Index

_

__init__() (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor method) (partycls.descriptors.ba.BondAngleDescriptor method) (partycls.descriptors.bo.BondOrientationalDescriptor method) (partycls.descriptors.compactness.CompactnessDescriptor method) (partycls.descriptors.coordination.CoordinationDescriptor method) (partycls.descriptors.radial.RadialDescriptor method) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor method) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor method) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor method) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor method)

A

accept_nans (partycls.descriptors.descriptor.StructuralDescriptor property) active_filters (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute)

add_filter() (partycls.descriptors.descriptor.StructuralDescriptor method) additional_fields (partycls.trajectory.Trajectory attribute) AMI() (in module partycls.helpers) ARI() (in module partycls.helpers) AutoEncoder (class in partycls.dim_reduction) average (partycls.descriptors.descriptor.StructuralDescriptor property)

B

backend (partycls.trajectory.Trajectory attribute) BoattiniDescriptor (class in partycls.descriptors.radial_bo) BondAngleDescriptor (class in partycls.descriptors.ba)

BondOrientationalDescriptor (class in partycls.descriptors.bo) bounds (partycls.descriptors.radial.RadialDescriptor property) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor property)

C

Cell (class in partycls.cell) cell (partycls.system.System attribute) centroids (partycls.workflow.Workflow property) centroids() (partycls.clustering.Clustering method) chemical_fractions (partycls.system.System property) clear_all_filters() (partycls.descriptors.descriptor.StructuralDescriptor method) clear_filters() (partycls.descriptors.descriptor.StructuralDescriptor method) Clustering (class in partycls.clustering) clustering (partycls.workflow.Workflow attribute) clustering_db (partycls.workflow.Workflow attribute) CommunityInference (class in partycls.clustering) CompactnessDescriptor (class in partycls.descriptors.compactness) compute() (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor method) (partycls.descriptors.ba.BondAngleDescriptor method) (partycls.descriptors.bo.BondOrientationalDescriptor method) (partycls.descriptors.compactness.CompactnessDescriptor method) (partycls.descriptors.coordination.CoordinationDescriptor method) (partycls.descriptors.descriptor.StructuralDescriptor method) (partycls.descriptors.dscribe.DscribeDescriptor method) (partycls.descriptors.radial.RadialDescriptor method) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor method) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor method) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor method) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor method)

compute_nearest_neighbors() (partycls.system.System method) (partycls.trajectory.Trajectory method) compute_nearest_neighbors_cutoffs() (partycls.trajectory.Trajectory method) compute_voronoi_signatures() (partycls.system.System method) (partycls.trajectory.Trajectory method) CoordinationDescriptor (class in partycls.descriptors.coordination)

D

density (partycls.system.System property) descriptor (partycls.workflow.Workflow attribute) descriptor_db (partycls.workflow.Workflow attribute) dim_reduction (partycls.workflow.Workflow attribute) dim_reduction_db (partycls.workflow.Workflow attribute) dimension (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute)

disable_output() (partycls.workflow.Workflow method) discard_nans() (partycls.descriptors.descriptor.StructuralDescriptor method) distance_grid (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor property) distinct_species (partycls.system.System property) dr (partycls.descriptors.radial.RadialDescriptor property) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor property) DscribeChemicalDescriptor (class in partycls.descriptors.dscribe) DscribeDescriptor (class in partycls.descriptors.dscribe) dtheta (partycls.descriptors.ba.BondAngleDescriptor property) DummyDescriptor (class in partycls.descriptors.descriptor) dump() (partycls.descriptors.descriptor.StructuralDescriptor method) (partycls.system.System method) (partycls.trajectory.Trajectory method)

F

features (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute) (partycls.workflow.Workflow attribute) filename (partycls.trajectory.Trajectory attribute) fit() (partycls.clustering.Clustering method) (partycls.clustering.CommunityInference method) (partycls.clustering.GaussianMixture method) (partycls.clustering.KMeans method)

fmt (partycls.trajectory.Trajectory attribute) fold() (partycls.particle.Particle method) (partycls.system.System method) (partycls.trajectory.Trajectory method) fractions (partycls.clustering.Clustering property) (partycls.workflow.Workflow property) full_name (partycls.dim_reduction.AutoEncoder attribute) (partycls.dim_reduction.LocallyLinearEmbedding attribute) (partycls.dim_reduction.PCA attribute) (partycls.dim_reduction.TSNE attribute) (partycls.feature_scaling.MaxAbs attribute) (partycls.feature_scaling.MinMax attribute) (partycls.feature_scaling.Robust attribute) (partycls.feature_scaling.ZScore attribute)

