chython 1.68__tar.gz → 3.0__tar.gz

chython-3.0/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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+
+
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+License, supplemented by the additional permissions listed below.
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chython-3.0/MANIFEST.in

@@ -0,0 +1,14 @@
+# What an sdist needs beyond the installed package, i.e. what it takes to BUILD rather than to run.
+#
+# `setup.py` cythonizes from source, so the .pyx modules and the .pxi layers they include must be in
+# the sdist or an install from it cannot compile.  `build_inchi.py` likewise: setup.py imports it.
+recursive-include chython *.pyx *.pxi
+include build_inchi.py
+
+# Generated C is excluded on purpose.  It is checked in for the developer loop, but shipping it lets
+# an sdist install compile a stale translation unit against fresh .pyx sources without saying so.
+recursive-exclude chython *.c
+
+# Nor do built artefacts belong in a source distribution -- that is the failure the migration away
+# from the copy-back build removed, and an sdist is the other door into it.
+recursive-exclude chython *.so *.pyd *.dylib *.dll

chython-3.0/PKG-INFO

@@ -0,0 +1,203 @@
+Metadata-Version: 2.4
+Name: chython
+Version: 3.0
+Summary: Library for processing molecules and reactions in python way
+Author-email: Ramil Nugmanov <nougmanoff@protonmail.com>
+License-Expression: LGPL-3.0-or-later
+Project-URL: homepage, https://github.com/chython/chython
+Project-URL: documentation, https://chython.readthedocs.io
+Classifier: Environment :: Plugins
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3 :: Only
+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
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: quickjs-ng>=0.16
+Provides-Extra: ml
+Requires-Dist: numpy>=1.21.0; extra == "ml"
+Provides-Extra: mapping
+Requires-Dist: numpy>=1.21.0; extra == "mapping"
+Requires-Dist: onnxruntime>=1.16; extra == "mapping"
+Requires-Dist: chython-rxnmap>=2.0; extra == "mapping"
+Provides-Extra: rdkit
+Requires-Dist: rdkit>=2025.9; extra == "rdkit"
+Provides-Extra: extra-clean2d
+Requires-Dist: jpype1>=1.6.0; extra == "extra-clean2d"
+Requires-Dist: openbabel-wheel>=3.1.1.22; extra == "extra-clean2d"
+Requires-Dist: epam.indigo>=1.45; extra == "extra-clean2d"
+Provides-Extra: extra-clean3d
+Requires-Dist: cdpkit>=1.2.3; extra == "extra-clean3d"
+Provides-Extra: iupac
+Requires-Dist: openclatura>=0.2; python_version >= "3.11" and extra == "iupac"
+Dynamic: license-file
+
+<p align="center">
+  <img src="docs/logo256.png" width="256" alt="chython logo"/>
+</p>
+
+<h1 align="center">Chython [ˈkʌɪθ(ə)n]</h1>
+
+<p align="center">
+  <a href="https://pypi.org/project/chython/"><img src="https://img.shields.io/pypi/v/chython.svg" alt="PyPI version"/></a>
+  <a href="https://pypi.org/project/chython/"><img src="https://img.shields.io/pypi/pyversions/chython.svg" alt="Python versions"/></a>
+  <a href="https://github.com/chython/chython/blob/master/LICENSE"><img src="https://img.shields.io/pypi/l/chython.svg" alt="License: LGPLv3"/></a>
+  <a href="https://chython.readthedocs.io"><img src="https://img.shields.io/readthedocs/chython.svg" alt="Documentation"/></a>
+  <a href="https://app.codecov.io/gh/chython/chython"><img src="https://img.shields.io/codecov/c/github/chython/chython/master?label=python%20coverage" alt="Coverage of the Python layers"/></a>
+</p>
+
+Library for processing molecules and reactions in a Python way.
