Everything


All Classes

edPDB.NullHandler
edPDB.cbook.PDB
edPDB.selections.NotProteinSelect
edPDB.selections.NotResidueSelect
edPDB.selections.ProteinSelect
edPDB.selections.ResidueSelect
edPDB.selections.ResnameSelect
edPDB.xpdb.AtomGroup
edPDB.xpdb.SloppyPDBIO
edPDB.xpdb.SloppyStructureBuilder
gromacs.AutoCorrectionWarning
gromacs.BadParameterWarning
gromacs.GromacsError
gromacs.GromacsFailureWarning
gromacs.GromacsImportWarning
gromacs.GromacsValueWarning
gromacs.LowAccuracyWarning
gromacs.MissingDataError
gromacs.MissingDataWarning
gromacs.NullHandler
gromacs.ParseError
gromacs.UsageWarning
gromacs.analysis.collections.Collection
gromacs.analysis.core.Plugin
gromacs.analysis.core.Simulation
gromacs.analysis.core.Worker
gromacs.analysis.plugins.com.COM
gromacs.analysis.plugins.com._COM
gromacs.analysis.plugins.cysaccessibility.CysAccessibility
gromacs.analysis.plugins.cysaccessibility._CysAccessibility
gromacs.analysis.plugins.dihedrals.Dihedrals
gromacs.analysis.plugins.dihedrals._Dihedrals
gromacs.analysis.plugins.dist.GdistData
gromacs.analysis.plugins.dist.Mindist
gromacs.analysis.plugins.distances.Distances
gromacs.analysis.plugins.distances._Distances
gromacs.analysis.plugins.energy.Energy
gromacs.analysis.plugins.energy._Energy
gromacs.analysis.plugins.gridmatmd.Grid2D
gromacs.analysis.plugins.gridmatmd.GridMatData
gromacs.analysis.plugins.gridmatmd.GridMatMD
gromacs.analysis.plugins.helixbundle.HelixBundle
gromacs.analysis.plugins.helixbundle._HelixBundle
gromacs.analysis.plugins.ls.Ls
gromacs.analysis.plugins.ls._Ls
gromacs.analysis.plugins.mindistances.MinDistances
gromacs.analysis.plugins.mindistances._MinDistances
gromacs.analysis.plugins.proteinonly.ProteinOnly
gromacs.analysis.plugins.proteinonly._ProteinOnly
gromacs.analysis.plugins.rmsd.RMSD
gromacs.analysis.plugins.rmsd._RMSD
gromacs.analysis.plugins.rmsf.RMSF
gromacs.analysis.plugins.rmsf._RMSF
gromacs.analysis.plugins.stripwater.StripWater
gromacs.analysis.plugins.stripwater._StripWater
gromacs.analysis.plugins.template_plugin.TEMPLATEplugin
gromacs.analysis.plugins.template_plugin._TEMPLATEplugin
gromacs.analysis.plugins.trajectories.Trajectories
gromacs.analysis.plugins.trajectories._Trajectories
gromacs.cbook.Frames
gromacs.cbook.IndexBuilder
gromacs.cbook.Transformer
gromacs.core.Command
gromacs.core.GromacsCommand
gromacs.core.PopenWithInput
gromacs.formats.GRO
gromacs.formats.IndexSet
gromacs.formats.MDP
gromacs.formats.NDX
gromacs.formats.XVG
gromacs.formats.uniqueNDX
gromacs.log'.NullHandler
gromacs.odict.odict
gromacs.qsub.Manager
gromacs.qsub.QueuingSystem
gromacs.run.MDrunner
gromacs.run.MDrunnerDoublePrecision
gromacs.run.MDrunnerMpich2Smpd
gromacs.run.MDrunnerOpenMP
gromacs.run.MDrunnerOpenMP64
gromacs.tools.A_gridcalc
gromacs.tools.A_ri3dc
gromacs.tools.Anadock
gromacs.tools.Do_dssp
gromacs.tools.Editconf
gromacs.tools.Eneconv
gromacs.tools.G_anaeig
gromacs.tools.G_analyze
gromacs.tools.G_angle
gromacs.tools.G_bond
gromacs.tools.G_bundle
gromacs.tools.G_chi
gromacs.tools.G_cluster
gromacs.tools.G_clustsize
gromacs.tools.G_confrms
gromacs.tools.G_count
gromacs.tools.G_covar
gromacs.tools.G_current
gromacs.tools.G_density
gromacs.tools.G_densmap
gromacs.tools.G_dielectric
gromacs.tools.G_dih
gromacs.tools.G_dipoles
gromacs.tools.G_disre
gromacs.tools.G_dist
gromacs.tools.G_dyndom
gromacs.tools.G_enemat
gromacs.tools.G_energy
gromacs.tools.G_filter
gromacs.tools.G_flux
gromacs.tools.G_gyrate
gromacs.tools.G_h2order
gromacs.tools.G_hbond
gromacs.tools.G_helix
gromacs.tools.G_helixorient
gromacs.tools.G_lie
gromacs.tools.G_mdmat
gromacs.tools.G_mindist
gromacs.tools.G_morph
gromacs.tools.G_msd
gromacs.tools.G_nmeig
gromacs.tools.G_nmens
gromacs.tools.G_nmtraj
gromacs.tools.G_order
gromacs.tools.G_polystat
gromacs.tools.G_potential
gromacs.tools.G_principal
gromacs.tools.G_rama
gromacs.tools.G_rdf
gromacs.tools.G_ri3dc
gromacs.tools.G_rms
gromacs.tools.G_rmsf
gromacs.tools.G_rotacf
gromacs.tools.G_saltbr
gromacs.tools.G_sas
gromacs.tools.G_sdf
gromacs.tools.G_sgangle
gromacs.tools.G_sham
gromacs.tools.G_sorient
gromacs.tools.G_spatial
gromacs.tools.G_spol
gromacs.tools.G_tcaf
gromacs.tools.G_traj
gromacs.tools.G_vanhove
gromacs.tools.G_velacc
gromacs.tools.G_wham
gromacs.tools.G_zcoord
gromacs.tools.Genbox
gromacs.tools.Genconf
gromacs.tools.Genion
gromacs.tools.Genrestr
gromacs.tools.Gmxcheck
gromacs.tools.Gmxdump
gromacs.tools.GridMAT_MD
gromacs.tools.GromacsCommandMultiIndex
gromacs.tools.Grompp
gromacs.tools.Luck
gromacs.tools.Make_edi
gromacs.tools.Make_ndx
gromacs.tools.Mdrun
gromacs.tools.Mdrun_d
gromacs.tools.Mk_angndx
gromacs.tools.Pdb2gmx
gromacs.tools.Protonate
gromacs.tools.Sigeps
gromacs.tools.Tpbconv
gromacs.tools.Trjcat
gromacs.tools.Trjconv
gromacs.tools.Trjorder
gromacs.tools.Wheel
gromacs.tools.X2top
gromacs.tools.Xpm2ps
gromacs.utilities.AttributeDict
gromacs.utilities.FileUtils
gromacs.utilities.Timedelta
vmd.control.client
vmd.control.command
vmd.control.interactive
vmd.control.server

