Identifier Index

[ A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ ]

A

A_gridcalc (in gromacs.tools)	analyze() (in _COM)	analyze_all() (in Simulation)
A_ri3dc (in gromacs.tools)	analyze() (in _CysAccessibility)	anyopen() (in gromacs.utilities)
activate_subplot() (in gromacs.utilities)	analyze() (in _Dihedrals)	array (in XVG)
add_mdp_includes() (in gromacs.cbook)	analyze() (in _Distances)	array() (in QueuingSystem)
add_plugin() (in Simulation)	analyze() (in _Energy)	array_flag() (in QueuingSystem)
align_ligand() (in edPDB.cbook)	analyze() (in _HelixBundle)	ashours (in Timedelta)
all_frames (in Frames)	analyze() (in _Ls)	asiterable() (in edPDB.utilities)
amino_acid_codes (in gromacs.utilities)	analyze() (in _ProteinOnly)	asiterable() (in gromacs.utilities)
anadock (in gromacs)	analyze() (in _RMSD)	AtomGroup (in edPDB.xpdb)
Anadock (in gromacs.tools)	analyze() (in _RMSF)	AttributeDict (in gromacs.utilities)
analysis (in gromacs)	analyze() (in _StripWater)	autoconvert() (in gromacs.formats)
analyze() (in Simulation)	analyze() (in _TEMPLATEplugin)	AutoCorrectionWarning (in gromacs)
analyze() (in Worker)	analyze() (in _Trajectories)

B

BadParameterWarning (in gromacs)	byindex() (in odict)

C

canonical() (in edPDB.selections)	command_name (in G_confrms)	command_name (in G_vanhove)
cat() (in IndexBuilder)	command_name (in G_count)	command_name (in G_velacc)
cat() (in gromacs.cbook)	command_name (in G_covar)	command_name (in G_wham)
cat() (in Manager)	command_name (in G_current)	command_name (in G_zcoord)
cat() (in gromacs.utilities)	command_name (in G_density)	command_name (in Genbox)
cbook (in edPDB)	command_name (in G_densmap)	command_name (in Genconf)
cbook (in gromacs)	command_name (in G_dielectric)	command_name (in Genion)
center_fit() (in Transformer)	command_name (in G_dih)	command_name (in Genrestr)
check_failure() (in GromacsCommand)	command_name (in G_dipoles)	command_name (in Gmxcheck)
check_file() (in Simulation)	command_name (in G_disre)	command_name (in Gmxdump)
check_file_exists() (in FileUtils)	command_name (in G_dist)	command_name (in GridMAT_MD)
check_mdpargs() (in gromacs.setup)	command_name (in G_dyndom)	command_name (in Grompp)
check_mdrun_success() (in gromacs.run)	command_name (in G_enemat)	command_name (in Luck)
check_output() (in IndexBuilder)	command_name (in G_energy)	command_name (in Make_edi)
check_plugin_name() (in Simulation)	command_name (in G_filter)	command_name (in Make_ndx)
check_setup() (in gromacs.config)	command_name (in G_flux)	command_name (in Mdrun)
check_success() (in MDrunner)	command_name (in G_gyrate)	command_name (in Mdrun_d)
cleanup() (in Frames)	command_name (in G_h2order)	command_name (in Mk_angndx)
clear() (in odict)	command_name (in G_hbond)	command_name (in Pdb2gmx)
clear_handlers() (in edPDB.log)	command_name (in G_helix)	command_name (in Protonate)
clear_handlers() (in gromacs.log')	command_name (in G_helixorient)	command_name (in Sigeps)
client (in vmd.control)	command_name (in G_lie)	command_name (in Tpbconv)
cmd() (in client)	command_name (in G_mdmat)	command_name (in Trjcat)
cmd() (in interactive)	command_name (in G_mindist)	command_name (in Trjconv)
collect_incoming_data() (in client)	command_name (in G_morph)	command_name (in Trjorder)
Collection (in gromacs.analysis.collections)	command_name (in G_msd)	command_name (in Wheel)
collections (in gromacs.analysis)	command_name (in G_nmeig)	command_name (in X2top)
com (in gromacs.analysis.plugins)	command_name (in G_nmens)	command_name (in Xpm2ps)
COM (in gromacs.analysis.plugins.com)	command_name (in G_nmtraj)	commandline() (in Command)
combine() (in IndexBuilder)	command_name (in G_order)	commandline() (in MDrunner)
Command (in gromacs.core)	command_name (in G_polystat)	commands() (in command)
command (in vmd.control)	command_name (in G_potential)	COMMENT (in MDP)
command() (in server)	command_name (in G_principal)	communicate() (in PopenWithInput)
command_name (in Command)	command_name (in G_rama)	CONC_WATER (in gromacs.setup)
command_name (in GromacsCommand)	command_name (in G_rdf)	config (in gromacs)
command_name (in A_gridcalc)	command_name (in G_ri3dc)	configdir (in gromacs.config)
command_name (in A_ri3dc)	command_name (in G_rms)	control (in vmd)
command_name (in Anadock)	command_name (in G_rmsf)	convert_aa_code() (in gromacs.utilities)
command_name (in Do_dssp)	command_name (in G_rotacf)	copy() (in odict)
command_name (in Editconf)	command_name (in G_saltbr)	core (in gromacs.analysis)
command_name (in Eneconv)	command_name (in G_sas)	core (in gromacs)
command_name (in G_anaeig)	command_name (in G_sdf)	create() (in edPDB.log)
command_name (in G_analyze)	command_name (in G_sgangle)	create() (in gromacs.log')
command_name (in G_angle)	command_name (in G_sham)	create_portable_topology() (in gromacs.cbook)
command_name (in G_bond)	command_name (in G_sorient)	current_framename (in Frames)
command_name (in G_bundle)	command_name (in G_spatial)	current_plugin() (in Simulation)
command_name (in G_chi)	command_name (in G_spol)	cysaccessibility (in gromacs.analysis.plugins)
command_name (in G_cluster)	command_name (in G_tcaf)	CysAccessibility (in gromacs.analysis.plugins.cysaccessibility)
command_name (in G_clustsize)	command_name (in G_traj)