+
+## Features
+
+**File formats**
+
+- Read and write MDL RDF/RXN and SDF/MOL (V2000 and V3000, including atom parity and enhanced stereo), Marvin MRV, CML, SMILES, and InChI with InChIKey (InChI Trust library)
+- Read SMARTS and SMIRKS, Tripos MOL2, PDBx/mmCIF, legacy PDB, XYZ, and IUPAC names through OPSIN
+- Compact binary (de)serialization — `pach` for a wire record, `mol.to_bytes()` for the arena buffer — and full pickle support
+- A coordinate format hands back a record of atoms and coordinates rather than a molecule, because it states no bond order: `build_molecule()` places the atoms, `perceive_bonds()` reads the connectivity out of a geometry, `saturate()` raises the orders, and all three are calls the caller makes
+
+**Input is unreliable by default**
+
+A reader stores and logs what a file says — an illegal valence, a nonsense charge, an underivable
+hydrogen count — and never rejects a record for being chemically wrong. Repair is a pipeline you run
+afterwards: `kekule()`, `standardize()`, `fix_resonance()`, `thiele()`.
+
+**Toolkit interoperability**
+
+Conversions build the target structure directly from the graph, so atom order matches
+`atoms()` and stereo is carried over without needing a 2D layout. Each toolkit has one callable in
+`chython.interop` that dispatches on its argument, and the export direction is also a container method.
+
+| Toolkit | API | Requires |
+|---------|-----|----------|
+| RDKit | `mol.to_rdkit()`, `rxn.to_rdkit()`, `chython.interop.rdkit()` both ways | extra `rdkit` |
+| Open Babel | `mol.to_openbabel()` | extra `extra-clean2d` |
+| Indigo | `mol.to_indigo()` | extra `extra-clean2d` |
+| CDK | `mol.to_cdk()` | extra `extra-clean2d` + `cdk.jar` (`CDK_PATH`) |
+| CDPKit | `mol.to_cdpkit()`, and 3D conformers (`conformer_engine = 'cdpkit'`) | extra `extra-clean3d` |
+
+RDKit is the only one of the five with a reaction form.
+
+Allene stereo is not portable through any of these toolkits. Indigo additionally omits
+cis-trans, which it derives from 2D coordinates.
+
+**IUPAC names, both directions**
+
+```python
+from chython import iupac
+
+mol = iupac('ethanol')   # name -> structure, via OPSIN
+mol.iupac                # 'ethanol' -- structure -> name, via openclatura
+```
+
+`iupac()` needs JPype and `opsin.jar` (`OPSIN_PATH`); the `.iupac` property needs the
+`iupac` extra (Python >= 3.11) and returns `None` when the structure cannot be named.
+
+**Molecules**
+
+- Atoms and bonds in one contiguous buffer, addressed by an id that survives editing; edits go through
+  an explicit session (`with mol.edit() as e:`) and derived data is recomputed on seal
+- Standardize, canonicalize, kekulize/aromatize, repair resonance forms, neutralize, put a mobile
+  hydrogen and charge where the canonical order says, check valences
+- Split and decompose salts, expand contracted groups, derive implicit hydrogen counts
+- Many 3D models per molecule in one conformer store
+- Tetrahedral, cis-trans, allene, atropisomer and helical stereo, with CIP labels
+- Descriptors: TPSA, Crippen logP and MR, hydrogen-bond donors and acceptors, rotatable bonds, ring
+  counts, Bertz CT, Randić and Zagreb indices
+- The 166 MACCS structural keys, one-based, and QED with its three published weight sets — both state
+  what they transcribe and neither claims parity with another implementation's bits or score
+- Morgan and linear fingerprints with Tanimoto similarity, as hash sets, folded bit vectors or count
+  vectors, and the graph matrices and distance-derived descriptors — extra `ml`
+- A molecule or a mapped reaction as `int32` arrays for a model: `mol.state_view()`,
+  `rxn.transition_view()` — extra `ml`
+
+**Search**
+
+- Subgraph isomorphism
+- SMARTS parser with chython-specific query semantics, including component grouping for intramolecular
+  patterns
+
+**Reactions**
+
+- Template application from SMIRKS: `mol.react(template)`, or `mol @ other` for a two-component join
+- Reaction enumeration over the shipped reaction corpus
+- Functional and protective group detection and deprotection, with the whole corpus in the docs
+- Sticky fragment / linker enumeration for combinatorial reassembly
+- Atom-to-atom mapping reconstruction against a template corpus: `rxn.reconstruct_mapping()`
+- Reaction-level standardization: each molecule pass once per molecule, plus the passes a loop cannot do
+
+**Depiction**
+
+- 2D coordinate generation, default [SmilesDrawer](https://github.com/reymond-group/smilesDrawer), switchable to RDKit/CDK/Open Babel/Indigo (`clean2d_engine`)
+- SVG and SVGZ output with Jupyter support, and scalar data overlaid on the same scene
+- 3D: a stored conformer as an X3DOM document (`mol.depict3d()`) or a notebook widget (`mol.view3d()`)
+- 3D conformer generation with RDKit or CDPKit (`conformer_engine`)
+
+Full documentation can be found [here](https://chython.readthedocs.io).
