Index

Symbols

$HOME

_

__add__() (gromacs.analysis.plugins.gridmatmd.Grid2D method) __call__() (gromacs.core.Command method) __del__() (gromacs.tools.GromacsCommandMultiIndex method) __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) _register_hook() (gromacs.analysis.core.Worker method) _setup_MD() (in module gromacs.setup)

A

activate_subplot() (in module gromacs.utilities) active (gromacs.fileformats.convert.Autoconverter attribute), [1] add_mdp_includes() (in module gromacs.cbook) add_plugin() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation method) add_section() (gromacs.manager.ManagerConfigParser method) all_frames (gromacs.cbook.Frames attribute) amino_acid_codes (in module gromacs.utilities) analyze() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation method) analyze_all() (gromacs.analysis.core.Simulation method) Angles (class in gromacs.fileformats.itp) anyopen() (in module gromacs.utilities) apply_histogrammed_function() (in module numkit.timeseries) array (gromacs.fileformats.xpm.XPM attribute) (gromacs.fileformats.xvg.XVG attribute) array() (gromacs.qsub.QueuingSystem method)

array_flag() (gromacs.qsub.QueuingSystem method) asiterable() (in module gromacs.utilities) asQuantityWithError() (numkit.observables.QuantityWithError static method) astuple() (numkit.observables.QuantityWithError method) Atoms (class in gromacs.fileformats.itp) Atomtypes (class in gromacs.fileformats.itp) AttributeDict (class in gromacs.utilities) autoconvert() (in module gromacs.utilities) Autoconverter (class in gromacs.fileformats.convert) Autoconverter.convert() (in module gromacs.fileformats.convert) AutoCorrectionWarning autocorrelation_fft() (in module numkit.timeseries) averages (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute)

B

BadParameterWarning besttype() (in module gromacs.fileformats.convert) Bonds (class in gromacs.fileformats.itp)

break_array() (in module gromacs.fileformats.xvg) buffer (gromacs.fileformats.preprocessor.Preprocessor attribute)

C

cat() (gromacs.manager.Manager method) (in module gromacs.cbook) center_fit() (gromacs.cbook.Transformer method) cfg (in module gromacs.config) check_file() (gromacs.analysis.core.Simulation method) check_file_exists() (gromacs.utilities.FileUtils method) check_mdpargs() (in module gromacs.setup) check_mdrun_success() (in module gromacs.run) check_plugin_name() (gromacs.analysis.core.Simulation method) check_setup() (in module gromacs.config) check_success() (gromacs.run.MDrunner method) circmean_histogrammed_function() (in module numkit.timeseries) circstd_histogrammed_function() (in module numkit.timeseries) cleanup() (gromacs.cbook.Frames method) (staging.SunGridEngine.Job method) col() (gromacs.fileformats.xpm.XPM method) Collection (class in gromacs.analysis.collections) COLOUR (gromacs.fileformats.xpm.XPM attribute) 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) compare_defines_and_conditions() (gromacs.fileformats.preprocessor.Preprocessor method) CONC_WATER (in module gromacs.setup) configdir (in module gromacs.config) CONFIGNAME (in module gromacs.config) configuration (gromacs.config.GMXConfigParser attribute) (in module gromacs.config) contains_preprocessor_constructs() (gromacs.fileformats.itp.ITP method) convert_aa_code() (in module gromacs.utilities) copy() (numkit.observables.QuantityWithError method) 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

data (gromacs.fileformats.itp.ITPdata attribute) 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) deepcopy() (numkit.observables.QuantityWithError method) default_color_cycle (gromacs.fileformats.xvg.XVG attribute) default_extension (gromacs.fileformats.xvg.XVG attribute) (gromacs.utilities.FileUtils attribute) defaults (in module gromacs.config)

define() (gromacs.fileformats.preprocessor.Preprocessor method) delete_frames() (gromacs.cbook.Frames method) detect_queuing_system() (in module gromacs.qsub) Dihedrals (class in gromacs.analysis.plugins) (class in gromacs.fileformats.itp) 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) doc() (gromacs.environment.Flags method) dtypes (gromacs.fileformats.itp.Angles attribute) (gromacs.fileformats.itp.Atoms attribute) (gromacs.fileformats.itp.Bonds attribute) (gromacs.fileformats.itp.Dihedrals attribute) Dummy (class in gromacs.fileformats.itp) dx (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) dy (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute)

