Index

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

_

__add__() (gromacs.analysis.plugins.gridmatmd.Grid2D method)
__call__() (gromacs.core.Command method)
__del__() (gromacs.tools.GromacsCommandMultiIndex method), [1]
__div__() (gromacs.analysis.plugins.gridmatmd.Grid2D method)
__iter__() (gromacs.analysis.plugins.dist.GdistData method)
__mul__() (gromacs.analysis.plugins.gridmatmd.Grid2D method)
__plugin_classes__ (in module gromacs.analysis.plugins)
__plugins__ (in module gromacs.analysis.plugins)
__sub__() (gromacs.analysis.plugins.gridmatmd.Grid2D method)
_apply_all() (gromacs.analysis.core.Simulation method)
_fake_multi_ndx() (gromacs.tools.GromacsCommandMultiIndex method), [1]
_hostname (gromacs.qsub.Manager attribute)
_qscript (gromacs.qsub.Manager attribute)
_register_hook() (gromacs.analysis.core.Worker method)
_scratchdir (gromacs.qsub.Manager attribute)
_setup_MD() (in module gromacs.setup)
_walltime (gromacs.qsub.Manager attribute)

A

activate_subplot() (in module gromacs.utilities)
add_mdp_includes() (in module gromacs.cbook)
add_plugin() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.Simulation method)
align_ligand() (in module edPDB.cbook)
all_frames (gromacs.cbook.Frames attribute)
amino_acid_codes (in module gromacs.utilities)
Anadock (class in gromacs.tools)
analyze() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.Simulation method)
analyze_all() (gromacs.analysis.core.Simulation method)
anyopen() (in module gromacs.utilities)
array (gromacs.formats.XVG attribute)
array() (gromacs.qsub.QueuingSystem method)
array_flag() (gromacs.qsub.QueuingSystem method)
asiterable() (in module edPDB.utilities)
(in module gromacs.utilities)
AtomGroup (class in edPDB.xpdb)
AttributeDict (class in gromacs.utilities)
AutoCorrectionWarning

B

BadParameterWarning

C

canonical() (in module edPDB.selections)
cat() (gromacs.qsub.Manager method)
(in module gromacs.cbook)
center_fit() (gromacs.cbook.Transformer method)
check_file() (gromacs.analysis.core.Simulation method)
check_file_exists() (gromacs.utilities.FileUtils method)
check_mdrun_success() (in module gromacs.run)
check_plugin_name() (gromacs.analysis.core.Simulation method)
check_success() (gromacs.run.MDrunner method)
cleanup() (gromacs.cbook.Frames method)
(staging.SunGridEngine.Job method)
Collection (class in gromacs.analysis.collections)
COM (class in gromacs.analysis.plugins)
COM.COM (class in gromacs.analysis.plugins)
combine() (gromacs.cbook.IndexBuilder method)
Command (class in gromacs.core)
command_name (gromacs.core.Command attribute)
commandline() (gromacs.core.GromacsCommand method)
(gromacs.run.MDrunner method)
communicate() (gromacs.core.PopenWithInput method)
configdir (in module gromacs.config)
convert_aa_code() (in module gromacs.utilities)
create_portable_topology() (in module gromacs.cbook)
current_plugin (gromacs.analysis.core.Simulation attribute)
CysAccessibility (class in gromacs.analysis.plugins)
CysAccessibility.CysAccessibility (class in gromacs.analysis.plugins)

D

default_extension (gromacs.utilities.FileUtils attribute)
delete_frames() (gromacs.cbook.Frames method)
detect_queuing_system() (in module gromacs.qsub)
Dihedrals (class in gromacs.analysis.plugins)
Dihedrals.Dihedrals (class in gromacs.analysis.plugins)
dist (gromacs.analysis.plugins.dist.Mindist attribute)
Distances (class in gromacs.analysis.plugins)
Distances.Distances (class in gromacs.analysis.plugins)
Do_dssp (class in gromacs.tools)