+
+## Install
+
+Only Python 3.10+.
+
+```bash
+pip install chython
+```
+
+The default 2D layout backend needs no extra: its JS engine (QuickJS) is a required dependency and
+costs under 2.5 MB.
+
+A plain install has **no numpy**, and that is deliberate — the base install is about 7.5 MB of runtime
+files, small enough for a serverless bundle. Reading and writing every format, `standardize()`,
+`kekule()`, `thiele()`, `canonicalize()`, stereo, substructure matching, template application and
+depiction all work without it. What needs `chython[ml]` is the surface that answers a numpy array: the
+fingerprints, `atom_invariants`, `adjacency_matrix`, `distance_matrix`, the distance-derived graph
+descriptors, `pharmacophore_invariants`, `maccs_keys()`/`maccs_bit_set()` and the ML views. Each of
+those raises an `ImportError` naming the extra when you call it, so nothing fails at import time.
+
+Optional extras, combinable (`chython[rdkit,iupac]`):
+
+| Extra | Enables |
+|-------|---------|
+| `ml` | numpy, and with it fingerprints, atom invariants, the graph matrices, the descriptors built on them and the ML views |
+| `rdkit` | RDKit conversion both ways, RDKit 2D layout and 3D conformers |
+| `iupac` | `molecule.iupac` name generation (Python >= 3.11) |
+| `extra-clean2d` | CDK, Open Babel and Indigo backends (CDK also needs `cdk.jar`) |
+| `extra-clean3d` | CDPKit conformer engine |
+
+## CGRtools
+
+Chython is a fork of [CGRtools](https://github.com/stsouko/CGRtools).
+
+## Copyright
+
+- 2014-2026 Ramil Nugmanov <nougmanoff@protonmail.com> main developer
+
+## Contributors
+
+CGRtools contributors are included too.
+
+- Adelia Fatykhova <adelik21979@gmail.com>
+- Aigul Khakimova
+- Aleksandr Sizov <murkyrussian@gmail.com>
+- Alexandre Varnek <varnek@unistra.fr>
+- Dinar Batyrshin <batyrshin-dinar@mail.ru>
+- Dmitrij Zanadvornykh <zandmitrij@gmail.com>
+- Philippe Gantzer
+- Ravil Mukhametgaleev <sonic-mc@mail.ru>
+- Tagir Akhmetshin <tagirshin@gmail.com>
+- Timur Gimadiev <timur.gimadiev@gmail.com>
+- Timur Madzhidov <tmadzhidov@gmail.com>
+- Zarina Ibragimova

chython-3.0/README.md

@@ -0,0 +1,157 @@
+<p align="center">
+  <img src="docs/logo256.png" width="256" alt="chython logo"/>
+</p>
+
+<h1 align="center">Chython [ˈkʌɪθ(ə)n]</h1>
+
+<p align="center">
+  <a href="https://pypi.org/project/chython/"><img src="https://img.shields.io/pypi/v/chython.svg" alt="PyPI version"/></a>
+  <a href="https://pypi.org/project/chython/"><img src="https://img.shields.io/pypi/pyversions/chython.svg" alt="Python versions"/></a>
+  <a href="https://github.com/chython/chython/blob/master/LICENSE"><img src="https://img.shields.io/pypi/l/chython.svg" alt="License: LGPLv3"/></a>
+  <a href="https://chython.readthedocs.io"><img src="https://img.shields.io/readthedocs/chython.svg" alt="Documentation"/></a>
+  <a href="https://app.codecov.io/gh/chython/chython"><img src="https://img.shields.io/codecov/c/github/chython/chython/master?label=python%20coverage" alt="Coverage of the Python layers"/></a>
+</p>
+
+Library for processing molecules and reactions in a Python way.
