rdkit-cli 0.1.0__tar.gz

rdkit_cli-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,82 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+  # Allow manual trigger
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Store distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/rdkit-cli
+
+    permissions:
+      id-token: write  # Required for trusted publishing
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch'
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/rdkit-cli
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

rdkit_cli-0.1.0/CHANGELOG.md

@@ -0,0 +1,43 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2026-01-06
+
+### Added
+
+- Initial release with 14 command categories
+- **descriptors**: Compute molecular descriptors (200+ available)
+- **fingerprints**: Generate molecular fingerprints (morgan, maccs, rdkit, atompair, torsion, pattern)
+- **filter**: Filter molecules by substructure, properties, drug-likeness (Lipinski/Veber/Ghose), PAINS
+- **convert**: Convert between molecular file formats (CSV, TSV, SMI, SDF, Parquet)
+- **standardize**: Standardize and canonicalize molecules
+- **similarity**: Similarity search, matrix computation, and clustering
+- **conformers**: Generate and optimize 3D conformers
+- **reactions**: SMIRKS transformations and reaction enumeration
+- **scaffold**: Murcko scaffold extraction and decomposition
+- **enumerate**: Stereoisomer and tautomer enumeration
+- **fragment**: BRICS/RECAP fragmentation and functional group analysis
+- **diversity**: MaxMin diversity picking and diversity analysis
+- **mcs**: Maximum Common Substructure finding
+- **depict**: SVG/PNG molecular depictions (single, batch, grid)
+
+### Features
+
+- Multi-core parallel processing via ProcessPoolExecutor
+- Ninja-style progress display with speed and ETA
+- Support for multiple I/O formats (CSV, TSV, SMI, SDF, Parquet)
+- Automatic format detection from file extensions
+- Lazy imports for fast CLI startup (~0.08s)
+- Comprehensive test suite (182 tests)
+
+### Dependencies
+
+- rdkit>=2024.3.1
+- rich-argparse>=1.4.0
+- pandas>=2.0.0
+- pyarrow>=14.0.0
+- numpy>=1.24.0

rdkit_cli-0.1.0/LICENSE

@@ -0,0 +1,190 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to the Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   Copyright 2026 Johan HG Natter
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

