smsd 5.0.1__tar.gz

smsd-5.0.1/.github/workflows/maven.yml

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+name: maven
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: '17'
+          cache: maven
+      - name: Build with Maven
+        run: mvn -U -B -DskipTests=false clean verify
+      - name: Package
+        run: mvn -B -DskipTests=false package
+      - name: Upload fat JAR and launchers
+        uses: actions/upload-artifact@v4
+        with:
+          name: smsd-jar-and-launchers
+          path: |
+            target/*-jar-with-dependencies.jar
+            src/scripts/
+

smsd-5.0.1/.github/workflows/python-publish.yml

@@ -0,0 +1,68 @@
+name: Publish Python Package to PyPI
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.21
+        with:
+          package-dir: .
+        env:
+          CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-*"
+          CIBW_SKIP: "*-musllinux_* *-win32 *-manylinux_i686"
+          CIBW_BEFORE_BUILD: "pip install pybind11 scikit-build-core cmake"
+          CIBW_BUILD_VERBOSITY: "1"
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: ""
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: ""
+          CIBW_ENVIRONMENT: "CMAKE_ARGS='-DCMAKE_BUILD_TYPE=Release -DSMSD_BUILD_PYTHON=ON -DSMSD_BUILD_TESTS=OFF -DSMSD_BUILD_OPENMP=OFF'"
+          CIBW_TEST_COMMAND: "python -c \"import smsd; print('SMSD imported OK'); m = smsd.parse_smiles('c1ccccc1'); print(f'Benzene: {len(m)} atoms')\""
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        run: |
+          pip install build
+          python -m build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish:
+    name: Publish to PyPI
+    needs: [build, build-sdist]
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

smsd-5.0.1/.github/workflows/release.yml

@@ -0,0 +1,28 @@
+name: release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: '17'
+          cache: maven
+      - name: Build
+        run: mvn -U -B -DskipTests=true clean package
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: |
+            target/*-jar-with-dependencies.jar
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+

smsd-5.0.1/.gitignore

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+# Build artifacts
+target/
+dependency-reduced-pom.xml
+*.jar
+*.war
+*.ear
+hs_err_pid*
+*.log
+
+# Python
+__pycache__/
+*.pyc
+*.egg-info/
+.venv/
+venv/
+dist/
+build/
+*.so
+*.pyd
+
+# C++ build
+cpp/build/
+cpp/cmake-build*/
+*.o
+*.a
+*.dylib
+
+# IDE
+.idea/
+*.iml
+.vscode/
+*.swp
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Generated (rebuild anytime)
+api/
+docs/
+src/scripts/lib/
+src/scripts/repo/
+
+# Not for public repo
+paper/
+legacy/

smsd-5.0.1/Dockerfile

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+FROM maven:3.9.9-eclipse-temurin-17 AS build
+WORKDIR /app
+COPY . .
+RUN mvn -U -B -DskipTests=false clean package
+
+FROM eclipse-temurin:17-jre
+WORKDIR /work
+COPY --from=build /app/target/smsd-5.0.0-jar-with-dependencies.jar /usr/local/bin/smsd.jar
+# Run the fat JAR directly (jar-first UX)
+ENTRYPOINT ["java","-jar","/usr/local/bin/smsd.jar"]
+CMD ["--help"]

smsd-5.0.1/HOWTO-INSTALL.md

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+# How to Build and Run
+
+## Requirements
+- Java 11+ (JDK 17 recommended)
+- Maven 3.9+
+
+## Build
+
+```bash
+mvn -U clean package
+```
+
+This produces `target/smsd-5.0.0-jar-with-dependencies.jar` (fat JAR with all dependencies).
+
+## Run Tests
+
+```bash
+mvn clean test
+```
+
+## Run the CLI
+
+```bash
+java -jar target/smsd-*-jar-with-dependencies.jar \
+  --Q SMI --q "CCN" \
+  --T SMI --t "CCCNC" \
+  -m --json - --json-pretty
+```
+
+## Docker
+
+```bash
+docker build -t smsd .
+docker run --rm smsd --Q SMI --q "c1ccccc1" --T SMI --t "c1ccc(O)cc1" --json -
+```
+
+## Notes
+- The test suite exercises substructure and MCS across 420 cases, including recursive SMARTS, adversarial edge cases, and large molecules.
+- Cross-platform launcher scripts are generated at `src/scripts/smsd` and `src/scripts/smsd.bat`.