+
+## Features
+
+**File formats**
+
+- Read and write MDL RDF/RXN and SDF/MOL (V2000 and V3000, including atom parity and enhanced stereo), Marvin MRV, CML, SMILES, and InChI with InChIKey (InChI Trust library)
+- Read SMARTS and SMIRKS, Tripos MOL2, PDBx/mmCIF, legacy PDB, XYZ, and IUPAC names through OPSIN
+- Compact binary (de)serialization — `pach` for a wire record, `mol.to_bytes()` for the arena buffer — and full pickle support
+- A coordinate format hands back a record of atoms and coordinates rather than a molecule, because it states no bond order: `build_molecule()` places the atoms, `perceive_bonds()` reads the connectivity out of a geometry, `saturate()` raises the orders, and all three are calls the caller makes
+
+**Input is unreliable by default**
+
+A reader stores and logs what a file says — an illegal valence, a nonsense charge, an underivable
+hydrogen count — and never rejects a record for being chemically wrong. Repair is a pipeline you run
+afterwards: `kekule()`, `standardize()`, `fix_resonance()`, `thiele()`.
+
+**Toolkit interoperability**
+
+Conversions build the target structure directly from the graph, so atom order matches
+`atoms()` and stereo is carried over without needing a 2D layout. Each toolkit has one callable in
+`chython.interop` that dispatches on its argument, and the export direction is also a container method.
+
+| Toolkit | API | Requires |
+|---------|-----|----------|
+| RDKit | `mol.to_rdkit()`, `rxn.to_rdkit()`, `chython.interop.rdkit()` both ways | extra `rdkit` |
+| Open Babel | `mol.to_openbabel()` | extra `extra-clean2d` |
+| Indigo | `mol.to_indigo()` | extra `extra-clean2d` |
+| CDK | `mol.to_cdk()` | extra `extra-clean2d` + `cdk.jar` (`CDK_PATH`) |
+| CDPKit | `mol.to_cdpkit()`, and 3D conformers (`conformer_engine = 'cdpkit'`) | extra `extra-clean3d` |
+
+RDKit is the only one of the five with a reaction form.
+
+Allene stereo is not portable through any of these toolkits. Indigo additionally omits
+cis-trans, which it derives from 2D coordinates.
+
+**IUPAC names, both directions**
+
+```python
+from chython import iupac
+
+mol = iupac('ethanol')   # name -> structure, via OPSIN
+mol.iupac                # 'ethanol' -- structure -> name, via openclatura
+```
+
+`iupac()` needs JPype and `opsin.jar` (`OPSIN_PATH`); the `.iupac` property needs the
+`iupac` extra (Python >= 3.11) and returns `None` when the structure cannot be named.
