rowan-python 1.1.9__tar.gz → 1.1.11__tar.gz

rowan_python-1.1.11/.envrc

@@ -0,0 +1,7 @@
+watch_file pixi.lock
+eval "$(pixi shell-hook -e dev)"
+
+if [ -f .env ]; then
+  watch_file .env
+  set -a && source .env && set +a
+fi

{rowan_python-1.1.9 → rowan_python-1.1.11}/.github/workflows/python-publish.yml

@@ -21,6 +21,12 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
+    - name: Skip if running with act
+      if: ${{ env.ACT == 'true' }}
+      run: |
+        echo "Skipping job because we're in act"
+        exit 1
+
     - uses: actions/checkout@v3
     - name: Set up Python
       uses: actions/setup-python@v3

rowan_python-1.1.11/.github/workflows/test.yml

@@ -0,0 +1,33 @@
+name: Pytest Dev
+
+on:
+  pull_request:
+  push:
+    branches:
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        python-version: ["3.13"]
+        os: [ubuntu-latest]
+
+    name: Python ${{ matrix.os }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: prefix-dev/setup-pixi@v0.8.7
+        with:
+          pixi-version: v0.45.0
+          cache: true
+          environments: dev
+
+      - run: pixi run fmt
+      - run: pixi run lint
+      - run: pixi run types

rowan_python-1.1.11/.gitignore

@@ -0,0 +1,200 @@
+# Ignore environment file with ROWAN_API_KEY
+.env
+
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+.vscode/
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+
+# Pixi
+.pixi
+
+# psi4 crap
+timer.dat
+psi*.clean
+
+*.CP
+*.CPC
+
+*.lprof
+
+# pyscf
+pyscf.chk
+local/
+
+.pixi/
+
+cyp/

rowan_python-1.1.11/.pre-commit-config.yaml

@@ -0,0 +1,36 @@
+# Exclude .pixi, data, and patches
+exclude: '(.pixi|\.dat$|\.patch$)'
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0  # this is optional, use `pre-commit autoupdate` to get the latest rev!
+  hooks:
+    - id: check-yaml
+    - id: check-toml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+
+- repo: local
+  hooks:
+  - id: ruff
+    name: ruff-format
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run fmt
+    types: [python]
+    pass_filenames: false
+
+  - id: ruff
+    name: ruff-check
+    stages: [pre-commit, pre-push]
+    language: system
+    entry: pixi run lint
+    types: [python]
+    pass_filenames: false
+
+  - id: Mypy
+    name: mypy
+    stages: [pre-commit]
+    language: system
+    entry: pixi run types
+    types: [python]
+    pass_filenames: false

{rowan_python-1.1.9 → rowan_python-1.1.11}/PKG-INFO

@@ -1,17 +1,17 @@
 Metadata-Version: 2.4
 Name: rowan-python
-Version: 1.1.9
+Version: 1.1.11
 Summary: Rowan Python Library
 Project-URL: Homepage, https://github.com/rowansci/rowan-client
 Project-URL: Bug Tracker, https://github.com/rowansci/rowan-client/issues
 Author-email: Corin Wagen <corin@rowansci.com>
 License-File: LICENSE
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 Requires-Dist: httpx
 Requires-Dist: nest-asyncio
 Requires-Dist: rdkit
 Requires-Dist: setuptools
-Requires-Dist: stjames>=0.0.62
+Requires-Dist: stjames>=0.0.83
 Description-Content-Type: text/markdown
 
 # Rowan Python Library
@@ -28,6 +28,11 @@ The Rowan Python library provides convenient access to the Rowan API from applic
 
 The documentation is available [here](https://docs.rowansci.com/python-api).
 
+## Running examples
+
+To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.
+If running the examples in a cloned version of the repository, you can add your api key to a local `.env` file, which will automatically be loaded into the environment by direnv (if installed).
+
 
 ## Issues
 

{rowan_python-1.1.9 → rowan_python-1.1.11}/README.md

@@ -12,6 +12,11 @@ The Rowan Python library provides convenient access to the Rowan API from applic
 
 The documentation is available [here](https://docs.rowansci.com/python-api).
 
+## Running examples
+
+To run the examples, you will need to set your ROWAN_API_KEY environment variable or set it directly in the script.
+If running the examples in a cloned version of the repository, you can add your api key to a local `.env` file, which will automatically be loaded into the environment by direnv (if installed).
+
 
