Index

A

add_vector() (ulamdyn.nma.vib_molden.vibration method) aggregate_data() (in module ulamdyn.statistics) align_geoms() (ulamdyn.data_loader.GetCoords method) (ulamdyn.GetCoords method) all_grads (ulamdyn.data_loader.GetGradients attribute) (ulamdyn.GetGradients attribute) all_nacs (ulamdyn.data_loader.GetCouplings attribute) (ulamdyn.GetCouplings attribute) angleconnectivity (ulamdyn.descriptors.ZMatrix attribute) (ulamdyn.ZMatrix attribute)

apply_to_delta (ulamdyn.descriptors.R2 attribute) (ulamdyn.R2 attribute) atom (class in ulamdyn.nma.vib_molden) atom_labels (ulamdyn.KineticEnergy attribute) (ulamdyn.kinetics.KineticEnergy attribute) atom_mass (ulamdyn.KineticEnergy attribute) (ulamdyn.kinetics.KineticEnergy attribute) atoms (ulamdyn.descriptors.SOAPDescriptor attribute) (ulamdyn.SOAPDescriptor attribute) (ulamdyn.wrappers.ring_analysis.RingAnalysis attribute)

B

Bootstrap (class in ulamdyn.wrappers.bootstrap) bootstrap() (in module ulamdyn.statistics) build_dataframe() (ulamdyn.data_loader.GetCoords method) (ulamdyn.data_loader.GetCouplings method) (ulamdyn.data_loader.GetGradients method) (ulamdyn.descriptors.RingParams method) (ulamdyn.GetCoords method) (ulamdyn.GetCouplings method) (ulamdyn.GetGradients method) (ulamdyn.GetVelocities method) (ulamdyn.KineticEnergy method) (ulamdyn.kinetics.GetVelocities method) (ulamdyn.kinetics.KineticEnergy method) (ulamdyn.kinetics.VibrationalSpectra method) (ulamdyn.RingParams method) (ulamdyn.VibrationalSpectra method)

build_descriptor() (ulamdyn.descriptors.R2 method) (ulamdyn.descriptors.ZMatrix method) (ulamdyn.R2 method) (ulamdyn.ZMatrix method)

C

calc_all_trajs() (ulamdyn.kinetics.VibrationalSpectra method) (ulamdyn.VibrationalSpectra method) calc_avg_occupations() (in module ulamdyn.statistics) calc_pdos() (ulamdyn.kinetics.VibrationalSpectra static method) (ulamdyn.VibrationalSpectra static method) calc_per_atom() (ulamdyn.KineticEnergy method) (ulamdyn.kinetics.KineticEnergy method) calc_per_molecule() (ulamdyn.KineticEnergy method) (ulamdyn.kinetics.KineticEnergy method) calc_rmsd() (in module ulamdyn.unsup_models.dist_metrics) check_nx_trajs() (in module ulamdyn.nx_utils)

ClusterGeoms (class in ulamdyn) (class in ulamdyn.unsup_models.geom_space) ClusteringAnalysis (class in ulamdyn.wrappers.clustering) ClusterTrajs (class in ulamdyn) (class in ulamdyn.unsup_models.traj_space) connectivity (ulamdyn.descriptors.ZMatrix attribute) (ulamdyn.ZMatrix attribute) convert_molden2xyz() (in module ulamdyn.nma.vib_molden) create_bootstrap_stats() (in module ulamdyn.statistics) create_features() (ulamdyn.descriptors.SOAPDescriptor method) (ulamdyn.SOAPDescriptor method) create_stats() (in module ulamdyn.statistics)

D

data_scaler (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) dataset (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.data_loader.GetProperties attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.GetProperties attribute) (ulamdyn.GetVelocities attribute) (ulamdyn.kinetics.GetVelocities attribute) (ulamdyn.kinetics.VibrationalSpectra attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute) (ulamdyn.VibrationalSpectra attribute) datasets (ulamdyn.data_loader.GetCouplings attribute) (ulamdyn.data_loader.GetGradients attribute) (ulamdyn.GetCouplings attribute) (ulamdyn.GetGradients attribute)

descriptor (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) dihedralconnectivity (ulamdyn.descriptors.ZMatrix attribute) (ulamdyn.ZMatrix attribute) DimensionReduction (class in ulamdyn) (class in ulamdyn.unsup_models.geom_space) DimensionReductionAnalysis (class in ulamdyn.wrappers.dim_reduction) displacement() (ulamdyn.descriptors.RingParams method) (ulamdyn.RingParams method) dist_metric (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) distancematrix (ulamdyn.descriptors.ZMatrix attribute) (ulamdyn.ZMatrix attribute)