D

data_pattern (in GdistData)	default_plot_columns (in _MinDistances)	dist (in Mindist)
DATANAME (in GridMatData)	delete_frames() (in Frames)	distances (in gromacs.analysis.plugins)
default_extension (in GRO)	detect_queuing_system() (in gromacs.qsub)	Distances (in gromacs.analysis.plugins.distances)
default_extension (in MDP)	dhours (in Timedelta)	dminutes (in Timedelta)
default_extension (in NDX)	dihedrals (in gromacs.analysis.plugins)	do_dssp (in gromacs)
default_extension (in XVG)	Dihedrals (in gromacs.analysis.plugins.dihedrals)	Do_dssp (in gromacs.tools)
default_extension (in FileUtils)	disable_gromacs_warnings() (in gromacs)	doc_pattern (in GromacsCommand)
default_plot_columns (in _Distances)	dist (in gromacs.analysis.plugins)	dseconds (in Timedelta)

E

edges (in Mindist)	emit() (in NullHandler)	exec_name (in gromacs.tools)
edit_mdp() (in gromacs.cbook)	enable_gromacs_warnings() (in gromacs)	extract() (in Frames)
edit_txt() (in gromacs.cbook)	eneconv (in gromacs)	extract_lipids() (in PDB)
editconf (in gromacs)	Eneconv (in gromacs.tools)	extract_lipids() (in edPDB.cbook)
Editconf (in gromacs.tools)	energy (in gromacs.analysis.plugins)	extract_notprotein() (in PDB)
edPDB	Energy (in gromacs.analysis.plugins.energy)	extract_protein() (in PDB)
em_schedule() (in gromacs.setup)	energy_minimize() (in gromacs.setup)	extract_protein() (in edPDB.cbook)
emit() (in NullHandler)	error (in XVG)	extract_resnames() (in PDB)
emit() (in NullHandler)	errorbar() (in XVG)	extract_resnames() (in edPDB.cbook)

F

failuremodes (in GromacsCommand)	find_first() (in gromacs.utilities)	found_terminator() (in client)
figdir() (in Simulation)	find_water() (in edPDB.selections)	found_terminator() (in interactive)
figdir() (in Worker)	fit() (in Transformer)	Frames (in gromacs.cbook)
filename() (in FileUtils)	flag() (in QueuingSystem)	fromkeys() (in odict)
FileUtils (in gromacs.utilities)	format (in NDX)
filter_gromacs_warnings() (in gromacs)	formats (in gromacs)

