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GromacsWrapper
Index
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Index
Symbols
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_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
Symbols
$HOME
_
__call__() (gromacs.core.Command method)
__version__ (in module gromacs)
_setup_MD() (in module gromacs.setup)
A
activate_subplot() (in module gromacs.utilities)
active (gromacs.fileformats.convert.Autoconverter attribute)
(gromacs.fileformats.convert.Autoconverter property)
add_mdp_includes() (in module gromacs.cbook)
all_frames (gromacs.cbook.Frames property)
amino_acid_codes (in module gromacs.utilities)
AngleType (class in gromacs.fileformats.blocks)
anumb_to_atom() (gromacs.fileformats.blocks.Molecule method)
anyopen() (in module gromacs.utilities)
array (gromacs.fileformats.xpm.XPM property)
(gromacs.fileformats.xvg.XVG property)
array() (gromacs.qsub.QueuingSystem method)
array_flag() (gromacs.qsub.QueuingSystem method)
asiterable() (in module gromacs.utilities)
assemble_topology() (gromacs.fileformats.top.SystemToGroTop method)
Atom (class in gromacs.fileformats.blocks)
AtomType (class in gromacs.fileformats.blocks)
AttributeDict (class in gromacs.utilities)
autoconvert() (in module gromacs.utilities)
Autoconverter (class in gromacs.fileformats.convert)
Autoconverter.convert() (in module gromacs.fileformats.convert)
AutoCorrectionWarning
B
BadParameterWarning
besttype() (in module gromacs.fileformats.convert)
BondType (class in gromacs.fileformats.blocks)
break_array() (in module gromacs.fileformats.xvg)
C
cat() (in module gromacs.cbook)
center_fit() (gromacs.cbook.Transformer method)
cfg (in module gromacs.config)
check_file_exists() (gromacs.utilities.FileUtils method)
check_mdpargs() (in module gromacs.setup)
check_mdrun_success() (in module gromacs.run)
check_setup() (in module gromacs.config)
check_success() (gromacs.run.MDrunner method)
cleanup() (gromacs.cbook.Frames method)
CMapType (class in gromacs.fileformats.blocks)
col() (gromacs.fileformats.xpm.XPM method)
Collection (class in gromacs.collections)
COLOUR (gromacs.fileformats.xpm.XPM attribute)
combine() (gromacs.cbook.IndexBuilder method)
Command (class in gromacs.core)
command_name (gromacs.core.Command attribute)
(gromacs.core.GromacsCommand attribute)
commandline() (gromacs.core.GromacsCommand method)
(gromacs.run.MDrunner method)
communicate() (gromacs.core.PopenWithInput method)
CONC_WATER (in module gromacs.setup)
configdir (in module gromacs.config)
CONFIGNAME (in module gromacs.config)
configuration (gromacs.config.GMXConfigParser property)
(in module gromacs.config)
ConstraintType (class in gromacs.fileformats.blocks)
convert_aa_code() (in module gromacs.utilities)
create_portable_topology() (in module gromacs.cbook)
D
decimate() (gromacs.fileformats.xvg.XVG method)
decimate_circmean() (gromacs.fileformats.xvg.XVG method)
decimate_error() (gromacs.fileformats.xvg.XVG method)
decimate_max() (gromacs.fileformats.xvg.XVG method)
decimate_mean() (gromacs.fileformats.xvg.XVG method)
decimate_min() (gromacs.fileformats.xvg.XVG method)
decimate_percentile() (gromacs.fileformats.xvg.XVG method)
decimate_rms() (gromacs.fileformats.xvg.XVG method)
decimate_smooth() (gromacs.fileformats.xvg.XVG method)