+
+**Molecules**
+
+- Atoms and bonds in one contiguous buffer, addressed by an id that survives editing; edits go through
+  an explicit session (`with mol.edit() as e:`) and derived data is recomputed on seal
+- Standardize, canonicalize, kekulize/aromatize, repair resonance forms, neutralize, put a mobile
+  hydrogen and charge where the canonical order says, check valences
+- Split and decompose salts, expand contracted groups, derive implicit hydrogen counts
+- Many 3D models per molecule in one conformer store
+- Tetrahedral, cis-trans, allene, atropisomer and helical stereo, with CIP labels
+- Descriptors: TPSA, Crippen logP and MR, hydrogen-bond donors and acceptors, rotatable bonds, ring
+  counts, Bertz CT, Randić and Zagreb indices
+- The 166 MACCS structural keys, one-based, and QED with its three published weight sets — both state
+  what they transcribe and neither claims parity with another implementation's bits or score
+- Morgan and linear fingerprints with Tanimoto similarity, as hash sets, folded bit vectors or count
+  vectors, and the graph matrices and distance-derived descriptors — extra `ml`
+- A molecule or a mapped reaction as `int32` arrays for a model: `mol.state_view()`,
+  `rxn.transition_view()` — extra `ml`
+
+**Search**
+
+- Subgraph isomorphism
+- SMARTS parser with chython-specific query semantics, including component grouping for intramolecular
+  patterns
+
+**Reactions**
+
+- Template application from SMIRKS: `mol.react(template)`, or `mol @ other` for a two-component join
+- Reaction enumeration over the shipped reaction corpus
+- Functional and protective group detection and deprotection, with the whole corpus in the docs
+- Sticky fragment / linker enumeration for combinatorial reassembly
+- Atom-to-atom mapping reconstruction against a template corpus: `rxn.reconstruct_mapping()`
+- Reaction-level standardization: each molecule pass once per molecule, plus the passes a loop cannot do
+
+**Depiction**
+
+- 2D coordinate generation, default [SmilesDrawer](https://github.com/reymond-group/smilesDrawer), switchable to RDKit/CDK/Open Babel/Indigo (`clean2d_engine`)
+- SVG and SVGZ output with Jupyter support, and scalar data overlaid on the same scene
+- 3D: a stored conformer as an X3DOM document (`mol.depict3d()`) or a notebook widget (`mol.view3d()`)
+- 3D conformer generation with RDKit or CDPKit (`conformer_engine`)
+
+Full documentation can be found [here](https://chython.readthedocs.io).
+
+## Install
+
+Only Python 3.10+.
+
+```bash
+pip install chython
+```
+
+The default 2D layout backend needs no extra: its JS engine (QuickJS) is a required dependency and
+costs under 2.5 MB.
+
+A plain install has **no numpy**, and that is deliberate — the base install is about 7.5 MB of runtime
+files, small enough for a serverless bundle. Reading and writing every format, `standardize()`,
+`kekule()`, `thiele()`, `canonicalize()`, stereo, substructure matching, template application and
+depiction all work without it. What needs `chython[ml]` is the surface that answers a numpy array: the
+fingerprints, `atom_invariants`, `adjacency_matrix`, `distance_matrix`, the distance-derived graph
+descriptors, `pharmacophore_invariants`, `maccs_keys()`/`maccs_bit_set()` and the ML views. Each of
+those raises an `ImportError` naming the extra when you call it, so nothing fails at import time.
+
+Optional extras, combinable (`chython[rdkit,iupac]`):
+
+| Extra | Enables |
+|-------|---------|
+| `ml` | numpy, and with it fingerprints, atom invariants, the graph matrices, the descriptors built on them and the ML views |
+| `rdkit` | RDKit conversion both ways, RDKit 2D layout and 3D conformers |
+| `iupac` | `molecule.iupac` name generation (Python >= 3.11) |
+| `extra-clean2d` | CDK, Open Babel and Indigo backends (CDK also needs `cdk.jar`) |
+| `extra-clean3d` | CDPKit conformer engine |
+
+## CGRtools
+
+Chython is a fork of [CGRtools](https://github.com/stsouko/CGRtools).
+
+## Copyright
+
+- 2014-2026 Ramil Nugmanov <nougmanoff@protonmail.com> main developer
+
+## Contributors
+
+CGRtools contributors are included too.
+
+- Adelia Fatykhova <adelik21979@gmail.com>
+- Aigul Khakimova
+- Aleksandr Sizov <murkyrussian@gmail.com>
+- Alexandre Varnek <varnek@unistra.fr>
+- Dinar Batyrshin <batyrshin-dinar@mail.ru>
+- Dmitrij Zanadvornykh <zandmitrij@gmail.com>
+- Philippe Gantzer
+- Ravil Mukhametgaleev <sonic-mc@mail.ru>
+- Tagir Akhmetshin <tagirshin@gmail.com>
+- Timur Gimadiev <timur.gimadiev@gmail.com>
+- Timur Madzhidov <tmadzhidov@gmail.com>
+- Zarina Ibragimova