Class Hierarchy

• logging.Filterer: A base class for loggers and handlers which allows them to share common code.
  • logging.Handler: Handler instances dispatch logging events to specific destinations.
    • gromacs.NullHandler
    • gromacs.log'.NullHandler: Silent Handler.
    • edPDB.NullHandler
• unreachable.PDBIO: Write a Structure object (or a subset of a Structure object) as a PDB file.
  • edPDB.xpdb.SloppyPDBIO: PDBIO class that can deal with large pdb files as used in MD simulations.
• Bio.PDB.PDBIO.Select: Default selection (everything) during writing - can be used as base class to implement selective output.
  • edPDB.selections.ProteinSelect: Select all amino acid residues.
  • edPDB.selections.ResidueSelect: Select all atoms that are in the *residues* list.
    • edPDB.selections.NotResidueSelect: Select all atoms that are *not* in the *residues* list.
  • edPDB.selections.ResnameSelect: Select all atoms that match *resnames*.
• Bio.PDB.StructureBuilder.StructureBuilder: Deals with contructing the Structure object.
  • edPDB.xpdb.SloppyStructureBuilder: Cope with resSeq < 10,000 limitation by just incrementing internally.
• asyncore.dispatcher
  • asynchat.async_chat: This is an abstract class.
    • vmd.control.client: one command -> response exchange between the client and vmd:
      • vmd.control.command: Send one or more tcl commands to VMD and return response:
      • vmd.control.interactive: Interactive remote session with vmd:
• object: The most base type
  • exceptions.BaseException: Common base class for all exceptions
    • exceptions.Exception: Common base class for all non-exit exceptions.
      • gromacs.MissingDataError: Error raised when prerequisite data are not available.
      • gromacs.ParseError: Error raised when parsing of a file failed.
      • exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        • exceptions.EnvironmentError: Base class for I/O related errors.
          • gromacs.GromacsError: Error raised when a gromacs tool fails.
      • exceptions.Warning: Base class for warning categories.
        • gromacs.AutoCorrectionWarning: Warns about cases when the code is choosing new values automatically.
        • gromacs.BadParameterWarning: Warns if some parameters or variables are unlikely to be appropriate or correct.
        • gromacs.GromacsFailureWarning: Warning about failure of a Gromacs tool.
        • gromacs.GromacsValueWarning: Warns about problems with the value of an option or variable.
        • exceptions.ImportWarning: Base class for warnings about probable mistakes in module imports
          • gromacs.GromacsImportWarning: Warns about problems with using a gromacs tool.
        • gromacs.MissingDataWarning: Warns when prerequisite data/files are not available.
        • gromacs.UsageWarning: Warns if usage is unexpected/documentation ambiguous.
  • gromacs.core.Command: Wrap simple script or command.
    • gromacs.tools.GridMAT_MD: External tool 'GridMAT-MD.pl'
    • gromacs.core.GromacsCommand: Base class for wrapping a g_* command.
      • gromacs.tools.Anadock: Gromacs tool 'anadock'.
      • gromacs.tools.Do_dssp: Gromacs tool 'do_dssp'.
      • gromacs.tools.Editconf: Gromacs tool 'editconf'.
      • gromacs.tools.Eneconv: Gromacs tool 'eneconv'.
      • gromacs.tools.G_anaeig: Gromacs tool 'g_anaeig'.
      • gromacs.tools.G_analyze: Gromacs tool 'g_analyze'.
      • gromacs.tools.G_angle: Gromacs tool 'g_angle'.
      • gromacs.tools.G_bond: Gromacs tool 'g_bond'.
      • gromacs.tools.G_bundle: Gromacs tool 'g_bundle'.
      • gromacs.tools.G_chi: Gromacs tool 'g_chi'.
      • gromacs.tools.G_cluster: Gromacs tool 'g_cluster'.
      • gromacs.tools.G_clustsize: Gromacs tool 'g_clustsize'.
      • gromacs.tools.G_confrms: Gromacs tool 'g_confrms'.