default_color_cycle (gromacs.fileformats.xvg.XVG attribute)
default_extension (gromacs.fileformats.mdp.MDP attribute)
(gromacs.fileformats.ndx.NDX attribute)
(gromacs.fileformats.xpm.XPM attribute)
(gromacs.fileformats.xvg.XVG attribute)
(gromacs.utilities.FileUtils attribute)
defaults (in module gromacs.config)
delete_frames() (gromacs.cbook.Frames method)
detect_queuing_system() (in module gromacs.qsub)
DihedralType (class in gromacs.fileformats.blocks)
doc() (gromacs.environment.Flags method)
E
edit_mdp() (in module gromacs.cbook)
,
[1]
edit_txt() (in module gromacs.cbook)
em_schedule() (in module gromacs.setup)
energy_minimize() (in module gromacs.setup)
environment variable
$HOME
GMXBIN
GMXDATA
GROMACSWRAPPER_SUPPRESS_SETUP_CHECK
,
[1]
,
[2]
GW_START_LOGGING
LD_LIBRARY_PATH
PATH
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
,
[8]
,
[9]
,
[10]
,
[11]
error (gromacs.fileformats.xvg.XVG property)
errorbar() (gromacs.fileformats.xvg.XVG method)
Exclusion (class in gromacs.fileformats.blocks)
extract() (gromacs.cbook.Frames method)
F
failuremode (gromacs.core.GromacsCommand property)
failuremodes (gromacs.core.GromacsCommand attribute)
filename() (gromacs.utilities.FileUtils method)
FileUtils (class in gromacs.utilities)
find_executables() (in module gromacs.tools)
find_first() (in module gromacs.utilities)
find_gromacs_command() (in module gromacs.run)
firstof() (in module gromacs.utilities)
fit() (gromacs.cbook.Transformer method)
Flag (class in gromacs.environment)
flag() (gromacs.qsub.QueuingSystem method)
Flags (class in gromacs.environment)
flags (in module gromacs.environment)
flagsDocs (class in gromacs.environment)
format (gromacs.fileformats.ndx.NDX attribute)
framenumber (gromacs.cbook.Frames attribute)
Frames (class in gromacs.cbook)
G
generate_submit_array() (in module gromacs.qsub)
generate_submit_scripts() (in module gromacs.qsub)
get() (gromacs.fileformats.ndx.NDX method)
get_configuration() (in module gromacs.config)
get_double_or_single_prec_mdrun() (in module gromacs.run)
get_lipid_vdwradii() (in module gromacs.setup)
get_ndx_groups() (in module gromacs.cbook)
get_template() (in module gromacs.config)
get_templates() (in module gromacs.config)
get_volume() (in module gromacs.cbook)
,
[1]
getLogLevel() (gromacs.config.GMXConfigParser method)
getpath() (gromacs.config.GMXConfigParser method)
gmx_resid() (gromacs.cbook.IndexBuilder method)
GMXBIN
GMXConfigParser (class in gromacs.config)
GMXDATA
gromacs
module
gromacs.cbook
module
gromacs.collections
module
gromacs.config
module
gromacs.core
module
gromacs.environment
module
gromacs.fileformats.blocks
module
gromacs.fileformats.convert
module
gromacs.fileformats.mdp
module
gromacs.fileformats.ndx
module
gromacs.fileformats.top
module
gromacs.fileformats.xpm
module
gromacs.fileformats.xvg
module
gromacs.qsub
module
gromacs.run
module
gromacs.scaling
module
gromacs.setup
module
gromacs.tools
module
gromacs.utilities
module
GromacsCommand (class in gromacs.core)
GromacsCommandMultiIndex (class in gromacs.tools)
GromacsError
GromacsFailureWarning
GromacsImportWarning
GromacsToolLoadingError
GromacsValueWarning
GROMACSWRAPPER_SUPPRESS_SETUP_CHECK
,
[1]
,
[2]
grompp_qtot() (in module gromacs.cbook)
,
[1]
groups (gromacs.fileformats.ndx.NDX property)
GW_START_LOGGING
H