G

g_anaeig (in gromacs)	g_mdmat (in gromacs)	G_wham (in gromacs.tools)
G_anaeig (in gromacs.tools)	G_mdmat (in gromacs.tools)	G_zcoord (in gromacs.tools)
g_analyze (in gromacs)	g_mindist (in gromacs)	GdistData (in gromacs.analysis.plugins.dist)
G_analyze (in gromacs.tools)	G_mindist (in gromacs.tools)	genbox (in gromacs)
g_angle (in gromacs)	g_morph (in gromacs)	Genbox (in gromacs.tools)
G_angle (in gromacs.tools)	G_morph (in gromacs.tools)	genconf (in gromacs)
g_bond (in gromacs)	g_msd (in gromacs)	Genconf (in gromacs.tools)
G_bond (in gromacs.tools)	G_msd (in gromacs.tools)	generate_submit_array() (in gromacs.qsub)
g_bundle (in gromacs)	g_nmeig (in gromacs)	generate_submit_scripts() (in gromacs.qsub)
G_bundle (in gromacs.tools)	G_nmeig (in gromacs.tools)	genion (in gromacs)
g_chi (in gromacs)	g_nmens (in gromacs)	Genion (in gromacs.tools)
G_chi (in gromacs.tools)	G_nmens (in gromacs.tools)	genrestr (in gromacs)
g_cluster (in gromacs)	g_nmtraj (in gromacs)	Genrestr (in gromacs.tools)
G_cluster (in gromacs.tools)	G_nmtraj (in gromacs.tools)	get() (in NDX)
g_clustsize (in gromacs)	g_order (in gromacs)	get() (in Manager)
G_clustsize (in gromacs.tools)	G_order (in gromacs.tools)	get_lipid_vdwradii() (in gromacs.setup)
g_confrms (in gromacs)	g_polystat (in gromacs)	get_ndx_groups() (in gromacs.cbook)
G_confrms (in gromacs.tools)	G_polystat (in gromacs.tools)	get_plugin() (in Simulation)
G_count (in gromacs.tools)	g_potential (in gromacs)	get_status() (in Manager)
g_covar (in gromacs)	G_potential (in gromacs.tools)	get_structure() (in edPDB.xpdb)
G_covar (in gromacs.tools)	g_principal (in gromacs)	get_template() (in gromacs.config)
g_current (in gromacs)	G_principal (in gromacs.tools)	get_templates() (in gromacs.config)
G_current (in gromacs.tools)	g_rama (in gromacs)	get_version() (in gromacs)
g_density (in gromacs)	G_rama (in gromacs.tools)	get_version_tuple() (in gromacs)
G_density (in gromacs.tools)	g_rdf (in gromacs)	get_volume() (in gromacs.cbook)
g_densmap (in gromacs)	G_rdf (in gromacs.tools)	getinput() (in interactive)
G_densmap (in gromacs.tools)	G_ri3dc (in gromacs.tools)	glob_parts() (in gromacs.cbook)
g_dielectric (in gromacs)	g_rms (in gromacs)	gmx_extra_tools (in gromacs.config)
G_dielectric (in gromacs.tools)	G_rms (in gromacs.tools)	gmx_resid() (in IndexBuilder)
g_dih (in gromacs)	g_rmsf (in gromacs)	gmx_tool_groups (in gromacs.config)
G_dih (in gromacs.tools)	G_rmsf (in gromacs.tools)	gmx_tools (in gromacs.config)
g_dipoles (in gromacs)	g_rotacf (in gromacs)	gmx_tools_402 (in gromacs.config)
G_dipoles (in gromacs.tools)	G_rotacf (in gromacs.tools)	gmxcheck (in gromacs)
g_disre (in gromacs)	g_saltbr (in gromacs)	Gmxcheck (in gromacs.tools)
G_disre (in gromacs.tools)	G_saltbr (in gromacs.tools)	gmxdoc (in GromacsCommand)
g_dist (in gromacs)	g_sas (in gromacs)	gmxdump (in gromacs)
G_dist (in gromacs.tools)	G_sas (in gromacs.tools)	Gmxdump (in gromacs.tools)
g_dyndom (in gromacs)	g_sdf (in gromacs)	gmxfatal_pattern (in GromacsCommand)
G_dyndom (in gromacs.tools)	G_sdf (in gromacs.tools)	Grid2D (in gromacs.analysis.plugins.gridmatmd)
g_enemat (in gromacs)	g_sgangle (in gromacs)	GridMAT_MD (in gromacs.config)
G_enemat (in gromacs.tools)	G_sgangle (in gromacs.tools)	gridMAT_MD (in gromacs)
g_energy (in gromacs)	g_sham (in gromacs)	GridMAT_MD (in gromacs.tools)
G_energy (in gromacs.tools)	G_sham (in gromacs.tools)	GridMatData (in gromacs.analysis.plugins.gridmatmd)
g_filter (in gromacs)	g_sorient (in gromacs)	gridmatmd (in gromacs.analysis.plugins)
G_filter (in gromacs.tools)	G_sorient (in gromacs.tools)	GridMatMD (in gromacs.analysis.plugins.gridmatmd)
G_flux (in gromacs.tools)	g_spatial (in gromacs)	GRO (in gromacs.formats)
g_gyrate (in gromacs)	G_spatial (in gromacs.tools)	gromacs
G_gyrate (in gromacs.tools)	g_spol (in gromacs)	GromacsCommand (in gromacs.core)
g_h2order (in gromacs)	G_spol (in gromacs.tools)	GromacsCommandMultiIndex (in gromacs.tools)
G_h2order (in gromacs.tools)	g_tcaf (in gromacs)	GromacsError (in gromacs)
g_hbond (in gromacs)	G_tcaf (in gromacs.tools)	GromacsFailureWarning (in gromacs)
G_hbond (in gromacs.tools)	g_traj (in gromacs)	GromacsImportWarning (in gromacs)
g_helix (in gromacs)	G_traj (in gromacs.tools)	GromacsValueWarning (in gromacs)
G_helix (in gromacs.tools)	g_vanhove (in gromacs)	grompp (in gromacs)
g_helixorient (in gromacs)	G_vanhove (in gromacs.tools)	Grompp (in gromacs.tools)
G_helixorient (in gromacs.tools)	g_velacc (in gromacs)	grompp_qtot() (in gromacs.cbook)
g_lie (in gromacs)	G_velacc (in gromacs.tools)	groups (in NDX)
G_lie (in gromacs.tools)	g_wham (in gromacs)