      • gromacs.tools.G_covar: Gromacs tool 'g_covar'.
      • gromacs.tools.G_current: Gromacs tool 'g_current'.
      • gromacs.tools.G_density: Gromacs tool 'g_density'.
      • gromacs.tools.G_densmap: Gromacs tool 'g_densmap'.
      • gromacs.tools.G_dielectric: Gromacs tool 'g_dielectric'.
      • gromacs.tools.G_dih: Gromacs tool 'g_dih'.
      • gromacs.tools.G_dipoles: Gromacs tool 'g_dipoles'.
      • gromacs.tools.G_disre: Gromacs tool 'g_disre'.
      • gromacs.tools.G_dyndom: Gromacs tool 'g_dyndom'.
      • gromacs.tools.G_enemat: Gromacs tool 'g_enemat'.
      • gromacs.tools.G_energy: Gromacs tool 'g_energy'.
      • gromacs.tools.G_filter: Gromacs tool 'g_filter'.
      • gromacs.tools.G_gyrate: Gromacs tool 'g_gyrate'.
      • gromacs.tools.G_h2order: Gromacs tool 'g_h2order'.
      • gromacs.tools.G_hbond: Gromacs tool 'g_hbond'.
      • gromacs.tools.G_helix: Gromacs tool 'g_helix'.
      • gromacs.tools.G_helixorient: Gromacs tool 'g_helixorient'.
      • gromacs.tools.G_lie: Gromacs tool 'g_lie'.
      • gromacs.tools.G_mdmat: Gromacs tool 'g_mdmat'.
      • gromacs.tools.G_morph: Gromacs tool 'g_morph'.
      • gromacs.tools.G_msd: Gromacs tool 'g_msd'.
      • gromacs.tools.G_nmeig: Gromacs tool 'g_nmeig'.
      • gromacs.tools.G_nmens: Gromacs tool 'g_nmens'.
      • gromacs.tools.G_nmtraj: Gromacs tool 'g_nmtraj'.
      • gromacs.tools.G_order: Gromacs tool 'g_order'.
      • gromacs.tools.G_polystat: Gromacs tool 'g_polystat'.
      • gromacs.tools.G_potential: Gromacs tool 'g_potential'.
      • gromacs.tools.G_principal: Gromacs tool 'g_principal'.
      • gromacs.tools.G_rama: Gromacs tool 'g_rama'.
      • gromacs.tools.G_rdf: Gromacs tool 'g_rdf'.
      • gromacs.tools.G_rms: Gromacs tool 'g_rms'.
      • gromacs.tools.G_rmsf: Gromacs tool 'g_rmsf'.
      • gromacs.tools.G_rotacf: Gromacs tool 'g_rotacf'.
      • gromacs.tools.G_saltbr: Gromacs tool 'g_saltbr'.
      • gromacs.tools.G_sas: Gromacs tool 'g_sas'.
      • gromacs.tools.G_sdf: Gromacs tool 'g_sdf'.
      • gromacs.tools.G_sgangle: Gromacs tool 'g_sgangle'.
      • gromacs.tools.G_sham: Gromacs tool 'g_sham'.
      • gromacs.tools.G_sorient: Gromacs tool 'g_sorient'.
      • gromacs.tools.G_spatial: Gromacs tool 'g_spatial'.
      • gromacs.tools.G_spol: Gromacs tool 'g_spol'.
      • gromacs.tools.G_tcaf: Gromacs tool 'g_tcaf'.
      • gromacs.tools.G_traj: Gromacs tool 'g_traj'.
      • gromacs.tools.G_vanhove: Gromacs tool 'g_vanhove'.
      • gromacs.tools.G_velacc: Gromacs tool 'g_velacc'.
      • gromacs.tools.G_wham: Gromacs tool 'g_wham'.
      • gromacs.tools.Genbox: Gromacs tool 'genbox'.
      • gromacs.tools.Genconf: Gromacs tool 'genconf'.
      • gromacs.tools.Genion: Gromacs tool 'genion'.