has_arrays() (gromacs.qsub.QueuingSystem method)
hasmethod() (in module gromacs.utilities)
help() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
I
ImproperType (class in gromacs.fileformats.blocks)
in_dir() (in module gromacs.utilities)
IndexBuilder (class in gromacs.cbook)
IndexSet (class in gromacs.fileformats.ndx)
infix_filename() (gromacs.utilities.FileUtils method)
InteractionType (class in gromacs.fileformats.blocks)
isMine() (gromacs.qsub.QueuingSystem method)
isstream() (in module gromacs.utilities)
items() (gromacs.environment.Flags method)
iterable() (in module gromacs.utilities)
J
join() (gromacs.fileformats.ndx.uniqueNDX method)
K
keep_protein_only() (gromacs.cbook.Transformer method)
L
LD_LIBRARY_PATH
load_v4_tools() (in module gromacs.tools)
load_v5_tools() (in module gromacs.tools)
logfilename (in module gromacs.config)
loglevel_console (in module gromacs.config)
loglevel_file (in module gromacs.config)
LowAccuracyWarning
M
ma (gromacs.fileformats.xvg.XVG property)
make_main_index() (in module gromacs.setup)
make_ndx_captured() (in module gromacs.cbook)
make_valid_identifier() (in module gromacs.tools)
max (gromacs.fileformats.xvg.XVG property)
maxpoints_default (gromacs.fileformats.xvg.XVG attribute)
MD() (in module gromacs.setup)
MD_restrained() (in module gromacs.setup)
MDP (class in gromacs.fileformats.mdp)
mdrun (gromacs.run.MDrunner attribute)
(gromacs.run.MDrunnerMpich2Smpd attribute)
(gromacs.run.MDrunnerOpenMP attribute)
MDrunner (class in gromacs.run)
MDrunnerDoublePrecision (class in gromacs.run)
MDrunnerMpich2Smpd (class in gromacs.run)
MDrunnerOpenMP (class in gromacs.run)
mean (gromacs.fileformats.xvg.XVG property)
merge_ndx() (in module gromacs.tools)
min (gromacs.fileformats.xvg.XVG property)
MissingDataError
MissingDataWarning
module
gromacs
gromacs.cbook
gromacs.collections
gromacs.config
gromacs.core
gromacs.environment
gromacs.fileformats.blocks
gromacs.fileformats.convert
gromacs.fileformats.mdp
gromacs.fileformats.ndx
gromacs.fileformats.top
gromacs.fileformats.xpm
gromacs.fileformats.xvg
gromacs.qsub
gromacs.run
gromacs.scaling
gromacs.setup
gromacs.tools
gromacs.utilities
Molecule (class in gromacs.fileformats.blocks)
mpicommand() (gromacs.run.MDrunner method)
mpiexec (gromacs.run.MDrunner attribute)
(gromacs.run.MDrunnerMpich2Smpd attribute)
(gromacs.run.MDrunnerOpenMP attribute)
N
NAMES5TO4 (in module gromacs.tools)
ncol (gromacs.fileformats.ndx.NDX attribute)
NDX (class in gromacs.fileformats.ndx)
ndxlist (gromacs.fileformats.ndx.NDX property)
NonbondedParamType (class in gromacs.fileformats.blocks)
number_pdbs() (in module gromacs.utilities)
O
openany() (in module gromacs.utilities)
outfile() (gromacs.cbook.Transformer method)
P
Param (class in gromacs.fileformats.blocks)
parse() (gromacs.fileformats.xpm.XPM method)
(gromacs.fileformats.xvg.XVG method)
parse_ndxlist() (in module gromacs.cbook)
,
[1]
ParseError
partial_tempering() (in module gromacs.scaling)
PATH
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
,
[8]
,
[9]
,
[10]
,
[11]
path (in module gromacs.config)
plot() (gromacs.fileformats.xvg.XVG method)
plot_coarsened() (gromacs.fileformats.xvg.XVG method)
Popen() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
PopenWithInput (class in gromacs.core)
posthook() (gromacs.run.MDrunner method)
