aerosolprops 0.1.0__tar.gz

aerosolprops-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 The aerosolprops developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

aerosolprops-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: aerosolprops
+Version: 0.1.0
+Summary: Structure-derived pure-component properties for atmospheric organic aerosol: vapour pressures and boiling points by group contribution
+Author: Fan Zhang
+License: MIT
+Project-URL: Homepage, https://github.com/openEarthModelling/aerosolprops
+Project-URL: Repository, https://github.com/openEarthModelling/aerosolprops
+Project-URL: Changelog, https://github.com/openEarthModelling/aerosolprops/blob/main/CHANGELOG.md
+Keywords: atmospheric chemistry,aerosol,SOA,vapour pressure,boiling point,group contribution,RDKit,thermo
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: thermo>=0.6.1
+Requires-Dist: rdkit>=2023.9
+Provides-Extra: test
+Requires-Dist: pytest>=7.0; extra == "test"
+Provides-Extra: docs
+Requires-Dist: mkdocs>=1.5; extra == "docs"
+Requires-Dist: mkdocs-material>=9.0; extra == "docs"
+Dynamic: license-file
+
+# aerosolprops
+
+[![CI](https://github.com/openEarthModelling/aerosolprops/actions/workflows/ci.yml/badge.svg)](https://github.com/openEarthModelling/aerosolprops/actions/workflows/ci.yml)
+
+Structure-derived pure-component properties for atmospheric organic aerosol.
+
+`aerosolprops` is a modern successor to the pure-component property methods of
+[UManSysProp](https://github.com/loftytopping/UManSysProp_public)
+(Topping et al., GMD 9, 899–911, 2016), rebuilt on
+[RDKit](https://www.rdkit.org/) as the structure engine and following the
+conventions of the [`thermo`](https://github.com/CalebBell/thermo) package
+family: strict SI units, estimators as pure functions of group counts where
+possible, and failures that return `None` rather than raise.
+
+**Status: pre-alpha.** The repository currently contains the packaging
+skeleton, CI, documentation scaffold, the structure/topology foundation
+layers, and the first estimator (SIMPOL.1). The remaining methods below
+land one at a time, each with coefficients entered from the published
+papers and tests against literature values.
+
+## Methods (v0.1)
+
+| Method | Property | Status | Reference |
+|---|---|---|---|
+| SIMPOL.1 | Vapour pressure | implemented | Pankow & Asher, [ACP 8, 2773 (2008)](https://doi.org/10.5194/acp-8-2773-2008) |
+| EVAPORATION | Vapour pressure | implemented | Compernolle et al., [ACP 11, 9431 (2011)](https://doi.org/10.5194/acp-11-9431-2011) |
+| Nannoolal Part 1 (+ SOA extension groups) | Normal boiling point | implemented | Nannoolal et al., [FPE 226, 45 (2004)](https://doi.org/10.1016/j.fluid.2004.09.001); Compernolle et al., [ACP 10, 6271 (2010)](https://doi.org/10.5194/acp-10-6271-2010) |
+| Nannoolal Part 3 | Vapour pressure | implemented | Nannoolal et al., [FPE 269, 117 (2008)](https://doi.org/10.1016/j.fluid.2008.04.020) |
+| Myrdal–Yalkowsky (+ H-bonding extension) | Vapour pressure | implemented | Myrdal & Yalkowsky, [IECR 36, 2494 (1997)](https://doi.org/10.1021/ie950242l); Compernolle et al., [ACP 10, 6271 (2010)](https://doi.org/10.5194/acp-10-6271-2010) |
+
+Boiling points used as inputs (by Myrdal–Yalkowsky and Nannoolal Part 3) can
+come from the self-implemented Nannoolal Part 1 route, from `thermo`'s
+built-in Joback method, or from experimental data — `aerosolprops` does **not**
+reimplement Joback.
+
+## Installation
+
+```bash
+pip install aerosolprops
+```
+
+RDKit and `thermo` are required dependencies.
+
+## Design notes
+
+- **Units are strictly SI** (Pa, K, mol); property failures return `None`.
+- **RDKit is the structure engine and a required dependency.** It is
+  imported lazily, and estimators ultimately consume group-count
+  dictionaries — the same interface `thermo` uses for its own
+  RDKit-optional group-contribution methods — so pieces remain extractable
+  upstream.
+- **No molecular descriptors.** Every method needs only 2D graph quantities:
+  SMARTS substructure counts, ring perception, composition, and a few
+  connectivity queries. No fingerprints, no 3D, no descriptor packages.
+- **No home-grown graph algorithms.** The graph primitives (connected
+  components, ring distances, neighbour queries) are RDKit built-ins;
+  `aerosolprops.topology` only wraps them. What is method-specific is the
+  translation of paper semantics (e.g. SIMPOL.1 "acid-side carbons",
+  EVAPORATION "in-chain oxygen") onto those primitives.
+- **`thermo` compatibility.** aerosolprops hard-depends on `thermo` and follows
+  its group-contribution conventions (`{group_id: coefficient record}`
+  catalogues, counts-based static estimators, Joback-style one-time
+  fragmenting wrappers). Where a method's counting semantics do not fit
+  `thermo`'s mutually-exclusive SMARTS partition (SIMPOL.1's groups overlap
+  and replace one another additively), aerosolprops ships its own fragmenter
+  but keeps the same interface, so pieces can still be contributed upstream
+  with minimal rework.
+
+## Licensing and data provenance
+
+`aerosolprops` is MIT-licensed. Coefficients are entered from the published
+papers cited above (facts, not copyrightable expression), and SMARTS
+patterns are authored from the group definitions in those papers.
+UManSysProp is used **only** as a behavioural test oracle during development;
+no code or data files are copied from it.
+
+## Development
+
+```bash
+uv venv && uv pip install -e ".[test,docs]"
+pytest                        # unit tests + doctests
+mkdocs serve                  # documentation
+```
+
+CI runs the full test matrix (with doctests) on Linux/macOS/Windows for
+Python 3.9–3.14, plus a strict docs build.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

