Index

_

__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) add_mdp_includes() (in module gromacs.cbook) add_plugin() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation 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) anyopen() (in module gromacs.utilities) 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) AttributeDict (class in gromacs.utilities) AutoCorrectionWarning autocorrelation_fft() (in module numkit.timeseries) averages (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute)

B

BadParameterWarning

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_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) 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) 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

DATANAME (gromacs.analysis.plugins.gridmatmd.GridMatData attribute) deepcopy() (numkit.observables.QuantityWithError method) default_extension (gromacs.utilities.FileUtils attribute) defaults (in module gromacs.config) 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) 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 JOB_NAME PATH, [1] SGE_TASK_ID error (numkit.observables.QuantityWithError attribute) extract() (gromacs.cbook.Frames method)

F

f_factory() (numkit.fitting.FitFunc method) 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) 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) FitLin (class in numkit.fitting) flag() (gromacs.qsub.QueuingSystem method) framenumber (gromacs.cbook.Frames attribute) Frames (class in gromacs.cbook)

G

GdistData (class in gromacs.analysis.plugins.dist) generate_submit_array() (in module gromacs.qsub) generate_submit_scripts() (in module gromacs.qsub) get() (gromacs.manager.Manager 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_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] getline_from_arraylist() (in module staging.SunGridEngine) getlist() (gromacs.config.GMXConfigParser method) getLogLevel() (gromacs.config.GMXConfigParser method) getpath() (gromacs.config.GMXConfigParser 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) 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.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 grompp_qtot() (in module gromacs.cbook), [1]

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)

initial_values() (numkit.fitting.FitFunc method) isMine() (gromacs.qsub.QueuingSystem method) isSame() (numkit.observables.QuantityWithError method) iterable() (in module gromacs.utilities)

J

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

JOB_NAME

K

keep_protein_only() (gromacs.cbook.Transformer method)

L

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

make_main_index() (in module gromacs.setup) make_ndx_captured() (in module gromacs.cbook) Manager (class in gromacs.manager) managerdir (in module gromacs.config) MD() (in module gromacs.setup) MD_restrained() (in module gromacs.setup) 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) midpoints (gromacs.analysis.plugins.dist.Mindist attribute) Mindist (class in gromacs.analysis.plugins.dist) MinDistances (class in gromacs.analysis.plugins) MinDistances.Distances (class in gromacs.analysis.plugins) MissingDataError MissingDataWarning mpicommand() (gromacs.run.MDrunner method) mpiexec (gromacs.run.MDrunner attribute)

N

ndependent() (gromacs.manager.Manager 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

openany() (in module gromacs.utilities)

P

parse_filename() (gromacs.analysis.plugins.gridmatmd.GridMatData method) parse_ndxlist() (in module gromacs.cbook), [1] ParseError PATH, [1] path (in module gromacs.config) pAVG (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) pBOT (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) Pearson_r() (in module numkit.fitting) plot() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation method) (gromacs.analysis.plugins.dist.Mindist 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)

pNX (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) pNY (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) Popen() (gromacs.core.Command method) (gromacs.core.GromacsCommand method) PopenWithInput (class in gromacs.core) posthook() (gromacs.run.MDrunner method) prehook() (gromacs.run.MDrunner method) ProteinOnly (class in gromacs.analysis.plugins) ProteinOnly.ProteinOnly (class in gromacs.analysis.plugins) pTOP (gromacs.analysis.plugins.gridmatmd.GridMatMD attribute) 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

realpath() (in module gromacs.utilities) register() (gromacs.analysis.core.Plugin method) remotepath() (gromacs.manager.Manager method) remoteuri() (gromacs.manager.Manager method) remove_legend() (in module gromacs.utilities) 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) set_plugin() (gromacs.analysis.core.Simulation method) (gromacs.analysis.Simulation 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) solvate() (in module gromacs.setup) stage() (staging.SunGridEngine.Job method) staging (module) staging.Local (module) staging.SunGridEngine (module) strip_water() (gromacs.cbook.Transformer method) StripWater (class in gromacs.analysis.plugins) StripWater.StripWater (class in gromacs.analysis.plugins)

T

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) 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

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

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) 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.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)