crisp-ase 1.1.2__py3-none-any.whl

CRISP/__init__.py

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+"""A python package for Post-simulation analysis and visualization"""
+
+__all__ = [
+    "cli",
+    "data_analysis",
+    "simulation_utility",
+]
+
+from ._version import __version__
+
+from . import cli
+from . import data_analysis
+from . import simulation_utility
+
+# Re-export commonly used classes and functions for convenience
+# This allows both import styles:
+# Old style: from CRISP.data_analysis.prdf import Analysis
+# New style: from CRISP import Analysis
+
+# Data analysis imports
+from .data_analysis.prdf import (
+    check_cell_and_r_max,
+    compute_pairwise_rdf,
+    plot_rdf,
+    animate_rdf,
+    analyze_rdf,
+    Analysis
+)
+
+from .data_analysis.clustering import (
+    analyze_frame, 
+    analyze_trajectory, 
+    cluster_analysis, 
+    save_analysis_results, 
+    plot_analysis_results,
+    cluster_analysis
+)
+
+from .data_analysis.contact_coordination import (
+    indices, 
+    coordination_frame, 
+    coordination, 
+    contacts_frame, 
+    contacts
+)
+
+from .data_analysis.h_bond import (
+    indices, 
+    count_hydrogen_bonds, 
+    aggregate_data, 
+    hydrogen_bonds
+)
+
+from .data_analysis.msd import (
+    read_trajectory_chunk, 
+    calculate_frame_msd, 
+    calculate_msd, 
+    calculate_save_msd, 
+    msd_analysis
+)
+
+from .data_analysis.volumetric_atomic_density import (
+    create_density_map, 
+    VDW_RADII, 
+    ELEMENT_COLORS
+)
+
+# Simulation utility imports
+from .simulation_utility.atomic_indices import (
+    atom_indices, 
+    run_atom_indices
+)
+
+from .simulation_utility.atomic_traj_linemap import (
+    plot_atomic_trajectory, 
+    VDW_RADII, 
+    ELEMENT_COLORS
+)
+
+from .simulation_utility.error_analysis import (
+    optimal_lag, 
+    vector_acf, 
+    autocorrelation_analysis, 
+    block_analysis
+)
+
+from .simulation_utility.interatomic_distances import (
+    indices, 
+    distance_calculation, 
+    save_distance_matrices, 
+    calculate_interatomic_distances
+)
+
+from .simulation_utility.subsampling import (
+    indices, 
+    compute_soap, 
+    create_repres, 
+    subsample
+)

CRISP/_version.py

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+__version__ = "1.1.2"

CRISP/cli.py

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+"""Command-line interface for CRISP."""
+
+import argparse
+import sys
+from CRISP._version import __version__
+
+
+def main():
+    """Main CLI entry point."""
+    parser = argparse.ArgumentParser(
+        prog='crisp',
+        description='CRISP: Computational Research Infrastructure for Spectroscopy and Properties'
+    )
+    
+    parser.add_argument(
+        '--version',
+        action='version',
+        version=f'CRISP {__version__}'
+    )
+    
+    subparsers = parser.add_subparsers(dest='command', help='Available commands')
+    
+    # Test command
+    test_parser = subparsers.add_parser('test', help='Run tests')
+    test_parser.add_argument('--verbose', '-v', action='store_true', help='Verbose output')
+    
+    args = parser.parse_args()
+    
+    if args.command == 'test':
+        run_tests(verbose=args.verbose)
+    elif args.command is None:
+        parser.print_help()
+        sys.exit(1)
+
+
+def run_tests(verbose=False):
+    """Run package tests."""
+    import pytest
+    args = ['-v'] if verbose else []
+    sys.exit(pytest.main(args))
+

CRISP/data_analysis/__init__.py

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+#  CRISP/data_analysis/__init__.py
+"""Data analysis module for molecular dynamics trajectory analysis."""
+
+from .contact_coordination import *
+from .h_bond import *
+from .prdf import *
+from .msd import *
+from .clustering import *
+from .volumetric_atomic_density import *
+
+__all__ = [
+    # Contact coordination functions
+    'indices',
+    'coordination_frame',
+    'coordination',
+    'contacts_frame',
+    'contacts',
+    # H-bond functions
+    'count_hydrogen_bonds',
+    'aggregate_data',
+    'hydrogen_bonds',
+    # RDF functions
+    'check_cell_and_r_max',
+    'compute_pairwise_rdf',
+    'analyze_rdf',
+    # MSD functions
+    'read_trajectory_chunk',
+    'calculate_frame_msd',
+    'calculate_msd',
+    'calculate_save_msd',
+    'msd_analysis',
+    # Clustering
+    'analyze_frame',
+    'analyze_trajectory',
+    # Volumetric density
+    'create_density_map',
+]
+