Everything


All Classes

edPDB.NullHandler
edPDB.cbook.PDB
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.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.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.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_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_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_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.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.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.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._have_g_commands
gromacs._missing_g_commands
gromacs.anadock
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_atoms
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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