E

edges (gromacs.analysis.plugins.dist.Mindist attribute) edit_mdp() (in module gromacs.cbook), [1] edit_txt() (in module gromacs.cbook) em_schedule() (in module gromacs.setup) Energy (class in gromacs.analysis.plugins) Energy.Energy (class in gromacs.analysis.plugins)

energy_minimize() (in module gromacs.setup) environment variable $HOME GROMACSWRAPPER_SUPPRESS_SETUP_CHECK, [1], [2] JOB_NAME PATH, [1] SGE_TASK_ID error (gromacs.fileformats.xvg.XVG attribute) (numkit.observables.QuantityWithError attribute) error_histogrammed_function() (in module numkit.timeseries) errorbar() (gromacs.fileformats.xvg.XVG method) extract() (gromacs.cbook.Frames method)

F

f_factory() (numkit.fitting.FitFunc method) failuremode (gromacs.core.GromacsCommand attribute) failuremodes (gromacs.core.GromacsCommand attribute) filename() (gromacs.utilities.FileUtils method) filenames (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) FileUtils (class in gromacs.utilities) find_first() (in module gromacs.utilities) find_manager_config() (in module gromacs.manager) firstof() (in module gromacs.utilities) fit() (gromacs.cbook.Transformer method) (numkit.fitting.FitFunc method) FitCompact (class in gromacs.analysis.plugins) FitCompact.FitCompact (class in gromacs.analysis.plugins) FitExp (class in numkit.fitting) FitExp2 (class in numkit.fitting)

FitFunc (class in numkit.fitting) FitGauss (class in numkit.fitting) FitLin (class in numkit.fitting) 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) flatten() (in module gromacs.fileformats.itp) fmt (gromacs.fileformats.itp.Angles attribute) (gromacs.fileformats.itp.Atoms attribute) (gromacs.fileformats.itp.Bonds attribute) (gromacs.fileformats.itp.Dihedrals attribute) format (gromacs.fileformats.ndx.NDX attribute) framenumber (gromacs.cbook.Frames attribute) Frames (class in gromacs.cbook) func() (in module numkit.timeseries), [1]

G

GdistData (class in gromacs.analysis.plugins.dist) generate_submit_array() (in module gromacs.qsub) generate_submit_scripts() (in module gromacs.qsub) get() (gromacs.fileformats.ndx.NDX method) (gromacs.manager.Manager method) (gromacs.manager.ManagerConfigParser method) get_configuration() (in module gromacs.config) get_dir() (gromacs.manager.Manager method) get_fields_from_arraylist() (in module staging.SunGridEngine) get_lipid_vdwradii() (in module gromacs.setup) get_manager_config() (in module gromacs.manager) get_ndx_groups() (in module gromacs.cbook) get_plugin() (gromacs.analysis.core.Simulation method) get_status() (gromacs.manager.Manager method) 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_version_tuple() (in module gromacs) get_volume() (in module gromacs.cbook), [1] getfloat() (gromacs.manager.ManagerConfigParser method) getline_from_arraylist() (in module staging.SunGridEngine) getlist() (gromacs.config.GMXConfigParser method) getLogLevel() (gromacs.config.GMXConfigParser method) getpath() (gromacs.config.GMXConfigParser method) (gromacs.manager.ManagerConfigParser method) gmx_resid() (gromacs.cbook.IndexBuilder method) GMXConfigParser (class in gromacs.config) gmxdoc (gromacs.core.GromacsCommand attribute) Grid2D (class in gromacs.analysis.plugins.gridmatmd) GridMAT_MD (class in gromacs.tools) GridMAT_MD.GridMAT_MD (class in gromacs.tools) GridMatData (class in gromacs.analysis.plugins.gridmatmd) GridMatMD (class in gromacs.analysis.plugins.gridmatmd) (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) GRO (class in gromacs.fileformats.gro) 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.environment (module) gromacs.fileformats.convert (module) gromacs.fileformats.gro (module) gromacs.fileformats.itp (module) gromacs.fileformats.mdp (module) gromacs.fileformats.ndx (module) gromacs.fileformats.preprocessor (module) gromacs.fileformats.xpm (module) gromacs.fileformats.xvg (module) gromacs.manager (module) gromacs.qsub (module) gromacs.run (module) gromacs.setup (module) gromacs.tools (module) gromacs.utilities (module) GromacsCommand (class in gromacs.core) GromacsCommandMultiIndex (class in gromacs.tools) GromacsError GromacsFailureWarning GromacsImportWarning GromacsValueWarning GROMACSWRAPPER_SUPPRESS_SETUP_CHECK, [1], [2] grompp_qtot() (in module gromacs.cbook), [1] groups (gromacs.fileformats.ndx.NDX attribute)