aerosolprops-0.1.0/README.md

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+# aerosolprops
+
+[![CI](https://github.com/openEarthModelling/aerosolprops/actions/workflows/ci.yml/badge.svg)](https://github.com/openEarthModelling/aerosolprops/actions/workflows/ci.yml)
+
+Structure-derived pure-component properties for atmospheric organic aerosol.
+
+`aerosolprops` is a modern successor to the pure-component property methods of
+[UManSysProp](https://github.com/loftytopping/UManSysProp_public)
+(Topping et al., GMD 9, 899–911, 2016), rebuilt on
+[RDKit](https://www.rdkit.org/) as the structure engine and following the
+conventions of the [`thermo`](https://github.com/CalebBell/thermo) package
+family: strict SI units, estimators as pure functions of group counts where
+possible, and failures that return `None` rather than raise.
+
+**Status: pre-alpha.** The repository currently contains the packaging
+skeleton, CI, documentation scaffold, the structure/topology foundation
+layers, and the first estimator (SIMPOL.1). The remaining methods below
+land one at a time, each with coefficients entered from the published
+papers and tests against literature values.
+
+## Methods (v0.1)
+
+| Method | Property | Status | Reference |
+|---|---|---|---|
+| SIMPOL.1 | Vapour pressure | implemented | Pankow & Asher, [ACP 8, 2773 (2008)](https://doi.org/10.5194/acp-8-2773-2008) |
+| EVAPORATION | Vapour pressure | implemented | Compernolle et al., [ACP 11, 9431 (2011)](https://doi.org/10.5194/acp-11-9431-2011) |
+| Nannoolal Part 1 (+ SOA extension groups) | Normal boiling point | implemented | Nannoolal et al., [FPE 226, 45 (2004)](https://doi.org/10.1016/j.fluid.2004.09.001); Compernolle et al., [ACP 10, 6271 (2010)](https://doi.org/10.5194/acp-10-6271-2010) |
+| Nannoolal Part 3 | Vapour pressure | implemented | Nannoolal et al., [FPE 269, 117 (2008)](https://doi.org/10.1016/j.fluid.2008.04.020) |
+| Myrdal–Yalkowsky (+ H-bonding extension) | Vapour pressure | implemented | Myrdal & Yalkowsky, [IECR 36, 2494 (1997)](https://doi.org/10.1021/ie950242l); Compernolle et al., [ACP 10, 6271 (2010)](https://doi.org/10.5194/acp-10-6271-2010) |
+
+Boiling points used as inputs (by Myrdal–Yalkowsky and Nannoolal Part 3) can
+come from the self-implemented Nannoolal Part 1 route, from `thermo`'s
+built-in Joback method, or from experimental data — `aerosolprops` does **not**
+reimplement Joback.
+
+## Installation
+
+```bash
+pip install aerosolprops
+```
+
+RDKit and `thermo` are required dependencies.
+
+## Design notes
+
+- **Units are strictly SI** (Pa, K, mol); property failures return `None`.
+- **RDKit is the structure engine and a required dependency.** It is
+  imported lazily, and estimators ultimately consume group-count
+  dictionaries — the same interface `thermo` uses for its own
+  RDKit-optional group-contribution methods — so pieces remain extractable
+  upstream.
+- **No molecular descriptors.** Every method needs only 2D graph quantities:
+  SMARTS substructure counts, ring perception, composition, and a few
+  connectivity queries. No fingerprints, no 3D, no descriptor packages.
+- **No home-grown graph algorithms.** The graph primitives (connected
+  components, ring distances, neighbour queries) are RDKit built-ins;
+  `aerosolprops.topology` only wraps them. What is method-specific is the
+  translation of paper semantics (e.g. SIMPOL.1 "acid-side carbons",
+  EVAPORATION "in-chain oxygen") onto those primitives.
+- **`thermo` compatibility.** aerosolprops hard-depends on `thermo` and follows
+  its group-contribution conventions (`{group_id: coefficient record}`
+  catalogues, counts-based static estimators, Joback-style one-time
+  fragmenting wrappers). Where a method's counting semantics do not fit
+  `thermo`'s mutually-exclusive SMARTS partition (SIMPOL.1's groups overlap
+  and replace one another additively), aerosolprops ships its own fragmenter
+  but keeps the same interface, so pieces can still be contributed upstream
+  with minimal rework.
+
+## Licensing and data provenance
+
+`aerosolprops` is MIT-licensed. Coefficients are entered from the published
+papers cited above (facts, not copyrightable expression), and SMARTS
+patterns are authored from the group definitions in those papers.
+UManSysProp is used **only** as a behavioural test oracle during development;
+no code or data files are copied from it.
+
+## Development
+
+```bash
+uv venv && uv pip install -e ".[test,docs]"
+pytest                        # unit tests + doctests
+mkdocs serve                  # documentation
+```
+
+CI runs the full test matrix (with doctests) on Linux/macOS/Windows for
+Python 3.9–3.14, plus a strict docs build.
+
+## License
+
+MIT — see [LICENSE](LICENSE).