H

handle_connect() (in client)	has_plugin() (in Simulation)	help() (in Command)
handle_connect() (in interactive)	helixbundle (in gromacs.analysis.plugins)	hist (in Mindist)
has_arrays() (in QueuingSystem)	HelixBundle (in gromacs.analysis.plugins.helixbundle)	histogram() (in Mindist)

I

identifiers (in AtomGroup)	infix_filename() (in FileUtils)	iterable() (in edPDB.utilities)
imshow() (in Grid2D)	init_residue() (in SloppyStructureBuilder)	iterable() (in gromacs.utilities)
imshow() (in GridMatMD)	interactive (in vmd.control)	iteritems() (in odict)
index() (in odict)	inverse_aa_codes (in gromacs.utilities)	iterkeys() (in odict)
IndexBuilder (in gromacs.cbook)	isMine() (in QueuingSystem)	itervalues() (in odict)
IndexSet (in gromacs.formats)	items() (in odict)

J

join() (in uniqueNDX)

K

keep_protein_only() (in Transformer)	keys() (in odict)

L

less_important_warnings (in gromacs)	logger (in gromacs.analysis.plugins.energy)	logger (in gromacs.qsub)
load() (in Collection)	logger (in gromacs.analysis.plugins.helixbundle)	logger (in gromacs.run)
load_scripts (in gromacs.config)	logger (in gromacs.analysis.plugins.ls)	logger (in gromacs.setup)
load_tools (in gromacs.config)	logger (in gromacs.analysis.plugins.rmsd)	logger (in gromacs.utilities)
local_get() (in Manager)	logger (in gromacs.analysis.plugins.rmsf)	loglevel_console (in gromacs.config)
log (in edPDB)	logger (in gromacs.analysis.plugins.template_plugin)	loglevel_file (in gromacs.config)
log' (in gromacs)	logger (in gromacs.analysis.plugins.trajectories)	LowAccuracyWarning (in gromacs)
log_RE (in Manager)	logger (in gromacs.cbook)	ls (in gromacs.analysis.plugins)
logfilename (in gromacs.config)	logger (in gromacs.core)	Ls (in gromacs.analysis.plugins.ls)
logger (in edPDB.cbook)	logger (in GRO)	luck (in gromacs)
logger (in edPDB)	logger (in MDP)	Luck (in gromacs.tools)
logger (in edPDB.xpdb)	logger (in XVG)
logger (in gromacs.analysis.plugins.com)	logger (in gromacs)