(gromacs.run.MDrunnerMpich2Smpd method)
prehook() (gromacs.run.MDrunner method)
(gromacs.run.MDrunnerMpich2Smpd method)
prop() (gromacs.environment.Flag method)
Q
qscript_template (in module gromacs.config)
qscriptdir (in module gromacs.config)
queuing_systems (in module gromacs.qsub)
QueuingSystem (class in gromacs.qsub)
R
read() (gromacs.fileformats.mdp.MDP method)
(gromacs.fileformats.ndx.NDX method)
(gromacs.fileformats.xpm.XPM method)
(gromacs.fileformats.xvg.XVG method)
realpath() (in module gromacs.utilities)
register() (gromacs.environment.Flags method)
registry (in module gromacs.tools)
Release (class in gromacs.tools)
remove_legend() (in module gromacs.utilities)
renumber_atoms() (gromacs.fileformats.blocks.Molecule method)
rmsd_backbone() (in module gromacs.cbook)
rp() (gromacs.cbook.Transformer method)
run() (gromacs.core.Command method)
(gromacs.core.GromacsCommand method)
(gromacs.run.MDrunner method)
run_check() (gromacs.run.MDrunner method)
S
scale_dihedrals() (in module gromacs.scaling)
scale_impropers() (in module gromacs.scaling)
set() (gromacs.fileformats.ndx.NDX method)
(gromacs.fileformats.xvg.XVG method)
set_correlparameters() (gromacs.fileformats.xvg.XVG method)
set_gmxrc_environment() (in module gromacs.config)
setdefault() (gromacs.environment.Flags method)
(gromacs.fileformats.ndx.NDX method)
SettleType (class in gromacs.fileformats.blocks)
setup() (in module gromacs.config)
signal_handler() (gromacs.run.MDrunner method)
size() (gromacs.fileformats.ndx.NDX method)
sizes (gromacs.fileformats.ndx.NDX property)
solvate() (in module gromacs.setup)
std (gromacs.fileformats.xvg.XVG property)
strip_fit() (gromacs.cbook.Transformer method)
strip_water() (gromacs.cbook.Transformer method)
System (class in gromacs.fileformats.blocks)
SystemToGroTop (class in gromacs.fileformats.top)
T
tc (gromacs.fileformats.xvg.XVG property)
templates (in module gromacs.config)
templatesdir (in module gromacs.config)
Timedelta (class in gromacs.utilities)
to_unicode() (in module gromacs.fileformats.convert)
tool_factory() (in module gromacs.tools)
TOP (class in gromacs.fileformats.top)
topology() (in module gromacs.setup)
totalframes (gromacs.cbook.Frames attribute)
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)
U
uncomment() (gromacs.fileformats.xpm.XPM static method)
uniqueNDX (class in gromacs.fileformats.ndx)
unlink_f() (in module gromacs.utilities)
unlink_gmx() (in module gromacs.utilities)
unlink_gmx_backups() (in module gromacs.utilities)
unquote() (gromacs.fileformats.xpm.XPM static method)
update() (gromacs.environment.Flags method)
UsageWarning
V
V4TOOLS (in module gromacs.tools)
values() (gromacs.environment.Flags method)
vdw_lipid_atom_radii (in module gromacs.setup)
vdw_lipid_resnames (in module gromacs.setup)
VirtualSites3Type (class in gromacs.fileformats.blocks)
W
which() (in module gromacs.utilities)
withextsep() (in module gromacs.utilities)
write() (gromacs.fileformats.mdp.MDP method)
(gromacs.fileformats.ndx.NDX method)
(gromacs.fileformats.top.TOP method)
(gromacs.fileformats.xvg.XVG method)
X
XPM (class in gromacs.fileformats.xpm)
xvalues (gromacs.fileformats.xpm.XPM attribute)
XVG (class in gromacs.fileformats.xvg)
Y
yvalues (gromacs.fileformats.xpm.XPM attribute)
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