smsd-5.0.1/LICENSE

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smsd-5.0.1/LICENSE-HEADER-JAVA.txt

@@ -0,0 +1,4 @@
+/*
+ * SPDX-License-Identifier: Apache-2.0
+ * © 2025 BioInception PVT LTD.
+ */

smsd-5.0.1/PKG-INFO

@@ -0,0 +1,261 @@
+Metadata-Version: 2.1
+Name: smsd
+Version: 5.0.1
+Summary: SMSD -- Substructure & MCS search for chemical graphs
+Keywords: cheminformatics,mcs,substructure,graph-matching,chemistry,smiles
+Author-Email: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
+License: Apache-2.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: C++
+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: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Project-URL: Homepage, https://github.com/asad/SMSD
+Project-URL: Repository, https://github.com/asad/SMSD
+Project-URL: Bug Tracker, https://github.com/asad/SMSD/issues
+Requires-Python: >=3.8
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-timeout>=2.0; extra == "dev"
+Description-Content-Type: text/markdown
+
+# SMSD Python Bindings
+
+Python interface for **SMSD** (Small Molecule Substructure Detector) -- a high-performance
+library for substructure search, Maximum Common Substructure (MCS), and molecular similarity.
+
+## Features
+
+- **SMILES parsing and writing** -- built-in OpenSMILES parser, no RDKit or CDK required
+- **Substructure search** -- VF2++ subgraph isomorphism
+- **MCS search** -- McSplit with seed-and-extend, orbit pruning, coverage-driven termination
+- **Tautomer-aware matching** -- keto/enol, amide, imidazole tautomer equivalence
+- **RASCAL screening** -- O(V+E) Tanimoto-like similarity upper bound
+- **Fingerprints** -- path-based and MCS-aware fingerprints for pre-screening
+
+## Requirements
+
+- Python >= 3.8
+- C++17 compiler (GCC 7+, Clang 5+, MSVC 2019+)
+- CMake >= 3.15
+- pybind11 >= 2.12
+
+## Installation
+
+### From source (recommended)
+
+```bash
+cd python/
+pip install .
+```
+
+### Development install
+
+```bash
+pip install -e ".[dev]"
+```
+
+### Build with specific compiler
+
+```bash
+CMAKE_ARGS="-DCMAKE_CXX_COMPILER=g++-13" pip install .
+```
+
+## Quick Start
+
+```python
+from smsd import parse_smiles, find_mcs, is_substructure, similarity
+
+# Parse SMILES strings
+benzene = parse_smiles("c1ccccc1")
+phenol  = parse_smiles("c1ccc(O)cc1")
+
+# Substructure search
+assert is_substructure(benzene, phenol)  # benzene is in phenol
+
+# Maximum Common Substructure
+mcs = find_mcs(benzene, phenol)
+print(f"MCS size: {len(mcs)} atoms")  # 6
+
+# Similarity
+sim = similarity(benzene, phenol)
+print(f"Similarity: {sim:.3f}")  # ~0.857
+```
+
+## API Reference
+
+### SMILES Parsing
+
+```python
+from smsd import parse_smiles, to_smiles
+
+mol = parse_smiles("c1ccccc1")
+print(mol.n)              # 6 atoms
+print(mol.atomic_num)     # [6, 6, 6, 6, 6, 6]
+print(mol.aromatic)       # [True, True, True, True, True, True]
+
+smi = to_smiles(mol)      # canonical SMILES string
+```
+
+### Substructure Search
+
+```python
+from smsd import is_substructure, find_substructure, ChemOptions
+
+query  = parse_smiles("c1ccccc1")
+target = parse_smiles("c1ccc(O)cc1")
+
+# Boolean check
+if is_substructure(query, target):
+    print("Query is a substructure of target")
+
+# Get atom mapping
+mapping = find_substructure(query, target)
+# Returns list of (query_atom, target_atom) pairs
+for qi, ti in mapping:
+    print(f"  query atom {qi} -> target atom {ti}")
+
+# Custom options