 ## Issues
 

rowan_python-1.1.11/examples/bde.py

@@ -0,0 +1,34 @@
+"""
+Calculate the Bond-Dissociation Energy (BDE) of a molecule using the Rowan API.
+
+| Calculation |   Initial    |    Final     |          Single        | Optimizes  |
+| Mode        | Optimization | Optimization |          Point         | Fragments? |
+|-------------|--------------|--------------|------------------------|------------|
+| Reckless    |              |    GFN-FF    |        GFN2-xTB        |     No     |
+| Rapid       |              |   GFN2-xTB   |        r²SCAN-3c       |     Yes    |
+| Careful     |              |   r²SCAN-3c  |        ωB97X-3c        |     Yes    |
+| Meticulous  |  r²SCAN-3c   |   ωB97X-3c   | ωB97M-D3BJ/def2-TZVPPD |     Yes    |
+
+Rapid is recommended for most work.
+
+See documentation at: https://docs.rowansci.com/science/workflows/bond-dissociation-energy
+"""
+
+import json
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.compute(
+    Molecule.from_smiles("CCCC"),
+    workflow_type="bde",
+    name="Butane BDE",
+    mode="reckless",
+    all_CH=True,
+)
+
+print(json.dumps(result, indent=4))

rowan_python-1.1.11/examples/conformers.py

@@ -0,0 +1,36 @@
+"""
+Calculate the conformers of a molecule using the Rowan API.
+
+| Mode                                          | Reckless | Rapid | Careful | Meticulous |
+|-----------------------------------------------|----------|-------|---------|------------|
+| Conformer generation program                  | RDKit    | RDKit | CREST   | CREST      |
+| Level of theory used for conformer generation | MMFF     | MMFF  | GFN-FF  | GFN2-xTB   |
+| CREST Mode                                    |          |       | quick   | normal     |
+| ETKDG number of initial conformers            | 200      | 300   |         |            |
+| Initial energy cutoff (kcal/mol)              | 10       | 15    | 10      | 15         |
+| RMSD similarity cutoff (Å)                    | 0.25     | 0.10  | 0.00    | 0.00       |
+| xTB screening max number of conformers        | 50       | 100   | 150     | 500        |
+| Final energy cutoff (kcal/mol)                | 5        | 5     | 5       | 10         |
+
+Rapid is recommended for most work.
+
+See documentation at: https://docs.rowansci.com/science/workflows/conformers
+"""
+
+import json
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.compute(
+    Molecule.from_smiles("CCOCC"),
+    workflow_type="conformers",
+    name="Diethyl ether conformers",
+    mode="reckless",
+)
+
+print(json.dumps(result, indent=4))

rowan_python-1.1.11/examples/multistage_opt.py

@@ -0,0 +1,21 @@
+from pprint import pprint
+
+import stjames
+
+import rowan
+
+# Set ROWAN_API_KEY environment variable to your API key or set rowan.api_key directly
+# rowan.api_key = "rowan-sk..."
+
+# load molecule by SMILES (stjames can load a variety of file formats)
+molecule = stjames.Molecule.from_smiles("C1CCC1")  # cyclobutane
+
+# run calculation remotely and return result
+result = rowan.compute(
+    molecule,
+    workflow_type="multistage_opt",
+    name="Multistage optimization cyclobutane",
+    mode="reckless",
+)
+
+pprint(result)

rowan_python-1.1.11/examples/optimization.py

@@ -0,0 +1,27 @@
+"""
+Run an optimization calculation on a molecule using Rowan.
+
+See documentation at: https://docs.rowansci.com/science/quantum-chemistry/geometry-optimization
+"""
+
+import json
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.compute(
+    Molecule.from_smiles("O"),
+    workflow_type="basic_calculation",
+    name="Water Optimization",
+    settings={
+        "method": "GFN2-xTB",
+        "tasks": ["optimize"],
+    },
+    engine="xtb",
+)
+
+print(json.dumps(result, indent=4))

rowan_python-1.1.11/examples/pka.py

@@ -0,0 +1,30 @@
+"""
+Calculate the pKa of the conjugate acid of pyridine using the Rowan API.
+
+Experimental value ≈5.23
+
+See documentiation at: https://docs.rowansci.com/science/workflows/pka
+and preprint at: https://rowansci.com/publications/pka-prediction
+"""
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.compute(
+    Molecule.from_smiles("n1ccccc1"),
+    workflow_type="pka",
+    name="Pyridine pKa",
+    mode="reckless",
+)
+
+logfile = result["object_logfile"]
+strongest_base = result["object_data"]["strongest_base"]
+
+print(f"""\
+{logfile}
+
+pKa of conjugate acid: {strongest_base:.2f}""")

rowan_python-1.1.11/examples/scan.py

@@ -0,0 +1,34 @@
+"""
+Run an scan calculation on a molecule using Rowan.
+
+See documentation at: https://docs.rowansci.com/science/workflows/scan
+"""
+
+import json
+
+from stjames import Molecule
+
+import rowan
+
+# rowan.api_key = ""
+
+# Run calculation remotely
+result = rowan.compute(
+    Molecule.from_smiles("O"),
+    workflow_type="scan",
+    name="Water Angle scan",
+    scan_settings={
+        "type": "angle",
+        "atoms": [2, 1, 3],  # 1-indexed
+        "start": 100,
+        "stop": 110,
+        "num": 5,
+    },
+    calc_settings={
+        "method": "GFN2-xTB",
+        "tasks": ["optimize"],
+    },
+    calc_engine="xtb",
+)
+
+print(json.dumps(result, indent=4))