E

edges (gromacs.analysis.plugins.dist.Mindist attribute)
edit_mdp() (in module gromacs.cbook), [1]
edit_txt() (in module gromacs.cbook)
Editconf (class in gromacs.tools)
edPDB (module)
edPDB.cbook (module)
edPDB.log (module)
edPDB.selections (module)
edPDB.utilities (module)
edPDB.xpdb (module)
Eneconv (class in gromacs.tools)
Energy (class in gromacs.analysis.plugins)
Energy.Energy (class in gromacs.analysis.plugins)
energy_minimize() (in module gromacs.setup)
environment variable
JOB_NAME
PATH, [1], [2]
SGE_TASK_ID
errorbar() (gromacs.formats.XVG method)
extract() (gromacs.cbook.Frames method)
extract_lipids() (edPDB.cbook.PDB method)
extract_protein() (edPDB.cbook.PDB method)
extract_resnames() (edPDB.cbook.PDB method)

F

failuremodes (gromacs.core.GromacsCommand attribute)
filename() (gromacs.utilities.FileUtils method)
FileUtils (class in gromacs.utilities)
find_first() (in module gromacs.utilities)
find_water() (in module edPDB.selections)
fit() (gromacs.cbook.Transformer method)
flag() (gromacs.qsub.QueuingSystem method)
format (gromacs.formats.NDX attribute)
Frames (class in gromacs.cbook)

G

G_anaeig (class in gromacs.tools)
G_analyze (class in gromacs.tools)
G_angle (class in gromacs.tools)
G_bond (class in gromacs.tools)
G_bundle (class in gromacs.tools)
G_chi (class in gromacs.tools)
G_cluster (class in gromacs.tools)
G_clustsize (class in gromacs.tools)
G_confrms (class in gromacs.tools)
G_covar (class in gromacs.tools)
G_current (class in gromacs.tools)
G_density (class in gromacs.tools)
G_densmap (class in gromacs.tools)
G_dielectric (class in gromacs.tools)
G_dih (class in gromacs.tools)
G_dipoles (class in gromacs.tools)
G_disre (class in gromacs.tools)
G_dist (class in gromacs.tools)
G_dyndom (class in gromacs.tools)
G_enemat (class in gromacs.tools)
G_energy (class in gromacs.tools)
G_filter (class in gromacs.tools)
G_gyrate (class in gromacs.tools)
G_h2order (class in gromacs.tools)
G_hbond (class in gromacs.tools)
G_helix (class in gromacs.tools)
G_helixorient (class in gromacs.tools)
G_lie (class in gromacs.tools)
G_mdmat (class in gromacs.tools)
G_mindist (class in gromacs.tools)
G_morph (class in gromacs.tools)
G_msd (class in gromacs.tools)
G_nmeig (class in gromacs.tools)
G_nmens (class in gromacs.tools)
G_nmtraj (class in gromacs.tools)
G_order (class in gromacs.tools)
G_polystat (class in gromacs.tools)
G_potential (class in gromacs.tools)
G_principal (class in gromacs.tools)
G_rama (class in gromacs.tools)
G_rdf (class in gromacs.tools)
G_rms (class in gromacs.tools)
G_rmsf (class in gromacs.tools)
G_rotacf (class in gromacs.tools)
G_saltbr (class in gromacs.tools)
G_sas (class in gromacs.tools)
G_sdf (class in gromacs.tools)
G_sgangle (class in gromacs.tools)
G_sham (class in gromacs.tools)
G_sorient (class in gromacs.tools)
G_spatial (class in gromacs.tools)
G_spol (class in gromacs.tools)
G_tcaf (class in gromacs.tools)
G_traj (class in gromacs.tools)
G_vanhove (class in gromacs.tools)
G_velacc (class in gromacs.tools)
G_wham (class in gromacs.tools)
GdistData (class in gromacs.analysis.plugins.dist)
Genbox (class in gromacs.tools)
Genconf (class in gromacs.tools)
generate_submit_array() (in module gromacs.qsub)
generate_submit_scripts() (in module gromacs.qsub)
Genion (class in gromacs.tools)
Genrestr (class in gromacs.tools)
get() (gromacs.formats.NDX method)
(gromacs.qsub.Manager method)
get_dir() (gromacs.qsub.Manager method)
get_fields_from_arraylist() (in module staging.SunGridEngine)
get_ndx_groups() (in module gromacs.cbook)
get_plugin() (gromacs.analysis.core.Simulation method)
get_status() (gromacs.qsub.Manager method)
get_structure() (in module edPDB.xpdb)
get_template() (in module gromacs.config)
get_templates() (in module gromacs.config)
get_value_from_arraylist() (in module staging.SunGridEngine)
get_version() (in module gromacs)
get_volume() (in module gromacs.cbook), [1]
getline_from_arraylist() (in module staging.SunGridEngine)
gmx_extra_tools (in module gromacs.config)
gmx_resid() (gromacs.cbook.IndexBuilder method)
gmx_tool_groups (in module gromacs.config)
gmx_tools (in module gromacs.config)
Gmxcheck (class in gromacs.tools)
gmxdoc (gromacs.core.GromacsCommand attribute)
Gmxdump (class in gromacs.tools)
Grid2D (class in gromacs.analysis.plugins.gridmatmd)
GridMAT_MD (class in gromacs.tools), [1]
GridMAT_MD.GridMAT_MD (class in gromacs.tools), [1]
GridMatData (class in gromacs.analysis.plugins.gridmatmd)
GridMatMD (class in gromacs.analysis.plugins.gridmatmd)
GRO (class in gromacs.formats)
gromacs (module)
gromacs.analysis (module)
gromacs.analysis.collections (module)
gromacs.analysis.core (module)
gromacs.analysis.plugins (module)
gromacs.analysis.plugins.dist (module)
gromacs.analysis.plugins.gridmatmd (module)
gromacs.cbook (module)
gromacs.config (module)
gromacs.core (module)
gromacs.formats (module)
gromacs.qsub (module)
gromacs.run (module)
gromacs.setup (module)
gromacs.tools (module), [1]
gromacs.utilities (module)
GromacsCommand (class in gromacs.core)
GromacsCommandMultiIndex (class in gromacs.tools), [1]
GromacsError
GromacsFailureWarning
GromacsImportWarning
GromacsValueWarning
Grompp (class in gromacs.tools)
grompp_qtot() (in module gromacs.cbook), [1]
groups (gromacs.formats.NDX attribute)