H

has_arrays() (gromacs.qsub.QueuingSystem method) has_option() (gromacs.manager.ManagerConfigParser method) has_plugin() (gromacs.analysis.core.Simulation method) has_section() (gromacs.manager.ManagerConfigParser method) HBonds (class in gromacs.analysis.plugins) HBonds.HBonds (class in gromacs.analysis.plugins)

Header (class in gromacs.fileformats.itp) 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) IndexSet (class in gromacs.fileformats.ndx) infix_filename() (gromacs.utilities.FileUtils method) initial_values() (numkit.fitting.FitFunc method) isMine() (gromacs.qsub.QueuingSystem method) isSame() (numkit.observables.QuantityWithError method)

items() (gromacs.manager.ManagerConfigParser method) iterable() (in module gromacs.utilities) ITP (class in gromacs.fileformats.itp) ITP.func() (in module gromacs.fileformats.itp) ITPdata (class in gromacs.fileformats.itp) ITPsection (class in gromacs.fileformats.itp) ITPsection.func() (in module gromacs.fileformats.itp)

J

Job (class in gromacs.manager) (class in staging.Local) (class in staging.SunGridEngine) job_done() (gromacs.manager.Manager method)

JOB_NAME join() (gromacs.fileformats.ndx.uniqueNDX method)

K

keep_protein_only() (gromacs.cbook.Transformer method)

L

lexer() (gromacs.fileformats.preprocessor.Preprocessor method) linfit() (in module numkit.fitting) load_scripts (in module gromacs.config) load_tools (in module gromacs.config) local_get() (gromacs.manager.Manager method) log_RE (gromacs.manager.Manager attribute)

logfilename (in module gromacs.config) loglevel_console (in module gromacs.config) loglevel_file (in module gromacs.config) LowAccuracyWarning, [1] Ls (class in gromacs.analysis.plugins) Ls.Ls (class in gromacs.analysis.plugins)

M

ma (gromacs.fileformats.xvg.XVG attribute) make_main_index() (in module gromacs.setup) make_ndx_captured() (in module gromacs.cbook) Manager (class in gromacs.manager) ManagerConfigParser (class in gromacs.manager) managerdir (in module gromacs.config) max (gromacs.fileformats.xvg.XVG attribute) max_histogrammed_function() (in module numkit.timeseries) 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 (class in gromacs.tools) mdrun (gromacs.run.MDrunner attribute) MDrunner (class in gromacs.run) MDrunnerMpich2Smpd (class in gromacs.run)