All Functions

edPDB.cbook.align_ligand
edPDB.cbook.extract_lipids
edPDB.cbook.extract_protein
edPDB.cbook.extract_resnames
edPDB.cbook.remove_overlap_water
edPDB.log.clear_handlers
edPDB.log.create
edPDB.selections.canonical
edPDB.selections.find_water
edPDB.selections.residues_by_resname
edPDB.selections.residues_by_selection
edPDB.utilities.asiterable
edPDB.utilities.iterable
edPDB.xpdb.get_structure
edPDB.xpdb.write_pdb
gromacs.analysis.plugins.ls.rulify
gromacs.cbook._mdp_include_string
gromacs.cbook.add_mdp_includes
gromacs.cbook.cat
gromacs.cbook.create_portable_topology
gromacs.cbook.edit_mdp
gromacs.cbook.edit_txt
gromacs.cbook.get_ndx_groups
gromacs.cbook.get_volume
gromacs.cbook.glob_parts
gromacs.cbook.grompp_qtot
gromacs.cbook.make_ndx_captured
gromacs.cbook.parse_groups
gromacs.cbook.parse_ndxlist
gromacs.cbook.trj_fitandcenter
gromacs.config._generate_template_dict
gromacs.config._get_template
gromacs.config.check_setup
gromacs.config.get_template
gromacs.config.get_templates
gromacs.config.resource_basename
gromacs.config.setup
gromacs.disable_gromacs_warnings
gromacs.enable_gromacs_warnings
gromacs.filter_gromacs_warnings
gromacs.formats.autoconvert
gromacs.get_version
gromacs.get_version_tuple
gromacs.log'.clear_handlers
gromacs.log'.create
gromacs.qsub.detect_queuing_system
gromacs.qsub.generate_submit_array
gromacs.qsub.generate_submit_scripts
gromacs.qsub.relpath
gromacs.run.check_mdrun_success
gromacs.setup.MD
gromacs.setup.MD_restrained
gromacs.setup._setup_MD
gromacs.setup.check_mdpargs
gromacs.setup.em_schedule
gromacs.setup.energy_minimize
gromacs.setup.get_lipid_vdwradii
gromacs.setup.make_main_index
gromacs.setup.solvate
gromacs.setup.topology
gromacs.utilities.Property
gromacs.utilities._get_stream
gromacs.utilities.activate_subplot
gromacs.utilities.anyopen
gromacs.utilities.asiterable
gromacs.utilities.cat
gromacs.utilities.convert_aa_code
gromacs.utilities.find_first
gromacs.utilities.iterable
gromacs.utilities.mkdir_p
gromacs.utilities.number_pdbs
gromacs.utilities.realpath
gromacs.utilities.remove_legend
gromacs.utilities.unlink_f
gromacs.utilities.unlink_gmx
gromacs.utilities.unlink_gmx_backups
gromacs.utilities.withextsep