      • gromacs.tools.Genrestr: Gromacs tool 'genrestr'.
      • gromacs.tools.Gmxcheck: Gromacs tool 'gmxcheck'.
      • gromacs.tools.Gmxdump: Gromacs tool 'gmxdump'.
      • gromacs.tools.GromacsCommandMultiIndex
        • gromacs.tools.G_dist: Gromacs tool 'g_dist' (with patch to handle multiple ndx files).
        • gromacs.tools.G_mindist: Gromacs tool 'g_mindist' (with patch to handle multiple ndx files).
      • gromacs.tools.Grompp: Gromacs tool 'grompp'.
      • gromacs.tools.Luck: Gromacs tool 'luck'.
      • gromacs.tools.Make_edi: Gromacs tool 'make_edi'.
      • gromacs.tools.Make_ndx: Gromacs tool 'make_ndx'.
      • gromacs.tools.Mdrun: Gromacs tool 'mdrun'.
      • gromacs.tools.Mdrun_d: Gromacs tool 'mdrun_d'.
      • gromacs.tools.Mk_angndx: Gromacs tool 'mk_angndx'.
      • gromacs.tools.Pdb2gmx: Gromacs tool 'pdb2gmx'.
      • gromacs.tools.Protonate: Gromacs tool 'protonate'.
      • gromacs.tools.Sigeps: Gromacs tool 'sigeps'.
      • gromacs.tools.Tpbconv: Gromacs tool 'tpbconv'.
      • gromacs.tools.Trjcat: Gromacs tool 'trjcat'.
      • gromacs.tools.Trjconv: Gromacs tool 'trjconv'.
      • gromacs.tools.Trjorder: Gromacs tool 'trjorder'.
      • gromacs.tools.Wheel: Gromacs tool 'wheel'.
      • gromacs.tools.X2top: Gromacs tool 'x2top'.
      • gromacs.tools.Xpm2ps: Gromacs tool 'xpm2ps'.
  • gromacs.utilities.FileUtils: Mixin class to provide additional file-related capabilities.
    • gromacs.formats.GRO: Class that represents a GROMOS (gro) structure file.
    • gromacs.formats.MDP: Class that represents a Gromacs mdp run input file.
    • gromacs.run.MDrunner: A class to manage running :program:`mdrun` in various ways.
      • gromacs.run.MDrunnerDoublePrecision: Manage running :program:`mdrun_d`.
      • gromacs.run.MDrunnerMpich2Smpd: Manage running :program:`mdrun` as mpich2_ multiprocessor job with the SMPD mechanism.
      • gromacs.run.MDrunnerOpenMP: Manage running :program:`mdrun` as an OpenMP_ multiprocessor job.
      • gromacs.run.MDrunnerOpenMP64: Manage running :program:`mdrun` as an OpenMP_ multiprocessor job (64-bit executable).
    • gromacs.formats.NDX: Gromacs index file.
      • gromacs.formats.uniqueNDX: Index that behaves like make_ndx, i.e.
    • gromacs.cbook.Transformer: Class to handle transformations of trajectories.
    • gromacs.analysis.core.Worker: Base class for a plugin worker.
      • gromacs.analysis.plugins.com._COM: COM worker class.
      • gromacs.analysis.plugins.cysaccessibility._CysAccessibility: Analysis of Cysteine accessibility.
      • gromacs.analysis.plugins.dihedrals._Dihedrals: Dihedrals worker class.
      • gromacs.analysis.plugins.distances._Distances: Analysis of distances.
        • gromacs.analysis.plugins.mindistances._MinDistances: Analysis of (multiple) minimum distances.
      • gromacs.analysis.plugins.energy._Energy: Energy worker class.
      • gromacs.analysis.plugins.helixbundle._HelixBundle: HelixBundle worker class.
      • gromacs.analysis.plugins.ls._Ls: ls worker class.
      • gromacs.analysis.plugins.rmsd._RMSD: RMSD worker class.
