sdfrust 0.7.0__cp313-cp313-win_amd64.whl

sdfrust/__init__.py

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+"""
+sdfrust - Fast Rust-based SDF, MOL2, and XYZ molecular structure file parser.
+
+This package provides high-performance parsing and writing of SDF (Structure Data File),
+MOL2 (TRIPOS), and XYZ molecular structure formats. It is implemented in Rust for speed
+and safety.
+
+Quick Start:
+    >>> import sdfrust
+    >>> mol = sdfrust.parse_sdf_file("molecule.sdf")
+    >>> print(f"Name: {mol.name}")
+    >>> print(f"Atoms: {mol.num_atoms}")
+    >>> print(f"Formula: {mol.formula()}")
+
+Features:
+    - Parse SDF V2000 and V3000 formats
+    - Parse TRIPOS MOL2 format
+    - Parse XYZ format
+    - Write SDF V2000 and V3000 formats
+    - Memory-efficient streaming iterators for large files
+    - Molecular descriptors (MW, exact mass, ring count, etc.)
+    - NumPy integration for coordinate arrays (optional)
+    - Transparent gzip decompression (optional, check with gzip_enabled())
+"""
+
+from sdfrust._sdfrust import (
+    # Version
+    __version__,
+    # Classes
+    Atom,
+    Bond,
+    BondOrder,
+    BondStereo,
+    Molecule,
+    SdfFormat,
+    SdfIterator,
+    SdfV3000Iterator,
+    Mol2Iterator,
+    XyzIterator,
+    # SDF V2000 parsing
+    parse_sdf_file,
+    parse_sdf_string,
+    parse_sdf_file_multi,
+    parse_sdf_string_multi,
+    # SDF V3000 parsing
+    parse_sdf_v3000_file,
+    parse_sdf_v3000_string,
+    parse_sdf_v3000_file_multi,
+    parse_sdf_v3000_string_multi,
+    # SDF auto-detection parsing (V2000/V3000)
+    parse_sdf_auto_file,
+    parse_sdf_auto_string,
+    parse_sdf_auto_file_multi,
+    parse_sdf_auto_string_multi,
+    # Unified auto-detection (SDF V2000, V3000, MOL2, XYZ)
+    detect_format,
+    parse_auto_file,
+    parse_auto_string,
+    parse_auto_file_multi,
+    parse_auto_string_multi,
+    # MOL2 parsing
+    parse_mol2_file,
+    parse_mol2_string,
+    parse_mol2_file_multi,
+    parse_mol2_string_multi,
+    # XYZ parsing
+    parse_xyz_file,
+    parse_xyz_string,
+    parse_xyz_file_multi,
+    parse_xyz_string_multi,
+    # SDF V2000 writing
+    write_sdf_file,
+    write_sdf_string,
+    write_sdf_file_multi,
+    # SDF V3000 writing
+    write_sdf_v3000_file,
+    write_sdf_v3000_string,
+    write_sdf_v3000_file_multi,
+    # SDF auto-format writing
+    write_sdf_auto_file,
+    write_sdf_auto_string,
+    # MOL2 writing
+    write_mol2_file,
+    write_mol2_string,
+    write_mol2_file_multi,
+    # Iterators
+    iter_sdf_file,
+    iter_sdf_v3000_file,
+    iter_mol2_file,
+    iter_xyz_file,
+    # Utility functions
+    gzip_enabled,
+)
+
+__all__ = [
+    # Version
+    "__version__",
+    # Classes
+    "Atom",
+    "Bond",
+    "BondOrder",
+    "BondStereo",
+    "Molecule",
+    "SdfFormat",
+    "SdfIterator",
+    "SdfV3000Iterator",
+    "Mol2Iterator",
+    "XyzIterator",
+    # SDF V2000 parsing
+    "parse_sdf_file",
+    "parse_sdf_string",
+    "parse_sdf_file_multi",
+    "parse_sdf_string_multi",
+    # SDF V3000 parsing
+    "parse_sdf_v3000_file",
+    "parse_sdf_v3000_string",
+    "parse_sdf_v3000_file_multi",
+    "parse_sdf_v3000_string_multi",
+    # SDF auto-detection parsing (V2000/V3000)
+    "parse_sdf_auto_file",
+    "parse_sdf_auto_string",
+    "parse_sdf_auto_file_multi",
+    "parse_sdf_auto_string_multi",
+    # Unified auto-detection (SDF V2000, V3000, MOL2, XYZ)
+    "detect_format",
+    "parse_auto_file",
+    "parse_auto_string",
+    "parse_auto_file_multi",
+    "parse_auto_string_multi",
+    # MOL2 parsing
+    "parse_mol2_file",
+    "parse_mol2_string",
+    "parse_mol2_file_multi",
+    "parse_mol2_string_multi",
+    # XYZ parsing
+    "parse_xyz_file",
+    "parse_xyz_string",
+    "parse_xyz_file_multi",
+    "parse_xyz_string_multi",
+    # SDF V2000 writing
+    "write_sdf_file",
+    "write_sdf_string",
+    "write_sdf_file_multi",
+    # SDF V3000 writing
+    "write_sdf_v3000_file",
+    "write_sdf_v3000_string",
+    "write_sdf_v3000_file_multi",
+    # SDF auto-format writing
+    "write_sdf_auto_file",
+    "write_sdf_auto_string",
+    # MOL2 writing
+    "write_mol2_file",
+    "write_mol2_string",
+    "write_mol2_file_multi",
+    # Iterators
+    "iter_sdf_file",
+    "iter_sdf_v3000_file",
+    "iter_mol2_file",
+    "iter_xyz_file",
+    # Utility functions
+    "gzip_enabled",
+]

