gmso

User Guide

  • Installation
    • Installing with conda
    • Installing from source conda
    • Install an editable version from source
    • Supported Python Versions
    • Testing your installation
    • Install pre-commit
    • Building the documentation
  • Design Principles
    • Scope and Features of GMSO
    • Structure of GMSO
  • Potential Templates
    • Non-bonded Potentials
      • LennardJonesPotential
      • BuckinghamPotential
      • MiePotential
    • Bond Potentials
      • HarmonicBondPotential
      • LAMMPSHarmonicBondPotential
      • FixedBondPotential
      • FENEBondPotential
      • LAMMPSFENEBondPotential
      • HOOMDFENEWCABondPotential
    • Angle Potentials
      • HarmonicAnglePotential
      • LAMMPSHarmonicAnglePotential
      • FixedAnglePotential
    • Torsion / Dihedral Potentials
      • PeriodicTorsionPotential
      • HarmonicTorsionPotential
      • OPLSTorsionPotential
      • FourierTorsionPotential
      • RyckaertBellemansTorsionPotential
      • LAMMPSHarmonicDihedralPotential
      • HOOMDPeriodicDihedralPotential
    • Improper Potentials
      • HarmonicImproperPotential
      • PeriodicImproperPotential
    • Virtual Sites
      • TIP4PPotential (MSite)
      • Type3fdVirtualPosition
    • Engine-Specific Potentials
      • HOOMDDPDForce
  • Contributing
    • Features
      • Implement functionality in a general and flexible fashion
    • Version control
      • Propose a single set of related changes
    • Source code
      • Use a consistent style
      • Document code with comments
    • Tests
      • Write unit tests
  • Using GMSO with Docker
    • Prerequisites
    • Quick Start
    • Persisting User Volumes
    • Running Python scripts in the container
    • Cleaning Up

API Reference

  • API Reference
    • Abstract Base Classes
      • GMSOBase
        • GMSOBase
      • Site
        • Site
        • Molecule
        • Residue
      • AbstractPotential
        • AbstractPotential
      • Connection
        • Connection
    • Core Classes
      • Topology
        • Summary
        • Reference
      • Sites
        • Atom
        • VirtualSite
      • Connections
        • Bond
        • Angle
        • Dihedral
        • Improper
      • Potential Types
        • AtomType
        • BondType
        • AngleType
        • DihedralType
        • ImproperType
        • PairPotentialType
        • VirtualType
      • ForceField
        • ForceField
      • Box
        • Box
      • Element
        • Element
    • File Format Readers and Writers
      • GROMACS
        • read_gro
        • write_gro
        • write_top
      • GSD
        • write_gsd
      • XYZ
        • read_xyz
        • write_xyz
      • LAMMPS DATA
        • write_lammpsdata
        • read_lammpsdata
      • MOL2
        • read_mol2
        • write_mol2
      • MCF
        • write_mcf
      • JSON
        • write_json
        • load_json
      • Format Registry
        • LoadersRegistry
        • SaversRegistry
    • External Library Conversions
      • mBuild
        • from_mbuild
        • from_mbuild_box
        • to_mbuild
      • ParmEd
        • from_parmed
        • to_parmed
      • OpenMM
        • to_openmm
      • HOOMD-blue
        • to_hoomd_snapshot
        • to_hoomd_forcefield
        • to_gsd_snapshot
      • NetworkX
        • from_networkx
        • to_networkx
    • Parameterization
      • apply
        • apply()
    • Utilities
      • identify_connections
        • identify_connections()
gmso
  • API Reference
  • Edit on GitHub

API Reference

This section provides comprehensive API documentation for all public modules in GMSO. Documentation is generated from docstrings in the source code.

API Reference

  • Abstract Base Classes
    • GMSOBase
    • Site
    • AbstractPotential
    • Connection
  • Core Classes
    • Topology
    • Sites
    • Connections
    • Potential Types
    • ForceField
    • Box
    • Element
  • File Format Readers and Writers
    • GROMACS
    • GSD
    • XYZ
    • LAMMPS DATA
    • MOL2
    • MCF
    • JSON
    • Format Registry
  • External Library Conversions
    • mBuild
    • ParmEd
    • OpenMM
    • HOOMD-blue
    • NetworkX
  • Parameterization
    • apply
  • Utilities
    • identify_connections
Previous Next

© Copyright 2024, mosdef-hub, Vanderbilt University.

Built with Sphinx using a theme provided by Read the Docs.