M

ma (in XVG)	mdrun (in MDrunner)	Mindist (in gromacs.analysis.plugins.dist)
make_edi (in gromacs)	mdrun (in MDrunnerDoublePrecision)	mindistances (in gromacs.analysis.plugins)
Make_edi (in gromacs.tools)	mdrun (in MDrunnerMpich2Smpd)	MinDistances (in gromacs.analysis.plugins.mindistances)
make_index() (in _Dihedrals)	mdrun (in MDrunnerOpenMP)	missing (in gromacs.odict)
make_index() (in _HelixBundle)	mdrun (in MDrunnerOpenMP64)	MissingDataError (in gromacs)
make_index_cys() (in _CysAccessibility)	Mdrun (in gromacs.tools)	MissingDataWarning (in gromacs)
make_main_index() (in gromacs.setup)	mdrun_d (in gromacs)	mk_angndx (in gromacs)
make_ndx (in gromacs)	Mdrun_d (in gromacs.tools)	Mk_angndx (in gromacs.tools)
Make_ndx (in gromacs.tools)	MDrunner (in gromacs.run)	mkdir_p() (in gromacs.utilities)
make_ndx_captured() (in gromacs.cbook)	MDrunnerDoublePrecision (in gromacs.run)	mpicommand() (in MDrunner)
Manager (in gromacs.qsub)	MDrunnerMpich2Smpd (in gromacs.run)	mpiexec (in MDrunner)
max (in XVG)	MDrunnerOpenMP (in gromacs.run)	mpiexec (in MDrunnerMpich2Smpd)
MD() (in gromacs.setup)	MDrunnerOpenMP64 (in gromacs.run)	mpiexec (in MDrunnerOpenMP)
MD_restrained() (in gromacs.setup)	mean (in XVG)	mpiexec (in MDrunnerOpenMP64)
MDP (in gromacs.formats)	midpoints (in Mindist)
mdrun (in gromacs)	min (in XVG)

N

names (in _Distances)	NDXGROUP (in gromacs.cbook)	NullHandler (in gromacs)
names (in _MinDistances)	NDXLIST (in gromacs.cbook)	NullHandler (in gromacs.log')
names (in IndexBuilder)	ndxlist (in NDX)	number_pdbs() (in gromacs.utilities)
ncol (in NDX)	NotProteinSelect (in edPDB.selections)	NUMBERED_PDB (in gromacs.utilities)
ndependent() (in Manager)	NotResidueSelect (in edPDB.selections)
NDX (in gromacs.formats)	NullHandler (in edPDB)

O

odict (in gromacs)	odict (in gromacs.odict)	one (in gromacs.utilities)

P

PARAMETER (in MDP)	plot() (in Mindist)	Popen() (in Command)
parse() (in XVG)	plot() (in _Distances)	PopenWithInput (in gromacs.core)
parse_filename() (in GridMatData)	plot() (in _Energy)	popitem() (in odict)
parse_groups() (in gromacs.cbook)	plot() (in _HelixBundle)	posthook() (in MDrunner)
parse_ndxlist() (in gromacs.cbook)	plot() (in _Ls)	posthook() (in MDrunnerMpich2Smpd)
parse_selection() (in IndexBuilder)	plot() (in _ProteinOnly)	prehook() (in MDrunner)
ParseError (in gromacs)	plot() (in _RMSD)	prehook() (in MDrunnerMpich2Smpd)
path (in gromacs.config)	plot() (in _RMSF)	Property() (in gromacs.utilities)
pAVG (in GridMatMD)	plot() (in _StripWater)	PROTEIN_RESNAMES (in edPDB.selections)
pBOT (in GridMatMD)	plot() (in _TEMPLATEplugin)	proteinonly (in gromacs.analysis.plugins)
PDB (in edPDB.cbook)	plot() (in _Trajectories)	ProteinOnly (in gromacs.analysis.plugins.proteinonly)
pdb2gmx (in gromacs)	plot() (in XVG)	ProteinSelect (in edPDB.selections)
Pdb2gmx (in gromacs.tools)	Plugin (in gromacs.analysis.core)	protonate (in gromacs)
ping() (in server)	plugindir() (in Simulation)	Protonate (in gromacs.tools)
plot() (in Simulation)	plugindir() (in Worker)	pTOP (in GridMatMD)
plot() (in Worker)	plugins (in gromacs.analysis)	put() (in Manager)
plot() (in _COM)	pNX (in GridMatMD)	putfile() (in Manager)
plot() (in _CysAccessibility)	pNY (in GridMatMD)
plot() (in _Dihedrals)	pop() (in odict)

