Index A | C | D | F | G | I | L | M | N | O | P | Q | R | S | T | U | W A ag (openfe_analysis.transformations.NoJump attribute) Aligner (class in openfe_analysis.transformations) apply_complex_alignment_transformations() (in module openfe_analysis.utils.apply_transformations) apply_ligand_alignment_transformations() (in module openfe_analysis.utils.apply_transformations) C close() (openfe_analysis.reader.FEReader method) ClosestImageShift (class in openfe_analysis.transformations) create_universe_single_state() (in module openfe_analysis.utils.universe_utils) D dt (openfe_analysis.reader.FEReader property) F FEReader (class in openfe_analysis.reader) format (openfe_analysis.reader.FEReader attribute) G gather_rms_data() (in module openfe_analysis.rmsd) guess_ligand_bonds() (in module openfe_analysis.utils.universe_utils) I index_method (openfe_analysis.reader.FEReader property) L LigandCOMDrift (class in openfe_analysis.rmsd) M module openfe_analysis openfe_analysis.reader openfe_analysis.rmsd openfe_analysis.transformations openfe_analysis.utils openfe_analysis.utils.apply_transformations openfe_analysis.utils.multistate openfe_analysis.utils.plotting openfe_analysis.utils.serialization openfe_analysis.utils.universe_utils multistate_index (openfe_analysis.reader.FEReader property) N n_atoms (openfe_analysis.reader.FEReader property) n_frames (openfe_analysis.reader.FEReader property) NoJump (class in openfe_analysis.transformations) O omm_quantity_string_to_offunit() (in module openfe_analysis.utils.serialization) openfe_analysis module openfe_analysis.reader module openfe_analysis.rmsd module openfe_analysis.transformations module openfe_analysis.utils module openfe_analysis.utils.apply_transformations module openfe_analysis.utils.multistate module openfe_analysis.utils.plotting module openfe_analysis.utils.serialization module openfe_analysis.utils.universe_utils module P parse_n_atoms() (openfe_analysis.reader.FEReader static method) plot_2D_rmsd() (in module openfe_analysis.utils.plotting) plot_ligand_COM_drift() (in module openfe_analysis.utils.plotting) plot_ligand_RMSD() (in module openfe_analysis.utils.plotting) prev (openfe_analysis.transformations.NoJump attribute) Protein2DRMSD (class in openfe_analysis.rmsd) Q quantity_constructor() (openfe_analysis.utils.serialization.UnitedYamlLoader static method) R ref_idx (openfe_analysis.transformations.Aligner attribute) ref_pos (openfe_analysis.transformations.Aligner attribute) RMSDAnalysis (class in openfe_analysis.rmsd) S select_state_atoms() (in module openfe_analysis.utils.universe_utils) SymmetryCorrectedLigandRMSD (class in openfe_analysis.rmsd) T trajectory_from_multistate() (in module openfe_analysis.utils.multistate) U UnitedYamlLoader (class in openfe_analysis.utils.serialization) units (openfe_analysis.reader.FEReader attribute) W weights (openfe_analysis.transformations.Aligner attribute)