Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | W A add_dummy_points() (nearl.io.traj.Trajectory method) agg (nearl.features.DynamicFeature property) append() (nearl.io.trajloader.TrajectoryLoader method) Aromaticity (class in nearl.features) AtomicNumber (class in nearl.features) AtomType (class in nearl.features) B Backbone (class in nearl.features) C cache() (nearl.features.Aromaticity method) (nearl.features.AtomType method) (nearl.features.Backbone method) (nearl.features.DynamicFeature method) (nearl.features.Electronegativity method) (nearl.features.Feature method) (nearl.features.HBondAcceptor method) (nearl.features.HBondDonor method) (nearl.features.HeavyAtom method) (nearl.features.Hybridization method) (nearl.features.Hydrophobicity method) (nearl.features.LabelAffinity method) (nearl.features.LabelIdentity method) (nearl.features.LabelPCDT method) (nearl.features.LabelRMSD method) (nearl.features.Mass method) (nearl.features.PartialCharge method) (nearl.features.Ring method) (nearl.features.Selection method) cache_properties() (in module nearl.features) center (nearl.features.Feature property) copy_traj() (nearl.io.traj.Trajectory method) D density_flow() (in module nearl.commands) DensityFlow (class in nearl.features) dims (nearl.features.Feature property) (nearl.featurizer.Featurizer property) dump() (nearl.features.Feature method) DynamicFeature (class in nearl.features) E Electronegativity (class in nearl.features) F Feature (class in nearl.features) Featurizer (class in nearl.featurizer) frame_observation() (in module nearl.commands) frame_offset (nearl.features.Feature property) frame_voxelize() (in module nearl.commands) G get_loading_options() (nearl.io.trajloader.TrajectoryLoader method) H HBondAcceptor (class in nearl.features) HBondDonor (class in nearl.features) HeavyAtom (class in nearl.features) hook() (nearl.features.Feature method) Hybridization (class in nearl.features) Hydrophobicity (class in nearl.features) I identity (nearl.io.traj.MisatoTraj property) (nearl.io.traj.Trajectory property) L LabelAffinity (class in nearl.features) LabelIdentity (class in nearl.features) LabelPCDT (class in nearl.features) LabelRMSD (class in nearl.features) lengths (nearl.features.Feature property) (nearl.featurizer.Featurizer property) loading_options (nearl.io.trajloader.TrajectoryLoader property) loop_by_residue() (nearl.featurizer.Featurizer method) M make_index() (nearl.io.traj.Trajectory method) marching_observer() (in module nearl.commands) MarchingObservers (class in nearl.features) Mass (class in nearl.features) MisatoTraj (class in nearl.io.traj) module nearl.commands nearl.features nearl.featurizer nearl.io.traj nearl.io.trajloader N nearl.commands module nearl.features module nearl.featurizer module nearl.io.traj module nearl.io.trajloader module O obs (nearl.features.MarchingObservers property) P padding (nearl.features.Feature property) params (nearl.features.Feature property) parms (nearl.featurizer.Featurizer property) parse_focus() (nearl.featurizer.Featurizer method) PartialCharge (class in nearl.features) Q query() (nearl.features.Aromaticity method) (nearl.features.AtomicNumber method) (nearl.features.AtomType method) (nearl.features.Backbone method) (nearl.features.DensityFlow method) (nearl.features.DynamicFeature method) (nearl.features.Electronegativity method) (nearl.features.Feature method) (nearl.features.HBondAcceptor method) (nearl.features.HBondDonor method) (nearl.features.HeavyAtom method) (nearl.features.Hybridization method) (nearl.features.Hydrophobicity method) (nearl.features.LabelAffinity method) (nearl.features.LabelIdentity method) (nearl.features.LabelPCDT method) (nearl.features.LabelRMSD method) (nearl.features.MarchingObservers method) (nearl.features.Mass method) (nearl.features.PartialCharge method) (nearl.features.Ring method) (nearl.features.Selection method) R register_feature() (nearl.featurizer.Featurizer method) register_features() (nearl.featurizer.Featurizer method) register_focus() (nearl.featurizer.Featurizer method) register_trajloader() (nearl.featurizer.Featurizer method) Ring (class in nearl.features) run() (nearl.features.DensityFlow method) (nearl.features.DynamicFeature method) (nearl.features.Feature method) (nearl.features.LabelAffinity method) (nearl.features.MarchingObservers method) (nearl.featurizer.Featurizer method) S search_baseline() (nearl.features.LabelAffinity method) Selection (class in nearl.features) spacing (nearl.features.Feature property) (nearl.featurizer.Featurizer property) T top (nearl.featurizer.Featurizer property) traj (nearl.featurizer.Featurizer property) Trajectory (class in nearl.io.traj) TrajectoryLoader (class in nearl.io.trajloader) W weight_type (nearl.features.DynamicFeature property) write_frame() (nearl.io.traj.Trajectory method)