Q

qscript_template (in gromacs.config)	qsub (in gromacs)	queuing_systems (in gromacs.qsub)
qscriptdir (in gromacs.config)	qsub() (in Manager)	QueuingSystem (in gromacs.qsub)

R

read() (in GRO)	ResidueSelect (in edPDB.selections)	run() (in _Dihedrals)
read() (in MDP)	ResnameSelect (in edPDB.selections)	run() (in _Distances)
read() (in NDX)	resource_basename() (in gromacs.config)	run() (in _Energy)
read() (in XVG)	response() (in client)	run() (in GridMatMD)
realpath() (in gromacs.utilities)	RESPONSE_TERMINATOR (in vmd.control)	run() (in _HelixBundle)
recommended_mdp_table (in gromacs.setup)	results() (in command)	run() (in _Ls)
register() (in Plugin)	reverse() (in odict)	run() (in _MinDistances)
registry (in gromacs.tools)	rmsd (in gromacs.analysis.plugins)	run() (in _ProteinOnly)
relpath() (in gromacs.qsub)	RMSD (in gromacs.analysis.plugins.rmsd)	run() (in _RMSD)
REMOTE_TCL (in vmd.control)	rmsd_backbone (in gromacs.cbook)	run() (in _RMSF)
remotepath() (in Manager)	rmsf (in gromacs.analysis.plugins)	run() (in _StripWater)
remoteuri() (in Manager)	RMSF (in gromacs.analysis.plugins.rmsf)	run() (in _TEMPLATEplugin)
remove_legend() (in gromacs.utilities)	rp() (in Transformer)	run() (in _Trajectories)
remove_overlap_water() (in edPDB.cbook)	rulify() (in gromacs.analysis.plugins.ls)	run() (in Command)
RESIDUE (in IndexBuilder)	run (in gromacs)	run() (in MDrunner)
residues_by_resname() (in PDB)	run() (in Simulation)	run() (in GromacsCommandMultiIndex)
residues_by_resname() (in edPDB.selections)	run() (in Worker)	run_all() (in Simulation)
residues_by_selection() (in PDB)	run() (in _COM)	run_check() (in MDrunner)
residues_by_selection() (in edPDB.selections)	run() (in _CysAccessibility)	run_frame() (in GridMatMD)

S

save() (in Collection)	setdefault() (in odict)	SloppyStructureBuilder (in edPDB.xpdb)
save() (in GridMatMD)	setup (in gromacs)	solvate() (in gromacs.setup)
savefig() (in Worker)	setup() (in gromacs.config)	sort() (in odict)
SECTION (in NDX)	setup_MD() (in Manager)	start() (in server)
selections (in edPDB)	setup_posres() (in Manager)	std (in XVG)
server (in vmd.control)	sigeps (in gromacs)	stop() (in server)
services (in vmd.control)	Sigeps (in gromacs.tools)	store_xvg() (in Worker)
set() (in NDX)	Simulation (in gromacs.analysis.core)	strftime() (in Timedelta)
set() (in XVG)	size() (in NDX)	strip_water() (in Transformer)
set_correlparameters() (in XVG)	sizes (in NDX)	stripwater (in gromacs.analysis.plugins)
set_plugin() (in Simulation)	sloppyparser (in edPDB.xpdb)	StripWater (in gromacs.analysis.plugins.stripwater)
setdefault() (in NDX)	SloppyPDBIO (in edPDB.xpdb)

