API Documentation

This is the API documentation for the main BuildAMol library.

• The core package
  • The Molecule module
  • The Linkage module
  • The Reaction module
  • The base module
• The resources package
  • PDBe Compounds
  • PubChem
  • CHARMM
  • CHARMMTopology
  • add_linkage()
  • add_patch()
  • available_linkages()
  • available_patches()
  • export_topology()
  • get_default_topology()
  • get_linkage()
  • get_patch()
  • has_linkage()
  • has_patch()
  • read_topology()
  • restore_default_topology()
  • save_topology()
  • set_default_topology()
  • PDBECompounds
  • add_compound()
  • export_compounds()
  • get_compound()
  • get_default_compounds()
  • has_compound()
  • load_all_compounds()
  • load_amino_acids()
  • load_lipids()
  • load_nucleotides()
  • load_small_molecules()
  • load_sugars()
  • read_compounds()
  • restore_default_compounds()
  • save_as_default_compounds()
  • save_compounds()
  • set_default_compounds()
  • subset_compounds_by_types()
  • unload_all_compounds()
  • unload_amino_acids()
  • unload_by_types()
  • unload_lipids()
  • unload_nucleotides()
  • unload_small_molecules()
  • unload_sugars()
  • pubchem_to_cif()
  • query()
• The optimizers package
  • The Rotatron Environments
  • The Translatron
  • Optimization algorithms
  • Optimization utilities
• The structural package
  • Basic structural operations
  • Inferring Structural Properties
  • Reactivities
  • Molecular Geometries
  • Functional Groups
  • Graph Neighborhood in Molecular Structures
  • Assembling Molecules
• The visual module
  • Visualizing from the Molecule class
  • Visualizing with Plotly
  • Visualizing with NglView
  • Visualizing with 3DMol.js
  • Visualizing 2D molecules
• The graphs package
  • The BaseGraph module
  • The AtomGraph module
  • The ResidueGraph module
• The utils package
  • Default settings and constants
  • File-format related utilities
  • Structure-related utilities
  • Other auxiliary utilities

Extensions

This is the API documentation for the BuildAMol extensions.

• The Extensions
  • Currently available extensions