MDrunnerOpenMP (class in gromacs.run) MDrunnerOpenMP64 (class in gromacs.run) mean (gromacs.fileformats.xvg.XVG attribute) mean_histogrammed_function() (in module numkit.timeseries) median_histogrammed_function() (in module numkit.timeseries) midpoints (gromacs.analysis.plugins.dist.Mindist attribute) min (gromacs.fileformats.xvg.XVG attribute) min_histogrammed_function() (in module numkit.timeseries) Mindist (class in gromacs.analysis.plugins.dist) MinDistances (class in gromacs.analysis.plugins) MinDistances.Distances (class in gromacs.analysis.plugins) MissingDataError MissingDataWarning Moleculetype (class in gromacs.fileformats.itp) mpicommand() (gromacs.run.MDrunner method) mpiexec (gromacs.run.MDrunner attribute)

N

ncol (gromacs.fileformats.ndx.NDX attribute) ndependent() (gromacs.manager.Manager method) NDX (class in gromacs.fileformats.ndx) ndxlist (gromacs.fileformats.ndx.NDX attribute) next() (gromacs.fileformats.itp.OneLineBuffer method) number_pdbs() (in module gromacs.utilities)

numkit.fitting (module) numkit.integration (module) numkit.observables (module) numkit.timeseries (module) nx (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) ny (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute)

O

OneLineBuffer (class in gromacs.fileformats.itp) open() (gromacs.fileformats.preprocessor.Preprocessor method) openany() (in module gromacs.utilities)

options() (gromacs.manager.ManagerConfigParser method) outfile() (gromacs.cbook.Transformer method)

P

Pairs (class in gromacs.fileformats.itp) parse() (gromacs.fileformats.itp.ITP method) (gromacs.fileformats.preprocessor.Preprocessor method) (gromacs.fileformats.xpm.XPM method) (gromacs.fileformats.xvg.XVG method) parse_filename() (gromacs.analysis.plugins.gridmatmd.GridMatData method) parse_ndxlist() (in module gromacs.cbook), [1] ParseError PATH, [1] path (in module gromacs.config) Pearson_r() (in module numkit.fitting) percentile_histogrammed_function() (in module numkit.timeseries) plot() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation method) (gromacs.analysis.plugins.dist.Mindist method) (gromacs.fileformats.xvg.XVG method) plot_coarsened() (gromacs.fileformats.xvg.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) Preprocessor (class in gromacs.fileformats.preprocessor) prop() (gromacs.environment.Flag method) ProteinOnly (class in gromacs.analysis.plugins) ProteinOnly.ProteinOnly (class in gromacs.analysis.plugins) put() (gromacs.manager.Manager method) putfile() (gromacs.manager.Manager method) Python Enhancement Proposals PEP 0372

Q

QID (class in numkit.observables) qscript_template (in module gromacs.config) qscriptdir (in module gromacs.config) qstat() (gromacs.manager.Manager method)

qsub() (gromacs.manager.Manager method) QuantityWithError (class in numkit.observables) queuing_systems (in module gromacs.qsub) QueuingSystem (class in gromacs.qsub)

R

raise_error() (gromacs.fileformats.preprocessor.Preprocessor method) read() (gromacs.fileformats.gro.GRO method) (gromacs.fileformats.itp.ITP method) (gromacs.fileformats.mdp.MDP method) (gromacs.fileformats.ndx.NDX method) (gromacs.fileformats.xpm.XPM method) (gromacs.fileformats.xvg.XVG method) (gromacs.manager.ManagerConfigParser method) readfp() (gromacs.manager.ManagerConfigParser method) realpath() (in module gromacs.utilities) register() (gromacs.analysis.core.Plugin method) (gromacs.environment.Flags method) regularized_function() (in module numkit.timeseries) remotepath() (gromacs.manager.Manager method) remoteuri() (gromacs.manager.Manager method) remove_legend() (in module gromacs.utilities) remove_option() (gromacs.manager.ManagerConfigParser method) remove_section() (gromacs.manager.ManagerConfigParser method)