      • gromacs.analysis.plugins.rmsf._RMSF: RMSF worker class.
      • gromacs.analysis.plugins.stripwater._StripWater: StripWater worker class.
      • gromacs.analysis.plugins.template_plugin._TEMPLATEplugin: TEMPLATE worker class.
      • gromacs.analysis.plugins.trajectories._Trajectories: Trajctories worker class.
    • gromacs.formats.XVG: Class that represents the numerical data in a grace xvg file.
  • gromacs.cbook.Frames: A iterator that transparently provides frames from a trajectory.
  • gromacs.analysis.plugins.dist.GdistData: Object that represents the standard output of g_dist -dist CUTOFF.
  • gromacs.analysis.plugins.gridmatmd.Grid2D: Represents a 2D array with bin sizes.
    • gromacs.analysis.plugins.gridmatmd.GridMatData: Represent GridMatMD data file.
  • gromacs.analysis.plugins.gridmatmd.GridMatMD: Analysis of lipid bilayers with GridMAT-MD.
  • gromacs.cbook.IndexBuilder: Build an index file with specified groups and the combined group.
  • gromacs.qsub.Manager: Base class to launch simulations remotely on computers with queuing systems.
  • gromacs.analysis.plugins.dist.Mindist: The Mindist class allows analysis of the output from ``g_dist -dist CUTOFF``.
  • edPDB.cbook.PDB: Class that represents a PDB file and allows extractions of interesting parts.
  • gromacs.analysis.core.Plugin: Plugin class that can be added to a :class:`Simulation` instance.
    • gromacs.analysis.plugins.com.COM: *COM* plugin.
    • gromacs.analysis.plugins.cysaccessibility.CysAccessibility: *CysAccessibility* plugin.
    • gromacs.analysis.plugins.dihedrals.Dihedrals: *Dihedrals* plugin.
    • gromacs.analysis.plugins.distances.Distances: *Distances* plugin.
    • gromacs.analysis.plugins.energy.Energy: *Energy* plugin.
    • gromacs.analysis.plugins.helixbundle.HelixBundle: *HelixBundle* plugin.
    • gromacs.analysis.plugins.ls.Ls: *ls* plugin.
    • gromacs.analysis.plugins.mindistances.MinDistances: *MinDistances* plugin.
    • gromacs.analysis.plugins.rmsd.RMSD: *RMSD* plugin.
    • gromacs.analysis.plugins.rmsf.RMSF: *RMSF* plugin.
    • gromacs.analysis.plugins.stripwater.StripWater: *StripWater* plugin.
    • gromacs.analysis.plugins.template_plugin.TEMPLATEplugin: *TEMPLATE* plugin.
    • gromacs.analysis.plugins.trajectories.Trajectories: *Trajectories* plugin.
  • subprocess.Popen
    • gromacs.core.PopenWithInput: Popen class that knows its input.
  • gromacs.qsub.QueuingSystem: Class that represents minimum information about a batch submission system.
  • gromacs.analysis.core.Simulation: Class that represents one simulation.
  • dict: dict() -> new empty dictionary.
    • gromacs.utilities.AttributeDict: A dictionary with pythonic access to keys as attributes --- useful for interactive work.
    • gromacs.odict.odict: Ordered dict example implementation.
      • gromacs.formats.MDP: Class that represents a Gromacs mdp run input file.
      • gromacs.formats.NDX: Gromacs index file.
        • gromacs.formats.uniqueNDX: Index that behaves like make_ndx, i.e.
  • list: list() -> new list list(sequence) -> new list initialized from sequence's items
    • gromacs.analysis.collections.Collection: Multiple objects (organized as a list).
  • set: set(iterable) --> set object
    • edPDB.xpdb.AtomGroup
    • gromacs.formats.IndexSet: set which defines '+' as union (OR) and '-' as intersection (AND).
  • datetime.timedelta: Difference between two datetime values.
    • gromacs.utilities.Timedelta: Extension of :class:`datetime.timedelta`.
• vmd.control.server: The VMD server process.