T

tc (in XVG)	topdir() (in Simulation)	trj_compact (in gromacs.cbook)
template_plugin (in gromacs.analysis.plugins)	topdir() (in Worker)	trj_compact_main (in gromacs.setup)
TEMPLATEplugin (in gromacs.analysis.plugins.template_plugin)	topology() (in gromacs.setup)	trj_fitandcenter() (in gromacs.cbook)
templates (in gromacs.config)	Tpbconv (in gromacs.tools)	trj_xyfitted (in gromacs.cbook)
templatesdir (in gromacs.config)	tpbconv (in gromacs)	Trjcat (in gromacs.tools)
terms (in _Energy)	trajectories (in gromacs.analysis.plugins)	trjcat (in gromacs)
three (in gromacs.utilities)	Trajectories (in gromacs.analysis.plugins.trajectories)	Trjconv (in gromacs.tools)
Timedelta (in gromacs.utilities)	transform_args() (in Command)	trjconv (in gromacs)
tolist() (in Collection)	transform_args() (in GromacsCommand)	Trjorder (in gromacs.tools)
tools (in gromacs)	Transformer (in gromacs.cbook)	trjorder (in gromacs)

U

uniqueNDX (in gromacs.formats)	unlink_gmx_backups() (in gromacs.utilities)	utilities (in edPDB)
unlink_f() (in gromacs.utilities)	update() (in odict)	utilities (in gromacs)
unlink_gmx() (in gromacs.utilities)	UsageWarning (in gromacs)

V

values() (in odict)	vdw_lipid_resnames (in gromacs.setup)	vmd
vdw_lipid_atom_radii (in gromacs.setup)	VERSION (in gromacs)

W

waitfor() (in Manager)	Worker (in gromacs.analysis.core)	write() (in NDX)
Wheel (in gromacs.tools)	worker_class (in Plugin)	write() (in XVG)
wheel (in gromacs)	write() (in PDB)	write_pdb() (in edPDB.xpdb)
withextsep() (in gromacs.utilities)	write() (in MDP)	writelogger (in edPDB.xpdb)

X

X2top (in gromacs.tools)	xpdb (in edPDB)	XVG (in gromacs.formats)
x2top (in gromacs)	Xpm2ps (in gromacs.tools)
xlabels (in _Distances)	xpm2ps (in gromacs)

Y

ylabels (in _Distances)