rms_histogrammed_function() (in module numkit.timeseries) 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) 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) search_defines() (gromacs.fileformats.preprocessor.Preprocessor method) section() (gromacs.fileformats.itp.ITPdata method) sections() (gromacs.manager.ManagerConfigParser method) set() (gromacs.fileformats.ndx.NDX method) (gromacs.fileformats.xvg.XVG method) (gromacs.manager.ManagerConfigParser method) set_correlparameters() (gromacs.fileformats.xvg.XVG method) set_data() (gromacs.fileformats.itp.ITPdata method) set_moleculename() (gromacs.fileformats.itp.Moleculetype method) set_plugin() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation method) set_resname() (gromacs.fileformats.itp.Atoms method) setup() (in module gromacs.config) setup_MD() (gromacs.manager.Manager method) setup_posres() (gromacs.manager.Manager method) SGE_TASK_ID simps_error() (in module numkit.integration) Simulation (class in gromacs.analysis) (class in gromacs.analysis.core)

simulation (gromacs.analysis.core.Plugin attribute) size() (gromacs.fileformats.ndx.NDX method) sizes (gromacs.fileformats.ndx.NDX attribute) smooth() (in module numkit.timeseries) smoothing_window_length() (in module numkit.timeseries) solvate() (in module gromacs.setup) stage() (staging.SunGridEngine.Job method) staging (module) staging.Local (module) staging.SunGridEngine (module) std (gromacs.fileformats.xvg.XVG attribute) StringIO() (gromacs.fileformats.preprocessor.Preprocessor method) strip_fit() (gromacs.cbook.Transformer method) strip_water() (gromacs.cbook.Transformer method) StripWater (class in gromacs.analysis.plugins) StripWater.StripWater (class in gromacs.analysis.plugins)

T

tc (gromacs.fileformats.xvg.XVG attribute) tc_histogrammed_function() (in module numkit.timeseries) tcorrel() (in module numkit.timeseries) templates (in module gromacs.config) templatesdir (in module gromacs.config) thickness (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) Timedelta (class in gromacs.utilities) to_unicode() (in module gromacs.fileformats.convert) topdir() (gromacs.analysis.core.Simulation method) (gromacs.analysis.core.Worker method)

topology() (in module gromacs.setup) totalframes (gromacs.cbook.Frames attribute) 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)

U

uncomment() (gromacs.fileformats.xpm.XPM static method) undefine() (gromacs.fileformats.preprocessor.Preprocessor 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) unread() (gromacs.fileformats.itp.OneLineBuffer method) unstage() (staging.SunGridEngine.Job method) update() (gromacs.environment.Flags method) UsageWarning

V

value (numkit.observables.QuantityWithError attribute) variance (numkit.observables.QuantityWithError attribute) vdw_lipid_atom_radii (in module gromacs.setup)

vdw_lipid_resnames (in module gromacs.setup) vmd (module) vmd.control (module)

W

waitfor() (gromacs.manager.Manager method) walk_sections() (gromacs.fileformats.itp.ITP method) (gromacs.fileformats.itp.ITPsection method) 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.FitCompact attribute) (gromacs.analysis.plugins.HBonds attribute) (gromacs.analysis.plugins.HelixBundle attribute) (gromacs.analysis.plugins.Ls attribute) (gromacs.analysis.plugins.MinDistances attribute) (gromacs.analysis.plugins.ProteinOnly attribute) (gromacs.analysis.plugins.RMSD attribute) (gromacs.analysis.plugins.RMSF attribute) (gromacs.analysis.plugins.StripWater attribute) (gromacs.analysis.plugins.Trajectories attribute) write() (gromacs.fileformats.itp.ITP method) (gromacs.fileformats.mdp.MDP method) (gromacs.fileformats.ndx.NDX method) (gromacs.fileformats.preprocessor.Preprocessor method) (gromacs.fileformats.xvg.XVG method) (gromacs.manager.ManagerConfigParser 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)