G

GaussianMixture (class in partycls.clustering) get_group_property() (partycls.descriptors.descriptor.StructuralDescriptor method) get_property() (partycls.system.System method) (partycls.trajectory.Trajectory method) grid (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute)

group_fraction() (partycls.descriptors.descriptor.StructuralDescriptor method) group_size() (partycls.descriptors.descriptor.StructuralDescriptor method) groups (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute)

K

KMeans (class in partycls.clustering)

L

label (partycls.particle.Particle attribute) labels (partycls.clustering.Clustering attribute) (partycls.workflow.Workflow property)

LechnerDellagoDescriptor (class in partycls.descriptors.averaged_bo) LocallyAveragedBondOrientationalDescriptor (class in partycls.descriptors.averaged_bo) LocallyLinearEmbedding (class in partycls.dim_reduction)

M

max_num_neighbors (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute) MaxAbs (class in partycls.feature_scaling) merge_clusters() (in module partycls.helpers) MinMax (class in partycls.feature_scaling) module partycls partycls.cell partycls.clustering partycls.core partycls.core.utils partycls.descriptors partycls.descriptors.averaged_bo partycls.descriptors.ba partycls.descriptors.bo partycls.descriptors.compactness partycls.descriptors.coordination partycls.descriptors.descriptor partycls.descriptors.dscribe partycls.descriptors.radial partycls.descriptors.radial_bo partycls.descriptors.smoothed_ba partycls.descriptors.smoothed_bo partycls.descriptors.tetrahedrality partycls.dim_reduction partycls.feature_scaling partycls.helpers partycls.particle partycls.system partycls.trajectory partycls.workflow

N

n_clusters (partycls.clustering.Clustering attribute) n_components (partycls.dim_reduction.AutoEncoder property) n_dimensions (partycls.system.System property) n_features (partycls.descriptors.descriptor.StructuralDescriptor property) n_init (partycls.clustering.Clustering attribute) n_samples (partycls.descriptors.descriptor.StructuralDescriptor property) n_shells (partycls.descriptors.radial.RadialDescriptor property) name (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.DummyDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute) naming_convention (partycls.workflow.Workflow attribute)

nearest_neighbors (partycls.particle.Particle attribute) nearest_neighbors_cutoffs (partycls.system.System attribute) (partycls.trajectory.Trajectory property) nearest_neighbors_method (partycls.system.System property) (partycls.trajectory.Trajectory property) neighbors_boost (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute) normalize() (partycls.descriptors.ba.BondAngleDescriptor method) (partycls.descriptors.descriptor.DummyDescriptor method) (partycls.descriptors.descriptor.StructuralDescriptor method) (partycls.descriptors.dscribe.DscribeDescriptor method) (partycls.descriptors.radial.RadialDescriptor method)

O

orders (partycls.descriptors.bo.BondOrientationalDescriptor property) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor property)

output_metadata (partycls.workflow.Workflow attribute)

P

pairs_of_species (partycls.system.System property) pairs_of_species_id (partycls.system.System property) partial (partycls.descriptors.coordination.CoordinationDescriptor property) Particle (class in partycls.particle) particle (partycls.system.System attribute) partycls module partycls.cell module partycls.clustering module partycls.core module partycls.core.utils module partycls.descriptors module partycls.descriptors.averaged_bo module partycls.descriptors.ba module partycls.descriptors.bo module partycls.descriptors.compactness module partycls.descriptors.coordination module partycls.descriptors.descriptor module partycls.descriptors.dscribe module

partycls.descriptors.radial module partycls.descriptors.radial_bo module partycls.descriptors.smoothed_ba module partycls.descriptors.smoothed_bo module partycls.descriptors.tetrahedrality module partycls.dim_reduction module partycls.feature_scaling module partycls.helpers module partycls.particle module partycls.system module partycls.trajectory module partycls.workflow module PCA (class in partycls.dim_reduction) periodic (partycls.cell.Cell attribute) populations (partycls.clustering.Clustering property) (partycls.workflow.Workflow property) position (partycls.particle.Particle attribute)