aerosolprops-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=64"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "aerosolprops"
+version = "0.1.0"
+description = "Structure-derived pure-component properties for atmospheric organic aerosol: vapour pressures and boiling points by group contribution"
+readme = "README.md"
+requires-python = ">=3.9"
+license = { text = "MIT" }
+authors = [{ name = "Fan Zhang" }]
+keywords = [
+    "atmospheric chemistry",
+    "aerosol",
+    "SOA",
+    "vapour pressure",
+    "boiling point",
+    "group contribution",
+    "RDKit",
+    "thermo",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Atmospheric Science",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+dependencies = [
+    "thermo>=0.6.1",
+    "rdkit>=2023.9",
+]
+
+[project.optional-dependencies]
+test = ["pytest>=7.0"]
+docs = ["mkdocs>=1.5", "mkdocs-material>=9.0"]
+
+[project.urls]
+Homepage = "https://github.com/openEarthModelling/aerosolprops"
+Repository = "https://github.com/openEarthModelling/aerosolprops"
+Changelog = "https://github.com/openEarthModelling/aerosolprops/blob/main/CHANGELOG.md"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+addopts = "--doctest-modules -q"
+testpaths = ["src", "tests"]

aerosolprops-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

aerosolprops-0.1.0/src/aerosolprops/__init__.py

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+# SPDX-License-Identifier: MIT
+"""Structure-derived pure-component properties for atmospheric organic
+aerosol.
+
+Successor to the pure-component property methods of UManSysProp
+(Topping et al., Geosci. Model Dev. 9, 899-911, 2016), rebuilt on RDKit as
+the structure engine and following the conventions of the ``thermo``
+package family: strict SI units (Pa, K, mol), estimators as pure functions
+of group counts where possible, and failures returned as ``None``.
+
+Method coverage for v0.1:
+
+- SIMPOL.1 vapour pressure (Pankow & Asher, ACP 8, 2773, 2008) —
+  implemented (see :class:`aerosolprops.vapour_pressure.SIMPOL1`)
+- EVAPORATION vapour pressure (Compernolle et al., ACP 11, 9431, 2011) —
+  implemented (see :class:`aerosolprops.vapour_pressure.EVAPORATION`)
+- Nannoolal Part 1 normal boiling point (Nannoolal et al., FPE 226, 45,
+  2004), including the SOA extension groups of Compernolle et al. (ACP 10,
+  6271, 2010) — implemented (see
+  :class:`aerosolprops.boiling_point.NannoolalBP`)
+- Nannoolal Part 3 vapour pressure (Nannoolal et al., FPE 269, 117, 2008) —
+  implemented (see :class:`aerosolprops.vapour_pressure.NannoolalVP`)
+- Myrdal-Yalkowsky vapour pressure (Myrdal & Yalkowsky, IECR 36, 2494,
+  1997) with the hydrogen-bonding extension of Compernolle et al. (2010) —
+  implemented (see :class:`aerosolprops.vapour_pressure.MyrdalYalkowsky`)
+
+Boiling-point inputs may instead come from ``thermo``'s built-in Joback
+method or from experimental data; aerosolprops does not reimplement Joback.
+
+RDKit is a required dependency but is imported lazily: importing this
+package pulls in neither RDKit nor ``thermo``'s group-contribution
+machinery. Estimators consume plain group-count dictionaries — the same
+interface ``thermo`` uses for its own RDKit-optional group-contribution
+methods — so pieces remain extractable upstream.
+"""
+
+__version__ = "0.1.0.dev0"
+
+from . import (
+    boiling_point,
+    fragmentation,
+    methods,
+    structure,
+    topology,
+    vapour_pressure,
+)
+
+__all__ = [
+    "__version__",
+    "boiling_point",
+    "fragmentation",
+    "methods",
+    "structure",
+    "topology",
+    "vapour_pressure",
+]