H

has_arrays() (gromacs.qsub.QueuingSystem method)
has_plugin() (gromacs.analysis.core.Simulation method)
HelixBundle (class in gromacs.analysis.plugins)
HelixBundle.HelixBundle (class in gromacs.analysis.plugins)
help() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
hist (gromacs.analysis.plugins.dist.Mindist attribute)
histogram() (gromacs.analysis.plugins.dist.Mindist method)

I

imshow() (gromacs.analysis.plugins.gridmatmd.Grid2D method)
(gromacs.analysis.plugins.gridmatmd.GridMatData method)
(gromacs.analysis.plugins.gridmatmd.GridMatMD method)
in_dir() (in module gromacs.utilities)
IndexBuilder (class in gromacs.cbook)
infix_filename() (gromacs.utilities.FileUtils method)
isMine() (gromacs.qsub.QueuingSystem method)
iterable() (in module edPDB.utilities)
(in module gromacs.utilities)

J

Job (class in staging.Local)
(class in staging.SunGridEngine)
job_done() (gromacs.qsub.Manager method)
JOB_NAME
join() (gromacs.formats.uniqueNDX method)

L

load_scripts (in module gromacs.config)
load_tools (in module gromacs.config)
local_get() (gromacs.qsub.Manager method)
log_RE (gromacs.qsub.Manager attribute)
logfilename (in module gromacs.config)
loglevel_console (in module gromacs.config)
loglevel_file (in module gromacs.config)
Ls (class in gromacs.analysis.plugins)
Ls.Ls (class in gromacs.analysis.plugins)
Luck (class in gromacs.tools)