R

RadialBondOrientationalDescriptor (class in partycls.descriptors.radial_bo) RadialDescriptor (class in partycls.descriptors.radial) radius (partycls.particle.Particle attribute) reduce() (partycls.dim_reduction.AutoEncoder method) (partycls.dim_reduction.LocallyLinearEmbedding method) (partycls.dim_reduction.PCA method) (partycls.dim_reduction.TSNE method)

reduced_features (partycls.workflow.Workflow attribute) remove() (partycls.trajectory.Trajectory method) Robust (class in partycls.feature_scaling) run() (partycls.workflow.Workflow method)

S

scale() (partycls.feature_scaling.MaxAbs method) (partycls.feature_scaling.MinMax method) (partycls.feature_scaling.Robust method) (partycls.feature_scaling.ZScore method) scaled_features (partycls.workflow.Workflow attribute) scaling (partycls.workflow.Workflow attribute) scaling_db (partycls.workflow.Workflow attribute) set_nearest_neighbors_cutoff() (partycls.trajectory.Trajectory method) set_output_metadata() (partycls.workflow.Workflow method) set_property() (partycls.system.System method) (partycls.trajectory.Trajectory method) shannon_entropy() (in module partycls.helpers) show() (partycls.system.System method) (partycls.trajectory.Trajectory method) show_3dmol() (in module partycls.helpers) show_matplotlib() (in module partycls.helpers) show_ovito() (in module partycls.helpers) side (partycls.cell.Cell attribute) silhouette_samples() (in module partycls.helpers) silhouette_score() (in module partycls.helpers) SmoothedBondAngleDescriptor (class in partycls.descriptors.smoothed_ba) SmoothedBondOrientationalDescriptor (class in partycls.descriptors.smoothed_bo) sort_clusters() (in module partycls.helpers)

species (partycls.particle.Particle attribute) standardize_condition() (in module partycls.core.utils) SteinhardtDescriptor (class in partycls.descriptors.bo) StructuralDescriptor (class in partycls.descriptors.descriptor) symbol (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.DummyDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute) (partycls.dim_reduction.AutoEncoder attribute) (partycls.dim_reduction.LocallyLinearEmbedding attribute) (partycls.dim_reduction.PCA attribute) (partycls.dim_reduction.TSNE attribute) (partycls.feature_scaling.MaxAbs attribute) (partycls.feature_scaling.MinMax attribute) (partycls.feature_scaling.Robust attribute) (partycls.feature_scaling.ZScore attribute) System (class in partycls.system)

T

tetrahedra() (partycls.descriptors.compactness.CompactnessDescriptor method) TetrahedralDescriptor (class in partycls.descriptors.tetrahedrality) tipify() (in module partycls.core.utils) TongTanakaDescriptor (class in partycls.descriptors.compactness) total (partycls.descriptors.coordination.CoordinationDescriptor property) Trajectory (class in partycls.trajectory) trajectory (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute) (partycls.workflow.Workflow attribute)

TSNE (class in partycls.dim_reduction)

V

verbose (partycls.descriptors.averaged_bo.LocallyAveragedBondOrientationalDescriptor attribute) (partycls.descriptors.ba.BondAngleDescriptor attribute) (partycls.descriptors.bo.BondOrientationalDescriptor attribute) (partycls.descriptors.compactness.CompactnessDescriptor attribute) (partycls.descriptors.coordination.CoordinationDescriptor attribute) (partycls.descriptors.descriptor.StructuralDescriptor attribute) (partycls.descriptors.radial.RadialDescriptor attribute) (partycls.descriptors.radial_bo.RadialBondOrientationalDescriptor attribute) (partycls.descriptors.smoothed_ba.SmoothedBondAngleDescriptor attribute) (partycls.descriptors.smoothed_bo.SmoothedBondOrientationalDescriptor attribute) (partycls.descriptors.tetrahedrality.TetrahedralDescriptor attribute)

volume (partycls.cell.Cell property)

W

Workflow (class in partycls.workflow) write() (partycls.trajectory.Trajectory method) write_centroids() (partycls.workflow.Workflow method)

write_dataset() (partycls.workflow.Workflow method) write_labels() (partycls.workflow.Workflow method) write_log() (partycls.workflow.Workflow method) write_trajectory() (partycls.workflow.Workflow method)

Z

ZScore (class in partycls.feature_scaling)