Module Hierarchy

• edPDB: :mod:`edPDB` -- editing PDB files =================================
  • edPDB.cbook: :mod:`edPDB.cbook` -- Recipes for editing PDB files ===================================================
  • edPDB.log: Configure logging for edPDB analysis.
  • edPDB.selections: Extensions to Bio.PDB, some useful selections.
  • edPDB.utilities: :mod:`edPDB.utilities` -- Helper functions and classes ========================================================
  • edPDB.xpdb: Extensions to Bio.PDB, such as handling of large pdb files and some useful selections (see :mod:`edPDB.selections`).
• gromacs: :mod:`gromacs` -- GromacsWrapper Package Overview =================================================
  • gromacs.analysis: :mod:`gromacs.analysis` -- Analysis Package Overview ====================================================
    • gromacs.analysis.collections: This module contains classes and functions that combine multiple :class:`gromacs.analysis.core.Simulation` objects.
    • gromacs.analysis.core: :mod:`analysis.core` -- Core classes for analysis of Gromacs trajectories =========================================================================
    • gromacs.analysis.plugins: :mod:`analysis.plugins` -- Plugin Modules =========================================
      • gromacs.analysis.plugins.com: Centre of mass ==============
      • gromacs.analysis.plugins.cysaccessibility: CysAccessibility plugin =======================
      • gromacs.analysis.plugins.dihedrals: Dihedrals plugin ================
      • gromacs.analysis.plugins.dist: ``analysis.plugins.dist`` --- Helper Class for ``g_dist`` =========================================================
      • gromacs.analysis.plugins.distances: Distance plugin ===============
      • gromacs.analysis.plugins.energy: Various terms from the energy (edr) file ========================================
      • gromacs.analysis.plugins.gridmatmd: :mod:`gromacs.analysis.plugins.gridmatmd` --- Lipid bilayer analysis helper ===========================================================================
      • gromacs.analysis.plugins.helixbundle: Helix bundle analysis =====================
      • gromacs.analysis.plugins.ls: ls plugin =========
      • gromacs.analysis.plugins.mindistances: MinDistance plugin ===============
      • gromacs.analysis.plugins.proteinonly: ProteinOnly ===========
      • gromacs.analysis.plugins.rmsd: RMSD calculation ================
      • gromacs.analysis.plugins.rmsf: RMSF calculation ================
      • gromacs.analysis.plugins.stripwater: StripWater ==========
      • gromacs.analysis.plugins.template_plugin: Template for a plugin ======================
      • gromacs.analysis.plugins.trajectories: Trajectories ============
  • gromacs.cbook: :mod:`gromacs.cbook` -- Gromacs Cook Book =========================================
  • gromacs.config: :mod:`gromacs.config` -- Configuration for GromacsWrapper ==========================================================
  • gromacs.core: :mod:`gromacs.core` -- Core functionality =========================================
  • gromacs.formats: :mod:`gromacs.formats` -- Accessing various files =================================================
  • gromacs.log
  • gromacs.log': Configure logging for gromacs.
  • gromacs.odict: odict ~~~~~
  • gromacs.qsub: :mod:`gromacs.qsub` -- utilities for batch submission systems =============================================================
  • gromacs.run: :mod:`gromacs.run` -- Running simulations =========================================
  • gromacs.setup: :mod:`gromacs.setup` -- Setting up a Gromacs MD run ===================================================
  • gromacs.tools: :mod:`gromacs.tools` -- Gromacs commands classes ================================================
  • gromacs.utilities: :mod:`gromacs.utilities` -- Helper functions and classes ========================================================
• vmd: ============= VMD control =============
  • vmd.control