rdkit_cli-0.1.0/PKG-INFO

@@ -0,0 +1,380 @@
+Metadata-Version: 2.4
+Name: rdkit-cli
+Version: 0.1.0
+Summary: A comprehensive CLI tool for RDKit cheminformatics operations
+Project-URL: Homepage, https://github.com/vitruves/rdkit-cli
+Project-URL: Repository, https://github.com/vitruves/rdkit-cli
+Project-URL: Issues, https://github.com/vitruves/rdkit-cli/issues
+Author: Vitruves
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: cheminformatics,chemistry,cli,fingerprints,molecular-descriptors,rdkit
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.24.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pyarrow>=14.0.0
+Requires-Dist: rdkit>=2024.3.1
+Requires-Dist: rich-argparse>=1.4.0
+Provides-Extra: dev
+Requires-Dist: mypy>=1.0.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
+Requires-Dist: pytest>=7.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.1.0; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# rdkit-cli
+
+A comprehensive, high-performance CLI tool wrapping RDKit functionality for cheminformatics workflows.
+
+## Features
+
+- **14 Command Categories**: descriptors, fingerprints, filter, convert, standardize, similarity, conformers, reactions, scaffold, enumerate, fragment, diversity, mcs, depict
+- **Multiple Input/Output Formats**: CSV, TSV, SMI, SDF, Parquet
+- **Parallel Processing**: Efficient multi-core support via ProcessPoolExecutor
+- **Ninja-style Progress**: Real-time progress display with speed and ETA
+
+## Installation
+
+```bash
+pip install rdkit-cli
+```
+
+Or with uv:
+
+```bash
+uv add rdkit-cli
+```
+
+## Quick Start
+
+```bash
+# Compute molecular descriptors
+rdkit-cli descriptors compute -i molecules.csv -o descriptors.csv -d MolWt,MolLogP,TPSA
+
+# Generate fingerprints
+rdkit-cli fingerprints compute -i molecules.csv -o fingerprints.csv --type morgan
+
+# Filter by drug-likeness
+rdkit-cli filter druglike -i molecules.csv -o filtered.csv --rule lipinski
+
+# Standardize molecules
+rdkit-cli standardize -i molecules.csv -o standardized.csv --cleanup --neutralize
+
+# Similarity search
+rdkit-cli similarity search -i library.csv -o hits.csv --query "c1ccccc1" --threshold 0.7
+```
+
+## Commands
+
+### descriptors
+
+Compute molecular descriptors.
+
+```bash
+# List available descriptors
+rdkit-cli descriptors list
+rdkit-cli descriptors list --all
+
+# Compute specific descriptors
+rdkit-cli descriptors compute -i input.csv -o output.csv -d MolWt,MolLogP,TPSA
+
+# Compute all descriptors
+rdkit-cli descriptors compute -i input.csv -o output.csv --all
+```
+
+### fingerprints
+
+Generate molecular fingerprints.
+
+```bash
+# List available fingerprint types
+rdkit-cli fingerprints list
+
+# Compute Morgan fingerprints (default)
+rdkit-cli fingerprints compute -i input.csv -o output.csv --type morgan
+
+# With options
+rdkit-cli fingerprints compute -i input.csv -o output.csv \
+    --type morgan --radius 3 --bits 4096 --use-chirality
+```
+
+Supported types: morgan, maccs, rdkit, atompair, torsion, pattern
+
+### filter
+
+Filter molecules by various criteria.
+
+```bash
+# Substructure filter
+rdkit-cli filter substructure -i input.csv -o output.csv --smarts "c1ccccc1"
+rdkit-cli filter substructure -i input.csv -o output.csv --smarts "c1ccccc1" --exclude
+
+# Property filter
+rdkit-cli filter property -i input.csv -o output.csv --rule "MolWt < 500"
+
+# Drug-likeness filters
+rdkit-cli filter druglike -i input.csv -o output.csv --rule lipinski
+rdkit-cli filter druglike -i input.csv -o output.csv --rule veber
+rdkit-cli filter druglike -i input.csv -o output.csv --rule ghose
+
+# PAINS filter
+rdkit-cli filter pains -i input.csv -o output.csv
+```
+
+### convert
+
+Convert between molecular file formats.
+
+```bash
+# Auto-detect formats from extensions
+rdkit-cli convert -i molecules.csv -o molecules.sdf
+
+# Explicit format specification
+rdkit-cli convert -i molecules.csv -o molecules.smi --out-format smi
+```
+
+Supported formats: csv, tsv, smi, sdf, parquet
+
+### standardize
+
+Standardize and canonicalize molecules.
+
+```bash
+# Basic standardization
+rdkit-cli standardize -i input.csv -o output.csv
+
+# With options
+rdkit-cli standardize -i input.csv -o output.csv \
+    --cleanup --neutralize --fragment-parent
+```
+
+### similarity
+
+Compute molecular similarity.
+
+```bash
+# Similarity search
+rdkit-cli similarity search -i library.csv -o hits.csv \
+    --query "CCO" --threshold 0.7
+
+# Similarity matrix
+rdkit-cli similarity matrix -i molecules.csv -o matrix.csv \
+    --metric tanimoto
+
+# Clustering
+rdkit-cli similarity cluster -i molecules.csv -o clustered.csv \
+    --cutoff 0.5