sdfrust-0.7.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: sdfrust
+Version: 0.7.0
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+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 :: Rust
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: pytest>=7.0 ; extra == 'dev'
+Requires-Dist: numpy>=1.20 ; extra == 'dev'
+Requires-Dist: numpy>=1.20 ; extra == 'numpy'
+Provides-Extra: dev
+Provides-Extra: numpy
+License-File: LICENSE
+Summary: Fast Rust-based SDF, MOL2, and XYZ molecular structure file parser
+Keywords: chemistry,sdf,mol2,xyz,cheminformatics,parsing,molecules
+Author-email: Hosein Fooladi <fooladi.hosein@gmail.com>
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Documentation, https://github.com/hfooladi/sdfrust#readme
+Project-URL: Homepage, https://github.com/hfooladi/sdfrust
+Project-URL: Repository, https://github.com/hfooladi/sdfrust
+
+# sdfrust - Python Bindings
+
+Fast Rust-based SDF, MOL2, and XYZ molecular structure file parser with Python bindings, including transparent gzip decompression.
+
+## Installation
+
+### From source (requires Rust toolchain)
+
+```bash
+cd sdfrust-python
+pip install maturin
+maturin develop --features numpy
+```
+
+### Build wheel
+
+```bash
+maturin build --release --features numpy
+pip install target/wheels/sdfrust-*.whl
+```
+
+## Quick Start
+
+```python
+import sdfrust
+
+# Parse a single SDF file
+mol = sdfrust.parse_sdf_file("molecule.sdf")
+print(f"Name: {mol.name}")
+print(f"Atoms: {mol.num_atoms}")
+print(f"Formula: {mol.formula()}")
+print(f"MW: {mol.molecular_weight():.2f}")
+
+# Parse multiple molecules
+mols = sdfrust.parse_sdf_file_multi("database.sdf")
+for mol in mols:
+    print(f"{mol.name}: {mol.num_atoms} atoms")
+
+# Memory-efficient iteration over large files
+for mol in sdfrust.iter_sdf_file("large_database.sdf"):
+    print(f"{mol.name}: MW={mol.molecular_weight():.2f}")
+```
+
+## Supported Formats
+
+- **SDF V2000**: Full support for reading and writing (up to 999 atoms/bonds)
+- **SDF V3000**: Full support for reading and writing (unlimited atoms/bonds)
+- **MOL2 TRIPOS**: Full support for reading and writing
+- **XYZ**: Read support for XYZ coordinate files (single and multi-molecule)
+- **Gzip**: Transparent decompression of `.gz` files for all formats
+
+## API Reference
+
+### Parsing Functions
+
+#### SDF Files
+
+```python
+# Single molecule
+mol = sdfrust.parse_sdf_file("file.sdf")      # V2000
+mol = sdfrust.parse_sdf_auto_file("file.sdf") # Auto-detect V2000/V3000
+mol = sdfrust.parse_sdf_v3000_file("file.sdf") # V3000 only
+
+# Multiple molecules
+mols = sdfrust.parse_sdf_file_multi("file.sdf")
+mols = sdfrust.parse_sdf_auto_file_multi("file.sdf")
+
+# From string
+mol = sdfrust.parse_sdf_string(content)
+mols = sdfrust.parse_sdf_string_multi(content)
+```
+
+#### MOL2 Files
+
+```python
+mol = sdfrust.parse_mol2_file("file.mol2")
+mols = sdfrust.parse_mol2_file_multi("file.mol2")
+mol = sdfrust.parse_mol2_string(content)
+```
+
+#### Iterators (Memory-Efficient)
+
+```python
+for mol in sdfrust.iter_sdf_file("large.sdf"):
+    process(mol)
+
+for mol in sdfrust.iter_mol2_file("large.mol2"):
+    process(mol)
+```
+
+### Writing Functions
+
+```python
+# Single molecule
+sdfrust.write_sdf_file(mol, "output.sdf")
+sdfrust.write_sdf_auto_file(mol, "output.sdf")  # Auto V2000/V3000
+sdf_string = sdfrust.write_sdf_string(mol)
+
+# Multiple molecules
+sdfrust.write_sdf_file_multi(mols, "output.sdf")
+```
+
+### Molecule Properties
+
+```python
+mol = sdfrust.parse_sdf_file("aspirin.sdf")
+
+# Basic info
+print(mol.name)           # Molecule name
+print(mol.num_atoms)      # Number of atoms
+print(mol.num_bonds)      # Number of bonds
+print(mol.formula())      # Molecular formula
+
+# Descriptors
+print(mol.molecular_weight())    # Molecular weight