_

__add__() (in Collection)	__init__() (in XVG)	_fake_multi_ndx() (in GromacsCommandMultiIndex)
__add__() (in Grid2D)	__init__() (in odict)	_generate_template_dict() (in gromacs.config)
__add__() (in IndexSet)	__init__() (in Manager)	_get_atom_line() (in SloppyPDBIO)
__call__() (in Command)	__init__() (in QueuingSystem)	_get_gmx_docs() (in GromacsCommand)
__cmp__() (in odict)	__init__() (in MDrunner)	_get_stream() (in gromacs.utilities)
__deepcopy__() (in odict)	__init__() (in GromacsCommandMultiIndex)	_get_template() (in gromacs.config)
__del__() (in Frames)	__init__() (in client)	_getarray() (in NDX)
__del__() (in IndexBuilder)	__init__() (in command)	_getarray() (in uniqueNDX)
__del__() (in GromacsCommandMultiIndex)	__init__() (in interactive)	_has_syntax_error() (in IndexBuilder)
__delitem__() (in odict)	__init__() (in server)	_have_g_commands (in gromacs)
__div__() (in Grid2D)	__iter__() (in GdistData)	_HelixBundle (in gromacs.analysis.plugins.helixbundle)
__eq__() (in odict)	__iter__() (in Frames)	_hostname (in Manager)
__getattribute__() (in Collection)	__mul__() (in Grid2D)	_init_filename() (in FileUtils)
__getattribute__() (in AttributeDict)	__ne__() (in odict)	_is_empty_group() (in IndexBuilder)
__getnewargs__() (in Collection)	__pickle_excluded (in XVG)	_Ls (in gromacs.analysis.plugins.ls)
__getstate__() (in XVG)	__plugin_classes__ (in gromacs.analysis.plugins)	_mdp_include_string() (in gromacs.cbook)
__getstate__() (in odict)	__plugins__ (in gromacs.analysis.plugins)	_midpoints() (in Grid2D)
__getstate__() (in AttributeDict)	__repr__() (in AtomGroup)	_mindist() (in _CysAccessibility)
__init__() (in PDB)	__repr__() (in Collection)	_MinDistances (in gromacs.analysis.plugins.mindistances)
__init__() (in NotProteinSelect)	__repr__() (in Simulation)	_missing_g_commands (in gromacs)
__init__() (in NotResidueSelect)	__repr__() (in odict)	_process_command() (in IndexBuilder)
__init__() (in ProteinSelect)	__repr__() (in QueuingSystem)	_process_range() (in IndexBuilder)
__init__() (in ResidueSelect)	__repr__() (in FileUtils)	_process_residue() (in IndexBuilder)
__init__() (in ResnameSelect)	__reversed__() (in odict)	_ProteinOnly (in gromacs.analysis.plugins.proteinonly)
__init__() (in AtomGroup)	__setattr__() (in AttributeDict)	_qscript (in Manager)
__init__() (in SloppyStructureBuilder)	__setitem__() (in NDX)	_register_hook() (in Worker)
__init__() (in Plugin)	__setitem__() (in odict)	_register_hook() (in _COM)
__init__() (in Simulation)	__setstate__() (in XVG)	_register_hook() (in _CysAccessibility)
__init__() (in Worker)	__setstate__() (in odict)	_register_hook() (in _Dihedrals)
__init__() (in _COM)	__setstate__() (in AttributeDict)	_register_hook() (in _Distances)
__init__() (in _CysAccessibility)	__str__() (in Simulation)	_register_hook() (in _Energy)
__init__() (in _Dihedrals)	__str__() (in PopenWithInput)	_register_hook() (in _HelixBundle)
__init__() (in GdistData)	__sub__() (in Grid2D)	_register_hook() (in _Ls)
__init__() (in Mindist)	__sub__() (in IndexSet)	_register_hook() (in _MinDistances)
__init__() (in _Distances)	__warningregistry__ (in gromacs)	_register_hook() (in _ProteinOnly)
__init__() (in _Energy)	_accept_not_residue() (in ProteinSelect)	_register_hook() (in _RMSD)
__init__() (in Grid2D)	_accept_not_residue() (in ResidueSelect)	_register_hook() (in _RMSF)
__init__() (in GridMatData)	_accept_not_residue() (in ResnameSelect)	_register_hook() (in _StripWater)
__init__() (in GridMatMD)	_accept_residue() (in ProteinSelect)	_register_hook() (in _TEMPLATEplugin)
__init__() (in _HelixBundle)	_accept_residue() (in ResidueSelect)	_register_hook() (in _Trajectories)
__init__() (in _Ls)	_accept_residue() (in ResnameSelect)	_RMSD (in gromacs.analysis.plugins.rmsd)
__init__() (in _ProteinOnly)	_apply_all() (in Simulation)	_RMSF (in gromacs.analysis.plugins.rmsf)
__init__() (in _RMSD)	_assertnotempty() (in Manager)	_run_command() (in Command)
__init__() (in _RMSF)	_ATOM_FORMAT_STRING (in SloppyPDBIO)	_run_command() (in GromacsCommand)
__init__() (in _StripWater)	_build_arg_list() (in GromacsCommand)	_scratchdir (in Manager)
__init__() (in _TEMPLATEplugin)	_canonicalize() (in Collection)	_setup_MD() (in gromacs.setup)
__init__() (in _Trajectories)	_COM (in gromacs.analysis.plugins.com)	_StripWater (in gromacs.analysis.plugins.stripwater)
__init__() (in Frames)	_combine_arglist() (in Command)	_sum() (in uniqueNDX)
__init__() (in IndexBuilder)	_combine_arglist() (in GromacsCommand)	_tcorrel() (in XVG)
__init__() (in Transformer)	_combineargs() (in GromacsCommand)	_TEMPLATEplugin (in gromacs.analysis.plugins.template_plugin)
__init__() (in Command)	_commandline() (in Command)	_Trajectories (in gromacs.analysis.plugins.trajectories)
__init__() (in GromacsCommand)	_correlprop() (in XVG)	_transform() (in MDP)
__init__() (in PopenWithInput)	_CysAccessibility (in gromacs.analysis.plugins.cysaccessibility)	_transform() (in NDX)
__init__() (in GRO)	_Dihedrals (in gromacs.analysis.plugins.dihedrals)	_transform() (in uniqueNDX)
__init__() (in MDP)	_Distances (in gromacs.analysis.plugins.distances)	_translate_residue() (in IndexBuilder)
__init__() (in NDX)	_Energy (in gromacs.analysis.plugins.energy)	_walltime (in Manager)