All Variables

edPDB.cbook.logger
edPDB.logger
edPDB.selections.PROTEIN_RESNAMES
edPDB.xpdb.logger
edPDB.xpdb.sloppyparser
edPDB.xpdb.writelogger
gromacs.VERSION
gromacs.__warningregistry__
gromacs._have_g_commands
gromacs._missing_g_commands
gromacs.anadock
gromacs.analysis.Simulation
gromacs.analysis.plugins
gromacs.analysis.plugins.__plugin_classes__
gromacs.analysis.plugins.__plugins__
gromacs.analysis.plugins.com.logger
gromacs.analysis.plugins.energy.logger
gromacs.analysis.plugins.helixbundle.logger
gromacs.analysis.plugins.ls.logger
gromacs.analysis.plugins.rmsd.logger
gromacs.analysis.plugins.rmsf.logger
gromacs.analysis.plugins.template_plugin.logger
gromacs.analysis.plugins.trajectories.logger
gromacs.cbook.NDXGROUP
gromacs.cbook.NDXLIST
gromacs.cbook.logger
gromacs.cbook.rmsd_backbone
gromacs.cbook.trj_compact
gromacs.cbook.trj_xyfitted
gromacs.config.GridMAT_MD
gromacs.config.configdir
gromacs.config.gmx_extra_tools
gromacs.config.gmx_tool_groups
gromacs.config.gmx_tools
gromacs.config.gmx_tools_402
gromacs.config.load_scripts
gromacs.config.load_tools
gromacs.config.logfilename
gromacs.config.loglevel_console
gromacs.config.loglevel_file
gromacs.config.path
gromacs.config.qscript_template
gromacs.config.qscriptdir
gromacs.config.templates
gromacs.config.templatesdir
gromacs.core.logger
gromacs.do_dssp
gromacs.editconf
gromacs.eneconv
gromacs.g_anaeig
gromacs.g_analyze
gromacs.g_angle
gromacs.g_bond
gromacs.g_bundle
gromacs.g_chi
gromacs.g_cluster
gromacs.g_clustsize
gromacs.g_confrms
gromacs.g_covar
gromacs.g_current
gromacs.g_density
gromacs.g_densmap
gromacs.g_dielectric
gromacs.g_dih
gromacs.g_dipoles
gromacs.g_disre
gromacs.g_dist
gromacs.g_dyndom
gromacs.g_enemat
gromacs.g_energy
gromacs.g_filter
gromacs.g_gyrate
gromacs.g_h2order
gromacs.g_hbond
gromacs.g_helix
gromacs.g_helixorient
gromacs.g_lie
gromacs.g_mdmat
gromacs.g_mindist
gromacs.g_morph
gromacs.g_msd
gromacs.g_nmeig
gromacs.g_nmens
gromacs.g_nmtraj
gromacs.g_order
gromacs.g_polystat
gromacs.g_potential
gromacs.g_principal
gromacs.g_rama
gromacs.g_rdf
gromacs.g_rms
gromacs.g_rmsf
gromacs.g_rotacf
gromacs.g_saltbr
gromacs.g_sas
gromacs.g_sdf
gromacs.g_sgangle
gromacs.g_sham
gromacs.g_sorient
gromacs.g_spatial
gromacs.g_spol
gromacs.g_tcaf
gromacs.g_traj
gromacs.g_vanhove
gromacs.g_velacc
gromacs.g_wham
gromacs.genbox
gromacs.genconf
gromacs.genion
gromacs.genrestr
gromacs.gmxcheck
gromacs.gmxdump
gromacs.gridMAT_MD
gromacs.grompp
gromacs.less_important_warnings
gromacs.logger
gromacs.luck
gromacs.make_edi
gromacs.make_ndx
gromacs.mdrun
gromacs.mdrun_d
gromacs.mk_angndx
gromacs.odict.missing
gromacs.pdb2gmx
gromacs.protonate
gromacs.qsub.logger
gromacs.qsub.queuing_systems
gromacs.run.logger
gromacs.setup.CONC_WATER
gromacs.setup.logger
gromacs.setup.recommended_mdp_table
gromacs.setup.trj_compact_main
gromacs.setup.vdw_lipid_atom_radii
gromacs.setup.vdw_lipid_resnames
gromacs.sigeps
gromacs.tools.exec_name
gromacs.tools.registry
gromacs.tpbconv
gromacs.trjcat
gromacs.trjconv
gromacs.trjorder
gromacs.utilities.NUMBERED_PDB
gromacs.utilities.amino_acid_codes
gromacs.utilities.inverse_aa_codes
gromacs.utilities.logger
gromacs.utilities.one
gromacs.utilities.three
gromacs.wheel
gromacs.x2top
gromacs.xpm2ps
vmd.control.REMOTE_TCL
vmd.control.RESPONSE_TERMINATOR
vmd.control.services

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