M

ma (gromacs.formats.XVG attribute)
Make_edi (class in gromacs.tools)
make_main_index() (in module gromacs.setup)
Make_ndx (class in gromacs.tools)
make_ndx_captured() (in module gromacs.cbook)
Manager (class in gromacs.qsub)
max (gromacs.formats.XVG attribute)
MD() (in module gromacs.setup)
MD_restrained() (in module gromacs.setup)
Mdrun (class in gromacs.tools), [1]
mdrun (gromacs.run.MDrunner attribute)
Mdrun_d (class in gromacs.tools)
MDrunner (class in gromacs.run)
MDrunnerMpich2Smpd (class in gromacs.run)
MDrunnerOpenMP (class in gromacs.run)
MDrunnerOpenMP64 (class in gromacs.run)
mean (gromacs.formats.XVG attribute)
midpoints (gromacs.analysis.plugins.dist.Mindist attribute)
min (gromacs.formats.XVG attribute)
Mindist (class in gromacs.analysis.plugins.dist)
MinDistances (class in gromacs.analysis.plugins)
MinDistances.Distances (class in gromacs.analysis.plugins)
MissingDataError
MissingDataWarning
Mk_angndx (class in gromacs.tools)
mpicommand() (gromacs.run.MDrunner method)
mpiexec (gromacs.run.MDrunner attribute)

N

ncol (gromacs.formats.NDX attribute)
ndependent() (gromacs.qsub.Manager method)
NDX (class in gromacs.formats)
ndxlist (gromacs.formats.NDX attribute)
NotResidueSelect (class in edPDB.selections)
number_pdbs() (in module gromacs.utilities)

O

openany() (in module gromacs.utilities)

P

parse() (gromacs.formats.XVG method)
parse_filename() (gromacs.analysis.plugins.gridmatmd.GridMatData method)
parse_ndxlist() (in module gromacs.cbook), [1]
ParseError
PATH, [1], [2]
path (in module gromacs.config)
PDB (class in edPDB.cbook)
Pdb2gmx (class in gromacs.tools)
plot() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.Simulation method)
(gromacs.analysis.plugins.dist.Mindist method)
(gromacs.formats.XVG method)
Plugin (class in gromacs.analysis.core)
plugin_name (gromacs.analysis.core.Plugin attribute)
plugindir() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.core.Worker method)
Popen() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
PopenWithInput (class in gromacs.core)
posthook() (gromacs.run.MDrunner method)
prehook() (gromacs.run.MDrunner method)
PROTEIN_RESNAMES (in module edPDB.selections)
ProteinSelect (class in edPDB.selections)
Protonate (class in gromacs.tools)
put() (gromacs.qsub.Manager method)
putfile() (gromacs.qsub.Manager method)
Python Enhancement Proposals!PEP 0372

Q

qscript_template (in module gromacs.config)
qscriptdir (in module gromacs.config)
qstat() (gromacs.qsub.Manager method)
qsub() (gromacs.qsub.Manager method)
queuing_systems (in module gromacs.qsub)
QueuingSystem (class in gromacs.qsub)

R

read() (gromacs.formats.GRO method)
(gromacs.formats.NDX method)
(gromacs.formats.XVG method)
realpath() (in module gromacs.utilities)
register() (gromacs.analysis.core.Plugin method)
remotepath() (gromacs.qsub.Manager method)
remoteuri() (gromacs.qsub.Manager method)
remove_legend() (in module gromacs.utilities)
remove_overlap_water() (in module edPDB.cbook)
residues_by_resname() (edPDB.cbook.PDB method)
(in module edPDB.selections)
residues_by_selection() (edPDB.cbook.PDB method)
(in module edPDB.selections)
ResidueSelect (class in edPDB.selections)
ResnameSelect (class in edPDB.selections)
RMSD (class in gromacs.analysis.plugins)
RMSD.RMSD (class in gromacs.analysis.plugins)
rmsd_backbone() (in module gromacs.cbook)
RMSF (class in gromacs.analysis.plugins)
RMSF.RMSF (class in gromacs.analysis.plugins)
rp() (gromacs.cbook.Transformer method)
run() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.Simulation method)
(gromacs.analysis.plugins.gridmatmd.GridMatMD method)
(gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
(gromacs.run.MDrunner method)
(gromacs.tools.GromacsCommandMultiIndex method), [1]
run_all() (gromacs.analysis.core.Simulation method)
run_check() (gromacs.run.MDrunner method)
run_frame() (gromacs.analysis.plugins.gridmatmd.GridMatMD method)