E

energies (ulamdyn.KineticEnergy attribute) (ulamdyn.kinetics.KineticEnergy attribute) energies() (ulamdyn.data_loader.GetProperties method) (ulamdyn.GetProperties method) eq_xyz (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute)

F

from_all_trajs() (ulamdyn.GetVelocities class method) (ulamdyn.kinetics.GetVelocities class method) from_dyn() (ulamdyn.data_loader.GetCoords method) (ulamdyn.GetCoords method) (ulamdyn.GetVelocities method) (ulamdyn.kinetics.GetVelocities method) from_h5() (ulamdyn.data_loader.GetCoords static method) (ulamdyn.data_loader.GetCouplings static method) (ulamdyn.data_loader.GetGradients static method) (ulamdyn.GetCoords static method) (ulamdyn.GetCouplings static method) (ulamdyn.GetGradients static method) (ulamdyn.GetVelocities method) (ulamdyn.kinetics.GetVelocities method)

from_nxlog() (ulamdyn.data_loader.GetCouplings static method) (ulamdyn.data_loader.GetGradients static method) (ulamdyn.GetCouplings static method) (ulamdyn.GetGradients static method) from_xyz() (ulamdyn.data_loader.GetCoords static method) (ulamdyn.GetCoords static method)

G

gaussian_mixture() (ulamdyn.ClusterGeoms method) (ulamdyn.unsup_models.geom_space.ClusterGeoms method) gen_geometries() (ulamdyn.GeomSampling method) Geometries (class in ulamdyn) (class in ulamdyn.data_writer) GeomSampling (class in ulamdyn) get_angle() (ulamdyn.descriptors.ZMatrix static method) (ulamdyn.ZMatrix static method) get_bending() (ulamdyn.descriptors.ZMatrix static method) (ulamdyn.ZMatrix static method) get_conf_5memb() (ulamdyn.descriptors.RingParams method) (ulamdyn.RingParams method) get_conf_6memb() (ulamdyn.descriptors.RingParams method) (ulamdyn.RingParams method) get_dataframes() (ulamdyn.wrappers.ring_analysis.RingAnalysis class method) get_dihedral() (ulamdyn.descriptors.ZMatrix static method) (ulamdyn.ZMatrix static method) get_distance() (ulamdyn.descriptors.ZMatrix static method) (ulamdyn.ZMatrix static method)

get_freqs() (ulamdyn.nma.vib_molden.VibMolden method) get_labels_masses() (in module ulamdyn.nx_utils) get_num_atoms() (in module ulamdyn.nx_utils) get_nx_version() (in module ulamdyn.nx_utils) get_pucker_coords() (ulamdyn.descriptors.RingParams method) (ulamdyn.RingParams method) get_traj_dirs() (in module ulamdyn.nx_utils) get_vib_data() (ulamdyn.nma.vib_molden.VibMolden method) get_vib_matrix() (ulamdyn.nma.vib_molden.VibMolden method) GetCoords (class in ulamdyn) (class in ulamdyn.data_loader) GetCouplings (class in ulamdyn) (class in ulamdyn.data_loader) GetGradients (class in ulamdyn) (class in ulamdyn.data_loader) GetProperties (class in ulamdyn) (class in ulamdyn.data_loader) GetVelocities (class in ulamdyn) (class in ulamdyn.kinetics)

H

hierarchical() (ulamdyn.ClusterGeoms method) (ulamdyn.unsup_models.geom_space.ClusterGeoms method)

I

inverse_transform() (ulamdyn.descriptors.R2 method) (ulamdyn.R2 method)

isomap() (ulamdyn.DimensionReduction method) (ulamdyn.unsup_models.geom_space.DimensionReduction method)

K

kernel (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) KineticEnergy (class in ulamdyn) (class in ulamdyn.kinetics) kmeans() (ulamdyn.ClusterGeoms method) (ulamdyn.ClusterTrajs method) (ulamdyn.unsup_models.geom_space.ClusterGeoms method) (ulamdyn.unsup_models.traj_space.ClusterTrajs method)

kpca() (ulamdyn.DimensionReduction method) (ulamdyn.unsup_models.geom_space.DimensionReduction method)

L

labels (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute)

