molr 0.0.1.dev2

Molecular Realm for Spatial Indexed Structures - Fast spatial operations for molecular data

MolR - Molecular Realm for Spatial Indexed Structures

A high-performance Python package that creates a spatial realm for molecular structures, providing lightning-fast neighbor searches, geometric queries, and spatial operations through integrated KDTree indexing.

Features

🚀 High-Performance Structure Representation

• NumPy-based Structure class with Structure of Arrays (SoA)
• Efficient spatial indexing with scipy KDTree integration for O(log n) neighbor queries
• Memory-efficient trajectory handling with StructureEnsemble
• Lazy initialization of optional annotations to minimize memory usage

🔗 Comprehensive Bond Detection

• Hierarchical bond detection with multiple providers:
  • File-based bonds from PDB CONECT records and mmCIF data
  • Template-based detection using standard residue topologies
  • Chemical Component Dictionary (CCD) lookup for ligands
  • Distance-based detection with Van der Waals radii
• Intelligent fallback system ensures complete bond coverage
• Partial processing support for incremental bond detection

🎯 Powerful Selection Language

• MDAnalysis/VMD-inspired syntax for complex atom queries
• Spatial selections with within, around, and center-of-geometry queries
• Boolean operations (and, or, not) for combining selections
• Residue-based selections with byres modifier

📁 Multi-Format I/O Support

• PDB format with multi-model support and CONECT record parsing
• mmCIF format with chemical bond information extraction
• Auto-detection of single structures vs. trajectories
• String-based parsing for in-memory structure creation

Installation

pip install molr

For development installation:

git clone https://github.com/abhishektiwari/molr.git
cd molr
pip install -e .[dev]

Quick Start

Basic Structure Loading and Analysis

import molr

# Load structure from PDB file
structure = molr.Structure.from_pdb("protein.pdb")
print(f"Loaded {structure.n_atoms} atoms")

# Detect bonds automatically
bonds = structure.detect_bonds()
print(f"Detected {len(bonds)} bonds")

# Use selection language
ca_atoms = structure.select("name CA")
active_site = structure.select("within 5.0 of (resname HIS)")
protein_backbone = structure.select("protein and backbone")

Spatial Queries and Neighbor Finding

# Fast spatial queries with built-in KDTree indexing
neighbors = structure.get_neighbors_within(atom_idx=100, radius=5.0)
atoms_in_sphere = structure.get_atoms_within_sphere([10, 15, 20], radius=8.0)

# Center of geometry-based selections
ligand = structure.select("resname LIG")
nearby = structure.get_atoms_within_cog_sphere(ligand, radius=10.0)

# Inter-selection contacts
protein = structure.select("protein")
contacts = structure.get_atoms_between_selections(protein, ligand, max_distance=4.0)

Bond Detection and Analysis

from molr import BondDetector

# Configure bond detection
detector = BondDetector(
    enable_residue_templates=True,
    enable_ccd_lookup=True,
    enable_distance_detection=True,
    vdw_factor=0.75
)

# Detect bonds with detailed statistics
bonds, stats = detector.detect_bonds_with_stats(structure)
print(f"Bond detection stats: {stats}")

# Access different bond sources
file_bonds = structure.file_bonds  # From PDB CONECT records
all_bonds = structure.bonds        # Complete bond set

Multi-Model Trajectories

# Load trajectory from multi-model PDB
ensemble = molr.StructureEnsemble.from_pdb("trajectory.pdb")
print(f"Loaded {ensemble.n_models} models with {ensemble.n_atoms} atoms each")

# Access individual frames
first_frame = ensemble[0]  # Returns Structure object
last_frame = ensemble[-1]

# Analyze trajectory
centers = [model.get_center() for model in ensemble]

Advanced Usage

Custom Bond Detection

from molr.bond_detection import (
    ResidueBondProvider,
    CCDBondProvider, 
    DistanceBondProvider
)

# Create custom detection pipeline
providers = [
    ResidueBondProvider(),      # Standard residues first
    CCDBondProvider(),          # CCD lookup for ligands  
    DistanceBondProvider(vdw_factor=0.8)  # Distance fallback
]

# Apply in sequence
final_bonds = BondList()
for provider in providers:
    if provider.is_applicable(structure):
        bonds = provider.detect_bonds(structure, existing_bonds=final_bonds)
        final_bonds.extend(bonds)

Structure Manipulation

# Subset structures
protein_only = structure[structure.select("protein")]
chain_a = structure[structure.chain_id == "A"]

# Coordinate transformations  
structure.translate([10.0, 0.0, 0.0])
structure.center_at_origin()

# Add custom annotations
structure.add_annotation("custom_prop", dtype=np.float32, default_value=1.0)

Performance

• Spatial indexing: O(log n) neighbor queries vs O(n²) brute force
• Memory efficient: SoA design minimizes memory overhead
• Vectorized operations: NumPy-based computations throughout
• Lazy evaluation: Optional data loaded only when needed

API Reference

Core Classes

• Structure: Single molecular structure with spatial indexing
• StructureEnsemble: Multi-model trajectory representation
• BondList: Efficient bond storage and manipulation
• BondDetector: Configurable hierarchical bond detection

I/O Parsers

• PDBParser: PDB format with CONECT record support
• mmCIFParser: mmCIF format with bond information

Selection System

• select(): Parse and evaluate selection expressions
• Spatial expressions: within, around, cog
• Boolean operators: and, or, not

Requirements

• Python ≥3.8
• NumPy ≥1.20.0
• SciPy ≥1.7.0 (for spatial indexing)
• pyparsing ≥3.0.0 (for selection language)

License

MIT License - see LICENSE file for details.

Contributing

Contributions welcome! Please see CONTRIBUTING.md for guidelines.