+```
+
+### conformers
+
+Generate and optimize 3D conformers.
+
+```bash
+# Generate conformers
+rdkit-cli conformers generate -i input.csv -o output.sdf --num 10
+
+# Optimize conformers
+rdkit-cli conformers optimize -i input.sdf -o optimized.sdf --force-field mmff
+```
+
+### reactions
+
+Apply chemical reactions and transformations.
+
+```bash
+# SMIRKS transformation
+rdkit-cli reactions transform -i input.csv -o output.csv \
+    --smirks "[OH:1]>>[O-:1]"
+
+# Reaction enumeration
+rdkit-cli reactions enumerate -i reactants.csv -o products.csv \
+    --template "reaction.rxn"
+```
+
+### scaffold
+
+Extract molecular scaffolds.
+
+```bash
+# Murcko scaffolds
+rdkit-cli scaffold murcko -i input.csv -o scaffolds.csv
+
+# Generic scaffolds
+rdkit-cli scaffold murcko -i input.csv -o scaffolds.csv --generic
+
+# Scaffold decomposition
+rdkit-cli scaffold decompose -i input.csv -o decomposed.csv
+```
+
+### enumerate
+
+Enumerate molecular variants.
+
+```bash
+# Stereoisomers
+rdkit-cli enumerate stereoisomers -i input.csv -o isomers.csv --max-isomers 32
+
+# Tautomers
+rdkit-cli enumerate tautomers -i input.csv -o tautomers.csv --max-tautomers 50
+
+# Canonical tautomer
+rdkit-cli enumerate canonical-tautomer -i input.csv -o canonical.csv
+```
+
+### fragment
+
+Fragment molecules.
+
+```bash
+# BRICS fragmentation
+rdkit-cli fragment brics -i input.csv -o fragments.csv
+
+# RECAP fragmentation
+rdkit-cli fragment recap -i input.csv -o fragments.csv
+
+# Functional group extraction
+rdkit-cli fragment functional-groups -i input.csv -o groups.csv
+
+# Fragment frequency analysis
+rdkit-cli fragment analyze -i fragments.csv -o analysis.csv
+```
+
+### diversity
+
+Analyze and select diverse molecules.
+
+```bash
+# Pick diverse subset
+rdkit-cli diversity pick -i input.csv -o diverse.csv -k 100
+
+# Analyze diversity
+rdkit-cli diversity analyze -i input.csv
+```
+
+### mcs
+
+Find Maximum Common Substructure.
+
+```bash
+# Find MCS across molecules
+rdkit-cli mcs -i molecules.csv -o mcs_result.csv
+
+# With options
+rdkit-cli mcs -i molecules.csv -o mcs_result.csv \
+    --timeout 60 --atom-compare elements
+```
+
+### depict
+
+Generate molecular depictions.
+
+```bash
+# Single molecule
+rdkit-cli depict single --smiles "c1ccccc1" -o benzene.svg
+
+# Batch depiction
+rdkit-cli depict batch -i molecules.csv -o images/ -f svg
+
+# Grid image
+rdkit-cli depict grid -i molecules.csv -o grid.svg --mols-per-row 4
+```
+
+## Global Options
+
+| Option | Description |
+|--------|-------------|
+| `-n, --ncpu N` | Number of CPUs (-1 = all, default: -1) |
+| `-i, --input FILE` | Input file |
+| `-o, --output FILE` | Output file |
+| `--smiles-column COL` | SMILES column name (default: "smiles") |
+| `--name-column COL` | Name column (optional) |
+| `--no-header` | Input has no header row |
+| `-q, --quiet` | Suppress progress output |
+| `-V, --version` | Show version |
+| `-h, --help` | Show help |
+
+## Input/Output Formats
+
+| Format | Extension | Notes |
+|--------|-----------|-------|
+| CSV | .csv | Comma-separated, with header |
+| TSV | .tsv | Tab-separated, with header |
+| SMI | .smi | SMILES format, space-separated |
+| SDF | .sdf | Structure-Data File |
+| Parquet | .parquet | Apache Parquet format |
+
+## Examples
+
+### Cheminformatics Pipeline
+
+```bash
+# 1. Standardize input molecules
+rdkit-cli standardize -i raw.csv -o std.csv --cleanup --neutralize
+
+# 2. Filter by drug-likeness
+rdkit-cli filter druglike -i std.csv -o druglike.csv --rule lipinski
+
+# 3. Compute descriptors
+rdkit-cli descriptors compute -i druglike.csv -o desc.csv -d MolWt,MolLogP,TPSA,HBD,HBA
+
+# 4. Select diverse subset
+rdkit-cli diversity pick -i druglike.csv -o diverse.csv -k 500
+
+# 5. Generate depictions
+rdkit-cli depict grid -i diverse.csv -o library.svg --mols-per-row 10
+```
+
+### Similarity Screening
+
+```bash
+# Search for similar compounds
+rdkit-cli similarity search -i library.csv -o hits.csv \
+    --query "CC(=O)Oc1ccccc1C(=O)O" \
+    --threshold 0.6 \
+    --type morgan
+
+# Cluster results
+rdkit-cli similarity cluster -i hits.csv -o clustered.csv --cutoff 0.4
+```
+
+### Scaffold Analysis
+
+```bash
+# Extract scaffolds
+rdkit-cli scaffold murcko -i library.csv -o scaffolds.csv
+
+# Analyze scaffold diversity
+rdkit-cli diversity analyze -i scaffolds.csv --smiles-column scaffold
+```
+
+## Development
+
+```bash
+# Clone repository
+git clone https://github.com/vitruves/rdkit-cli
+cd rdkit-cli
+
+# Install with dev dependencies
+uv sync --dev
+
+# Run tests
+uv run pytest
+
+# Run with coverage
+uv run pytest --cov=rdkit_cli
+```
+
+## License
+
+Apache 2.0