M

make_molden_file() (in module ulamdyn.nma.vib_molden) make_stats() (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis method) (ulamdyn.NormalModeAnalysis method) mass_weights (ulamdyn.descriptors.R2 attribute) (ulamdyn.R2 attribute) mcscf_coefs() (ulamdyn.data_loader.GetProperties method) (ulamdyn.GetProperties method) method (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) module ulamdyn ulamdyn.data_loader ulamdyn.data_writer ulamdyn.descriptors ulamdyn.kinetics ulamdyn.nma ulamdyn.nma.normal_mode_analysis ulamdyn.nma.vib_molden ulamdyn.nx_utils ulamdyn.statistics ulamdyn.unsup_models ulamdyn.unsup_models.dist_metrics ulamdyn.unsup_models.geom_space ulamdyn.unsup_models.traj_space ulamdyn.unsup_models.utilities ulamdyn.wrappers ulamdyn.wrappers.bootstrap ulamdyn.wrappers.clustering ulamdyn.wrappers.dim_reduction ulamdyn.wrappers.ring_analysis ulamdyn.wrappers.save_datasets ulamdyn.wrappers.save_xyz

mwc (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute)

N

n_atoms (ulamdyn.GetVelocities attribute) (ulamdyn.KineticEnergy attribute) (ulamdyn.kinetics.GetVelocities attribute) (ulamdyn.kinetics.KineticEnergy attribute) (ulamdyn.kinetics.VibrationalSpectra attribute) (ulamdyn.VibrationalSpectra attribute) n_clusters (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) n_cpus (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) n_dim (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) n_samples (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute)

nac_norm() (ulamdyn.data_loader.GetProperties method) (ulamdyn.GetProperties method) norm_factor (ulamdyn.descriptors.R2 attribute) (ulamdyn.R2 attribute) NormalModeAnalysis (class in ulamdyn) (class in ulamdyn.nma.normal_mode_analysis) num_states (ulamdyn.data_loader.GetProperties attribute) (ulamdyn.GetProperties attribute) nx_version (ulamdyn.data_loader.GetProperties attribute) (ulamdyn.GetProperties attribute)

O

oscillator_strength() (ulamdyn.data_loader.GetProperties method) (ulamdyn.GetProperties method)

P

pca() (ulamdyn.DimensionReduction method) (ulamdyn.unsup_models.geom_space.DimensionReduction method) perplexity (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute)

populations() (ulamdyn.data_loader.GetProperties method) (ulamdyn.GetProperties method) print_xyz_file() (ulamdyn.nma.vib_molden.VibMolden method) properties_data (ulamdyn.GeomSampling property)

R

R2 (class in ulamdyn) (class in ulamdyn.descriptors) r2_descriptor (ulamdyn.descriptors.R2 attribute) (ulamdyn.R2 attribute) r2_ref_geom (ulamdyn.descriptors.R2 attribute) (ulamdyn.R2 attribute) read_all_trajs() (ulamdyn.data_loader.GetCoords method) (ulamdyn.data_loader.GetCouplings method) (ulamdyn.data_loader.GetGradients method) (ulamdyn.GetCoords method) (ulamdyn.GetCouplings method) (ulamdyn.GetGradients method) (ulamdyn.GetVelocities method) (ulamdyn.kinetics.GetVelocities method) read_eq_geom() (ulamdyn.data_loader.GetCoords method) (ulamdyn.GetCoords method) read_h5_nx() (in module ulamdyn.nx_utils) read_molden_file() (ulamdyn.nma.vib_molden.VibMolden method) read_nx_control() (in module ulamdyn.nx_utils) reconstruct_xyz() (ulamdyn.descriptors.R2 static method) (ulamdyn.R2 static method) ret_Atoms_table() (in module ulamdyn.nma.vib_molden)

ret_eff_mass() (ulamdyn.nma.vib_molden.vibration method) ret_eff_masses() (ulamdyn.nma.vib_molden.VibMolden method) ret_FRCOORD_table() (in module ulamdyn.nma.vib_molden) ret_joined_vector() (ulamdyn.nma.vib_molden.vibration method) ring_coords (ulamdyn.descriptors.RingParams property) (ulamdyn.RingParams property) RingAnalysis (class in ulamdyn.wrappers.ring_analysis) RingParams (class in ulamdyn) (class in ulamdyn.descriptors) rmsd (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute) run() (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis method) (ulamdyn.NormalModeAnalysis method) (ulamdyn.wrappers.bootstrap.Bootstrap class method) (ulamdyn.wrappers.clustering.ClusteringAnalysis class method) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis class method) (ulamdyn.wrappers.ring_analysis.RingAnalysis class method) (ulamdyn.wrappers.save_datasets.SaveDataset class method) (ulamdyn.wrappers.save_xyz.SaveXYZ class method)