S

save() (gromacs.analysis.plugins.gridmatmd.GridMatMD method)
(staging.Local.Job method)
(staging.SunGridEngine.Job method)
savefig() (gromacs.analysis.core.Worker method)
set() (gromacs.formats.NDX method)
(gromacs.formats.XVG method)
set_plugin() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.Simulation method)
setup() (in module gromacs.config)
setup_MD() (gromacs.qsub.Manager method)
setup_posres() (gromacs.qsub.Manager method)
SGE_TASK_ID
Sigeps (class in gromacs.tools)
Simulation (class in gromacs.analysis)
(class in gromacs.analysis.core)
simulation (gromacs.analysis.core.Plugin attribute)
size() (gromacs.formats.NDX method)
sizes (gromacs.formats.NDX attribute)
SloppyPDBIO (class in edPDB.xpdb)
SloppyStructureBuilder (class in edPDB.xpdb)
solvate() (in module gromacs.setup)
stage() (staging.SunGridEngine.Job method)
staging (module)
staging.Local (module)
staging.SunGridEngine (module)
std (gromacs.formats.XVG attribute)
strip_water() (gromacs.cbook.Transformer method)
StripWater (class in gromacs.analysis.plugins)
StripWater.StripWater (class in gromacs.analysis.plugins)

T

templates (in module gromacs.config)
templatesdir (in module gromacs.config)
Timedelta (class in gromacs.utilities)
topdir() (gromacs.analysis.core.Simulation method)
(gromacs.analysis.core.Worker method)
topology() (in module gromacs.setup)
Tpbconv (class in gromacs.tools)
Trajectories (class in gromacs.analysis.plugins)
Trajectories.Trajectories (class in gromacs.analysis.plugins)
transform_args() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
Transformer (class in gromacs.cbook)
trj_compact() (in module gromacs.cbook)
trj_fitandcenter() (in module gromacs.cbook)
trj_xyfitted() (in module gromacs.cbook)
Trjcat (class in gromacs.tools)
Trjconv (class in gromacs.tools)
Trjorder (class in gromacs.tools)

U

uniqueNDX (class in gromacs.formats)
unlink_f() (in module gromacs.utilities)
unlink_gmx() (in module gromacs.utilities)
unlink_gmx_backups() (in module gromacs.utilities)
unstage() (staging.SunGridEngine.Job method)
UsageWarning

V

vmd (module)
vmd.control (module)

W

waitfor() (gromacs.qsub.Manager method)
Wheel (class in gromacs.tools)
withextsep() (in module gromacs.utilities)
Worker (class in gromacs.analysis.core)
worker (gromacs.analysis.core.Plugin attribute)
worker_class (gromacs.analysis.core.Plugin attribute)
(gromacs.analysis.plugins.COM attribute)
(gromacs.analysis.plugins.CysAccessibility attribute)
(gromacs.analysis.plugins.Dihedrals attribute)
(gromacs.analysis.plugins.Distances attribute)
(gromacs.analysis.plugins.Energy attribute)
(gromacs.analysis.plugins.HelixBundle attribute)
(gromacs.analysis.plugins.Ls attribute)
(gromacs.analysis.plugins.MinDistances attribute)
(gromacs.analysis.plugins.RMSD attribute)
(gromacs.analysis.plugins.RMSF attribute)
(gromacs.analysis.plugins.StripWater attribute)
(gromacs.analysis.plugins.Trajectories attribute)
write() (edPDB.cbook.PDB method)
(gromacs.formats.NDX method)
(gromacs.formats.XVG method)
write_pdb() (in module edPDB.xpdb)

X

X2top (class in gromacs.tools)
Xpm2ps (class in gromacs.tools)
XVG (class in gromacs.formats)