1
+  - libzip=1.10.1=h2629f0a_3
+  - libzlib=1.2.13=hd590300_5
+  - lz4-c=1.9.4=hcb278e6_0
+  - lzo=2.10=h516909a_1000
+  - markupsafe=2.1.4=py311h459d7ec_0
+  - matplotlib-base=3.8.2=py311h54ef318_0
+  - matplotlib-inline=0.1.6=pyhd8ed1ab_0
+  - mda-xdrlib=0.2.0=pyhd8ed1ab_0
+  - mdtraj=1.9.9=py311h90fe790_1
+  - mistune=3.0.2=pyhd8ed1ab_0
+  - msgpack-python=1.0.7=py311h9547e67_0
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - nbclient=0.8.0=pyhd8ed1ab_0
+  - nbconvert-core=7.14.2=pyhd8ed1ab_0
+  - nbformat=5.9.2=pyhd8ed1ab_0
+  - ncurses=6.5=h59595ed_0
+  - nest-asyncio=1.6.0=pyhd8ed1ab_0
+  - netcdf-fortran=4.6.1=nompi_hacb5139_103
+  - networkx=3.2.1=pyhd8ed1ab_0
+  - nomkl=1.0=h5ca1d4c_0
+  - notebook=7.0.7=pyhd8ed1ab_0
+  - notebook-shim=0.2.3=pyhd8ed1ab_0
+  - numexpr=2.8.8=py311h039bad6_100
+  - numpy=1.26.3=py311h64a7726_0
+  - ocl-icd=2.3.1=h7f98852_0
+  - ocl-icd-system=1.0.0=1
+  - openeye-toolkits=2023.1.1=py311_0
+  - openff-amber-ff-ports=0.0.4=pyhca7485f_0
+  - openff-forcefields=2024.01.0=pyhca7485f_0
+  - openff-interchange=0.3.18=pyhd8ed1ab_0
+  - openff-interchange-base=0.3.18=pyhd8ed1ab_0
+  - openff-models=0.1.1=pyhca7485f_0
+  - openff-qcsubmit=0.50.2=pyhd8ed1ab_0
+  - openff-toolkit=0.15.1=pyhd8ed1ab_0
+  - openff-toolkit-base=0.15.1=pyhd8ed1ab_0
+  - openff-units=0.2.1=pyh1a96a4e_0
+  - openff-utilities=0.1.12=pyhd8ed1ab_0
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+  - openmm=8.1.1=py311h9766050_0
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+  - overrides=7.7.0=pyhd8ed1ab_0
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+  - 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