+print(mol.exact_mass())          # Monoisotopic mass
+print(mol.heavy_atom_count())    # Non-hydrogen atoms
+print(mol.ring_count())          # Number of rings
+print(mol.rotatable_bond_count()) # Rotatable bonds
+print(mol.total_charge())        # Sum of formal charges
+
+# Geometry
+centroid = mol.centroid()        # (x, y, z) center
+mol.translate(1.0, 0.0, 0.0)     # Move molecule
+mol.center()                     # Center at origin
+
+# Properties (from SDF data block)
+cid = mol.get_property("PUBCHEM_CID")
+mol.set_property("SOURCE", "generated")
+```
+
+### Atom Access
+
+```python
+# Iterate over atoms
+for atom in mol.atoms:
+    print(f"{atom.element} at ({atom.x}, {atom.y}, {atom.z})")
+
+# Get specific atom
+atom = mol.get_atom(0)
+print(atom.element)
+print(atom.formal_charge)
+print(atom.coords())  # (x, y, z) tuple
+
+# Filter atoms
+carbons = mol.atoms_by_element("C")
+neighbors = mol.neighbors(0)  # Atom indices bonded to atom 0
+```
+
+### Bond Access
+
+```python
+# Iterate over bonds
+for bond in mol.bonds:
+    print(f"{bond.atom1}-{bond.atom2}: {bond.order}")
+
+# Filter bonds
+double_bonds = mol.bonds_by_order(sdfrust.BondOrder.double())
+aromatic = mol.has_aromatic_bonds()
+
+# Bond properties
+bond = mol.bonds[0]
+print(bond.is_aromatic())
+print(bond.contains_atom(0))
+print(bond.other_atom(0))  # Other atom in bond
+```
+
+### NumPy Integration
+
+```python
+import numpy as np
+import sdfrust
+
+mol = sdfrust.parse_sdf_file("molecule.sdf")
+
+# Get coordinates as NumPy array
+coords = mol.get_coords_array()  # Shape: (N, 3)
+print(coords.shape)
+
+# Modify and set back
+coords[:, 0] += 10.0  # Translate in x
+mol.set_coords_array(coords)
+
+# Get atomic numbers
+atomic_nums = mol.get_atomic_numbers()  # Shape: (N,)
+```
+
+### Creating Molecules
+
+```python
+import sdfrust
+
+# Create empty molecule
+mol = sdfrust.Molecule("water")
+
+# Add atoms
+mol.add_atom(sdfrust.Atom(0, "O", 0.0, 0.0, 0.0))
+mol.add_atom(sdfrust.Atom(1, "H", 0.96, 0.0, 0.0))
+mol.add_atom(sdfrust.Atom(2, "H", -0.24, 0.93, 0.0))
+
+# Add bonds
+mol.add_bond(sdfrust.Bond(0, 1, sdfrust.BondOrder.single()))
+mol.add_bond(sdfrust.Bond(0, 2, sdfrust.BondOrder.single()))
+
+# Write to file
+sdfrust.write_sdf_file(mol, "water.sdf")
+```
+
+## Examples
+
+The `examples/` directory contains runnable scripts demonstrating real-world usage:
+
+| Script | Description |
+|--------|-------------|
+| [`basic_usage.py`](examples/basic_usage.py) | Core API: parsing, writing, atoms, bonds, descriptors, NumPy |
+| [`format_conversion.py`](examples/format_conversion.py) | Multi-format detection, XYZ parsing, SDF/MOL2 conversion, round-trips |
+| [`batch_analysis.py`](examples/batch_analysis.py) | Drug library processing: filtering, sorting, Lipinski analysis |
+| [`geometry_analysis.py`](examples/geometry_analysis.py) | 3D geometry: distance matrices, RMSD, rotation, transforms |
+
+```bash
+cd sdfrust-python
+maturin develop --features numpy,geometry
+python examples/basic_usage.py
+python examples/format_conversion.py
+python examples/batch_analysis.py
+python examples/geometry_analysis.py
+```
+
+## Performance
+
+sdfrust is implemented in Rust for maximum performance. Benchmarks show it is
+significantly faster than pure Python parsers and comparable to C++ implementations.
+
+For large files, use the iterator API (`iter_sdf_file`) to process molecules
+one at a time without loading the entire file into memory.
+
+## License
+
+MIT License
+

sdfrust-0.7.0.dist-info/RECORD

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sdfrust-0.7.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: maturin (1.15.0)
+Root-Is-Purelib: false
+Tag: cp313-cp313-win_amd64

sdfrust-0.7.0.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2025-2026 Hosein Fooladi
+
+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.