+opts = ChemOptions()
+opts.ring_matches_ring_only = True
+is_substructure(query, target, opts=opts, timeout_ms=5000)
+```
+
+### MCS Search
+
+```python
+from smsd import find_mcs, ChemOptions, McsOptions
+
+g1 = parse_smiles("CC(=O)Oc1ccccc1C(=O)O")   # aspirin
+g2 = parse_smiles("CC(=O)Nc1ccc(O)cc1")       # acetaminophen
+
+# Default MCS
+mapping = find_mcs(g1, g2)
+print(f"MCS size: {len(mapping)}")
+
+# Tautomer-aware MCS
+taut = ChemOptions.tautomer_profile()
+mapping = find_mcs(g1, g2, chem=taut)
+
+# With MCS options
+mcs_opts = McsOptions()
+mcs_opts.timeout_ms = 5000
+mcs_opts.connected_only = True
+mapping = find_mcs(g1, g2, opts=mcs_opts)
+
+# Convenience wrapper (accepts SMILES strings directly)
+from smsd import mcs
+mapping = mcs("c1ccccc1", "Cc1ccccc1", tautomer_aware=True)
+```
+
+### Similarity and Screening
+
+```python
+from smsd import similarity_upper_bound, screen_targets, similarity
+
+g1 = parse_smiles("c1ccccc1")
+g2 = parse_smiles("Cc1ccccc1")
+
+# Single pair
+sim = similarity_upper_bound(g1, g2)
+print(f"Similarity: {sim:.3f}")
+
+# Convenience wrapper (accepts SMILES)
+sim = similarity("c1ccccc1", "Cc1ccccc1")
+
+# Batch screening
+library = [parse_smiles(s) for s in smiles_list]
+query = parse_smiles("c1ccccc1")
+hits = screen_targets(query, library, threshold=0.5)
+# Returns indices of molecules with similarity >= 0.5
+```
+
+### Fingerprints
+
+```python
+from smsd import (
+    path_fingerprint, mcs_fingerprint,
+    fingerprint_subset, analyze_fp_quality,
+    fingerprint, tanimoto,
+)
+
+mol = parse_smiles("c1ccccc1")
+
+# Path fingerprint (returns set bit positions)
+fp = path_fingerprint(mol, path_length=7, fp_size=2048)
+
+# MCS-aware fingerprint
+fp_mcs = mcs_fingerprint(mol, path_length=7, fp_size=2048)
+
+# Subset check (for substructure pre-screening)
+query_fp = path_fingerprint(parse_smiles("c1ccccc1"))
+target_fp = path_fingerprint(parse_smiles("c1ccc(O)cc1"))
+assert fingerprint_subset(query_fp, target_fp)
+
+# Quality analysis
+quality = analyze_fp_quality(fp)
+print(quality)  # {'set_bits': 12, 'density': 0.006, ...}
+
+# Convenience wrappers
+fp = fingerprint("CCO", kind="mcs")
+sim = tanimoto(fp, fingerprint("CCCO"))
+```
+
+### MolGraph Builder
+
+Build molecules directly without SMILES:
+
+```python
+from smsd import MolGraphBuilder
+
+builder = MolGraphBuilder(6)  # 6 atoms
+for i in range(6):
+    builder.atom(i, 6, charge=0, aromatic=True, in_ring=True)
+for i in range(6):
+    builder.bond(i, (i + 1) % 6, order=1, in_ring=True, aromatic=True)
+benzene = builder.build()
+```
+
+### Configuration
+
+```python
+from smsd import ChemOptions, McsOptions, BondOrderMode, RingFusionMode
+
+# ChemOptions controls atom/bond matching
+chem = ChemOptions()
+chem.match_atom_type = True
+chem.match_formal_charge = True
+chem.tautomer_aware = True
+chem.complete_rings_only = True
+chem.match_bond_order = BondOrderMode.LOOSE
+chem.ring_fusion_mode = RingFusionMode.STRICT
+
+# Named profiles
+chem = ChemOptions.tautomer_profile()   # tautomer-aware defaults
+chem = ChemOptions.profile("strict")    # strict matching
+
+# McsOptions controls MCS algorithm behavior
+opts = McsOptions()
+opts.connected_only = True
+opts.timeout_ms = 10000
+opts.maximize_bonds = True  # MCES mode
+```
+
+## Running Tests
+
+```bash
+cd python/
+pip install -e ".[dev]"
+pytest tests/ -v
+```
+
+## License
+
+Apache 2.0. Copyright (c) 2009-2026 Syed Asad Rahman, BioInception Labs.