S

save_csv (ulamdyn.data_loader.GetProperties property) (ulamdyn.GetProperties property) save_csv() (ulamdyn.data_loader.GetCoords method) (ulamdyn.GetCoords method) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis method) (ulamdyn.NormalModeAnalysis method) save_xyz (ulamdyn.wrappers.save_xyz.SaveXYZ attribute) save_xyz() (ulamdyn.data_writer.Geometries method) (ulamdyn.Geometries method) (ulamdyn.GeomSampling method) SaveDataset (class in ulamdyn.wrappers.save_datasets) SaveXYZ (class in ulamdyn.wrappers.save_xyz)

select_points (ulamdyn.wrappers.save_xyz.SaveXYZ attribute) soap (ulamdyn.descriptors.SOAPDescriptor attribute) (ulamdyn.SOAPDescriptor attribute) SOAPDescriptor (class in ulamdyn) (class in ulamdyn.descriptors) space (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) species (ulamdyn.descriptors.SOAPDescriptor attribute) (ulamdyn.SOAPDescriptor attribute) spectral() (ulamdyn.ClusterGeoms method) (ulamdyn.unsup_models.geom_space.ClusterGeoms method) stats_by (ulamdyn.wrappers.ring_analysis.RingAnalysis attribute) stats_hopping() (in module ulamdyn.statistics)

T

time_step (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) traj_time (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute) trajectories (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.data_loader.GetCouplings attribute) (ulamdyn.data_loader.GetGradients attribute) (ulamdyn.data_loader.GetProperties attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.GetCouplings attribute) (ulamdyn.GetGradients attribute) (ulamdyn.GetProperties attribute) (ulamdyn.GetVelocities attribute) (ulamdyn.KineticEnergy attribute) (ulamdyn.kinetics.GetVelocities attribute) (ulamdyn.kinetics.KineticEnergy attribute) (ulamdyn.kinetics.VibrationalSpectra attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute) (ulamdyn.VibrationalSpectra attribute)

transform (ulamdyn.wrappers.clustering.ClusteringAnalysis attribute) (ulamdyn.wrappers.dim_reduction.DimensionReductionAnalysis attribute) transform() (ulamdyn.ClusterTrajs method) (ulamdyn.unsup_models.traj_space.ClusterTrajs method) tsne() (ulamdyn.DimensionReduction method) (ulamdyn.unsup_models.geom_space.DimensionReduction method)

U

ulamdyn module ulamdyn.data_loader module ulamdyn.data_writer module ulamdyn.descriptors module ulamdyn.kinetics module ulamdyn.nma module ulamdyn.nma.normal_mode_analysis module ulamdyn.nma.vib_molden module ulamdyn.nx_utils module ulamdyn.statistics module ulamdyn.unsup_models module ulamdyn.unsup_models.dist_metrics module

ulamdyn.unsup_models.geom_space module ulamdyn.unsup_models.traj_space module ulamdyn.unsup_models.utilities module ulamdyn.wrappers module ulamdyn.wrappers.bootstrap module ulamdyn.wrappers.clustering module ulamdyn.wrappers.dim_reduction module ulamdyn.wrappers.ring_analysis module ulamdyn.wrappers.save_datasets module ulamdyn.wrappers.save_xyz module use_au (ulamdyn.wrappers.save_xyz.SaveXYZ attribute) Utils (class in ulamdyn.unsup_models.utilities)

V

variant (ulamdyn.descriptors.R2 attribute) (ulamdyn.R2 attribute) veloc (ulamdyn.GetVelocities attribute) (ulamdyn.kinetics.GetVelocities attribute) (ulamdyn.kinetics.VibrationalSpectra attribute) (ulamdyn.VibrationalSpectra attribute)

VibMolden (class in ulamdyn.nma.vib_molden) vibration (class in ulamdyn.nma.vib_molden) VibrationalSpectra (class in ulamdyn) (class in ulamdyn.kinetics)

X

xyz (ulamdyn.data_loader.GetCoords attribute) (ulamdyn.descriptors.RingParams attribute) (ulamdyn.GetCoords attribute) (ulamdyn.nma.normal_mode_analysis.NormalModeAnalysis attribute) (ulamdyn.NormalModeAnalysis attribute) (ulamdyn.RingParams attribute)

xyz_to_distances() (ulamdyn.descriptors.R2 static method) (ulamdyn.R2 static method)

Z

zmat_ref_geom (ulamdyn.descriptors.ZMatrix attribute) (ulamdyn.ZMatrix attribute)

ZMatrix (class in ulamdyn) (class in ulamdyn.descriptors)