Index

Symbols

--dirname mdpow-equilibrium command line option mdpow-fep command line option --energies mdpow-pow command line option mdpow-solvationenergy command line option --estimator mdpow-pow command line option mdpow-solvationenergy command line option --force mdpow-pow command line option mdpow-solvationenergy command line option --help mdpow-check command line option mdpow-equilibrium command line option mdpow-fep command line option mdpow-pow command line option mdpow-rebuild-fep command line option mdpow-rebuild-simulation command line option mdpow-solvationenergy command line option --ignore-corrupted mdpow-pow command line option mdpow-solvationenergy command line option --method mdpow-pow command line option mdpow-solvationenergy command line option --no-SI mdpow-pow command line option mdpow-solvationenergy command line option --outfile mdpow-check command line option mdpow-pow command line option mdpow-solvationenergy command line option --plotfile mdpow-pow command line option mdpow-solvationenergy command line option --setup mdpow-rebuild-fep command line option --SI mdpow-pow command line option mdpow-solvationenergy command line option

--solvent mdpow-equilibrium command line option mdpow-fep command line option mdpow-rebuild-fep command line option mdpow-rebuild-simulation command line option mdpow-solvationenergy command line option --start mdpow-pow command line option mdpow-solvationenergy command line option --stop mdpow-pow command line option mdpow-solvationenergy command line option --stride mdpow-pow command line option mdpow-solvationenergy command line option -d mdpow-equilibrium command line option mdpow-fep command line option -e mdpow-pow command line option mdpow-solvationenergy command line option -h mdpow-check command line option mdpow-equilibrium command line option mdpow-fep command line option mdpow-pow command line option mdpow-rebuild-fep command line option mdpow-rebuild-simulation command line option mdpow-solvationenergy command line option -o mdpow-check command line option mdpow-pow command line option mdpow-solvationenergy command line option -S mdpow-equilibrium command line option mdpow-fep command line option mdpow-solvationenergy command line option -s mdpow-pow command line option mdpow-solvationenergy command line option

_

__version__ (in module mdpow) _build_ensemble() (mdpow.analysis.ensemble.Ensemble method) _conclude_ensemble() (mdpow.analysis.ensemble.EnsembleAnalysis method) _conclude_universe() (mdpow.analysis.ensemble.EnsembleAnalysis method)

_load_universe_from_dir() (mdpow.analysis.ensemble.Ensemble static method) _prepare_ensemble() (mdpow.analysis.ensemble.EnsembleAnalysis method) _prepare_universe() (mdpow.analysis.ensemble.EnsembleAnalysis method) _single_frame() (mdpow.analysis.ensemble.EnsembleAnalysis method) _single_universe() (mdpow.analysis.ensemble.EnsembleAnalysis method)

A

add_system() (mdpow.analysis.ensemble.Ensemble method)

automated_dihedral_analysis() (in module mdpow.workflows.dihedrals) automated_project_analysis() (in module mdpow.workflows.base)

B

build_svg() (in module mdpow.workflows.dihedrals)

build_universe() (in module mdpow.workflows.dihedrals)

C

check_groups_from_common_ensemble() (mdpow.analysis.ensemble.EnsembleAnalysis static method) checkpoint() (in module mdpow.restart)

clear() (mdpow.restart.Journal method) completed() (mdpow.restart.Journal method) current (mdpow.restart.Journal property)

D

dihedral_groups_ensemble() (in module mdpow.workflows.dihedrals) dihedral_violins() (in module mdpow.workflows.dihedrals) DihedralAnalysis (class in mdpow.analysis.dihedral)

DIRECTORY mdpow-pow command line option mdpow-solvationenergy command line option

E

Ensemble (class in mdpow.analysis.ensemble) ensemble (mdpow.analysis.ensemble.EnsembleAtomGroup property) EnsembleAnalysis (class in mdpow.analysis.ensemble)

EnsembleAtomGroup (class in mdpow.analysis.ensemble) environment variable GMXLIB PATH

G

get_atom_indices() (in module mdpow.workflows.dihedrals) get_bond_indices() (in module mdpow.workflows.dihedrals) get_dihedral_groups() (in module mdpow.workflows.dihedrals)

get_paired_indices() (in module mdpow.workflows.dihedrals) get_protocol() (mdpow.restart.Journalled method) GMXLIB guess_elements() (in module mdpow.workflows.base)

H

has_completed() (mdpow.restart.Journal method)

has_not_completed() (mdpow.restart.Journal method) history (mdpow.restart.Journal property)

I

incomplete (mdpow.restart.Journal property)

INTERACTIONS_DEFAULT (in module mdpow.workflows.dihedrals)

J

Journal (class in mdpow.restart) Journalled (class in mdpow.restart)

Journalled.dummy_protocol() (in module mdpow.restart) JournalSequenceError

K

keys() (mdpow.analysis.ensemble.Ensemble method) (mdpow.analysis.ensemble.EnsembleAtomGroup method)

L

load() (mdpow.restart.Journalled method)

M

mdpow-check command line option --help --outfile -h -o mdpow-equilibrium command line option --dirname --help --solvent -d -h -S RUNFILE mdpow-fep command line option --dirname --help --solvent -d -h -S RUNFILE mdpow-pow command line option --energies --estimator --force --help --ignore-corrupted --method --no-SI --outfile --plotfile --SI --start --stop --stride -e -h -o -s DIRECTORY mdpow-rebuild-fep command line option --help --setup --solvent -h

mdpow-rebuild-simulation command line option --help --solvent -h mdpow-solvationenergy command line option --energies --estimator --force --help --ignore-corrupted --method --no-SI --outfile --plotfile --SI --solvent --start --stop --stride -e -h -o -S -s DIRECTORY mdpow.log module mdpow.restart module mdpow.workflows.base module mdpow.workflows.dihedrals module mdpow.workflows.registry module module mdpow.log mdpow.restart mdpow.workflows.base mdpow.workflows.dihedrals mdpow.workflows.registry

P

PATH periodic_angle_padding() (in module mdpow.workflows.dihedrals) plot_dihedral_violins() (in module mdpow.workflows.dihedrals) PLOT_WIDTH_DEFAULT (in module mdpow.workflows.dihedrals)

pop() (mdpow.analysis.ensemble.Ensemble method) positions() (mdpow.analysis.ensemble.EnsembleAtomGroup method) project_paths() (in module mdpow.workflows.base) protocols (mdpow.restart.Journalled attribute)

R

rdkit_conversion() (in module mdpow.workflows.dihedrals) registry (in module mdpow.workflows.registry) run() (mdpow.analysis.dihedral.DihedralAnalysis method) (mdpow.analysis.ensemble.EnsembleAnalysis method) (mdpow.analysis.solvation.SolvationAnalysis method)

RUNFILE mdpow-equilibrium command line option mdpow-fep command line option

S

save() (mdpow.restart.Journalled method) save_df() (in module mdpow.workflows.dihedrals) select_atoms() (mdpow.analysis.ensemble.Ensemble method) (mdpow.analysis.ensemble.EnsembleAtomGroup method)

select_systems() (mdpow.analysis.ensemble.Ensemble method) SMARTS_DEFAULT (in module mdpow.workflows.dihedrals) SolvationAnalysis (class in mdpow.analysis.solvation) SOLVENTS_DEFAULT (in module mdpow.workflows.dihedrals) start() (mdpow.restart.Journal method)