Index

Symbols

--config command line option

-c command line option

_

__init__() (crystal_analyzer.CrystalAnalyzer method), [1], [2], [3], [4] (csa_config.ExtractionConfig method), [1], [2], [3] (csd_operations.CSDOperations method), [1], [2], [3], [4] (csd_operations.SimilaritySettings method), [1] (csd_structure_validator.StructureValidationResult method), [1] (data_reader.RawDataReader method), [1], [2] (data_writer.ComputedDataWriter method), [1], [2] (data_writer.RawDataWriter method), [1], [2] (structure_data_extractor.StructureDataExtractor method), [1], [2], [3], [4] (structure_post_extraction_processor.AtomParams method) (structure_post_extraction_processor.BondParams method) (structure_post_extraction_processor.CrystalParams method) (structure_post_extraction_processor.StructurePostExtractionProcessor method), [1], [2], [3], [4] _check_structure() (csd_operations.CSDOperations method) _cluster_refcode_families() (crystal_analyzer.CrystalAnalyzer method) _compute_contact_com_vectors() (structure_post_extraction_processor.StructurePostExtractionProcessor method)

_compute_fragment_com_centroid() (structure_post_extraction_processor.StructurePostExtractionProcessor method) _compute_rigid_fragments() (structure_post_extraction_processor.StructurePostExtractionProcessor method) _expand_inter_contacts() (structure_post_extraction_processor.StructurePostExtractionProcessor method) _extract_one() (in module structure_data_extractor) _extract_refcode_families() (crystal_analyzer.CrystalAnalyzer method) _extract_structure_data() (crystal_analyzer.CrystalAnalyzer method) _extract_unique_structures() (crystal_analyzer.CrystalAnalyzer method) _flag_hbond_contacts() (structure_post_extraction_processor.StructurePostExtractionProcessor method) _identify_contact_fragments() (structure_post_extraction_processor.StructurePostExtractionProcessor method) _load_refcodes() (structure_data_extractor.StructureDataExtractor method) _post_extraction_process() (crystal_analyzer.CrystalAnalyzer method) _process_batch() (structure_data_extractor.StructureDataExtractor method) (structure_post_extraction_processor.StructurePostExtractionProcessor method) _process_single_family() (in module csd_operations) _representative_for_cluster() (in module csd_operations) _save_unique_structures() (csd_operations.CSDOperations method)

A

actions (csa_config.ExtractionConfig attribute), [1], [2] add_inter_cc_symmetry() (in module symmetry_utils), [1] add_inter_hb_symmetry() (in module symmetry_utils), [1] add_symmetry_matrices() (in module symmetry_utils), [1]

angle_tolerance (csd_operations.SimilaritySettings attribute), [1] angles (structure_post_extraction_processor.InterHBParams attribute), [1] atom1_idx (structure_post_extraction_processor.BondParams attribute), [1], [2], [3], [4], [5] atom2_idx (structure_post_extraction_processor.BondParams attribute), [1], [2], [3], [4], [5] AtomParams (class in structure_post_extraction_processor), [1], [2]

B

batch_size (structure_data_extractor.StructureDataExtractor attribute), [1], [2]

bond_type (structure_post_extraction_processor.BondParams attribute), [1], [2], [3], [4], [5] BondParams (class in structure_post_extraction_processor), [1], [2]

C

cell_angles (structure_post_extraction_processor.CrystalParams attribute), [1], [2], [3], [4], [5] cell_lengths (structure_post_extraction_processor.CrystalParams attribute), [1], [2], [3], [4], [5] cell_utils module central_atom (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] central_atom_frac_coords (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] central_atom_idx (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] charges (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] cluster_families() (csd_operations.CSDOperations method), [1], [2], [3] command line option --config -c compute_angles_between_bonds_and_crystallographic_planes_frac_batch() (in module geometry_utils), [1] compute_atom_vectors_to_point_batch() (in module geometry_utils), [1] compute_best_fit_plane_batch() (in module geometry_utils), [1] compute_bond_angles_batch() (in module geometry_utils), [1], [2] compute_bond_rotatability_batch() (in module geometry_utils), [1] compute_cell_matrix_batch() (in module cell_utils), [1], [2] compute_center_of_mass_batch() (in module fragment_utils), [1] compute_centroid_batch() (in module fragment_utils), [1] compute_contact_atom_to_central_fragment_com_batch() (in module contact_utils), [1] compute_contact_fragment_indices_batch() (in module contact_utils), [1] compute_contact_is_hbond() (in module contact_utils), [1] compute_distances_to_crystallographic_planes_frac_batch() (in module geometry_utils), [1] compute_fragment_pairwise_vectors_and_distances_batch() (in module geometry_utils), [1] compute_global_steinhardt_order_parameters_batch() (in module geometry_utils), [1] compute_inertia_tensor_batch() (in module fragment_utils), [1] compute_planarity_metrics_batch() (in module geometry_utils), [1] compute_quadrupole_tensor_batch() (in module fragment_utils), [1]

compute_quaternions_from_rotation_matrices() (in module geometry_utils), [1] compute_scaled_cell() (in module cell_utils), [1] compute_symmetric_contacts_batch() (in module contact_utils), [1], [2] compute_symmetric_hbonds_batch() (in module contact_utils), [1] compute_torsion_angles_batch() (in module geometry_utils), [1] ComputedDataWriter (class in data_writer), [1] contact_atom (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] contact_atom_frac_coords (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] contact_atom_idx (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] contact_utils module coords (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] count() (structure_post_extraction_processor.AtomParams method), [1], [2] (structure_post_extraction_processor.BondParams method), [1], [2] (structure_post_extraction_processor.CrystalParams method), [1], [2] (structure_post_extraction_processor.InterCCParams method) (structure_post_extraction_processor.InterHBParams method) crystal_analyzer module CrystalAnalyzer (class in crystal_analyzer), [1], [2] CrystalParams (class in structure_post_extraction_processor), [1], [2] csa_config module csa_main module csd_operations module csd_ops (crystal_analyzer.CrystalAnalyzer attribute), [1], [2] CSDOperations (class in csd_operations), [1], [2]

D

data_dir (crystal_analyzer.CrystalAnalyzer attribute), [1], [2] data_directory (csa_config.ExtractionConfig attribute), [1], [2] (csd_operations.CSDOperations attribute), [1], [2] data_prefix (csa_config.ExtractionConfig attribute), [1], [2] (csd_operations.CSDOperations attribute), [1], [2] data_reader module

data_writer module dimension_scanner module distance_tolerance (csd_operations.SimilaritySettings attribute), [1]

E

extract_data() (crystal_analyzer.CrystalAnalyzer method), [1], [2], [3] extraction_batch_size (csa_config.ExtractionConfig attribute), [1], [2]

extraction_config (crystal_analyzer.CrystalAnalyzer attribute), [1], [2] ExtractionConfig (class in csa_config), [1], [2] extractor (crystal_analyzer.CrystalAnalyzer attribute), [1], [2]

F

failure_reason (csd_structure_validator.StructureValidationResult attribute), [1] filter_families_by_size() (csd_operations.CSDOperations method), [1], [2], [3] filters (csa_config.ExtractionConfig attribute), [1], [2] (structure_data_extractor.StructureDataExtractor attribute), [1], [2]

frac_coords (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] fragment_utils module from_json() (csa_config.ExtractionConfig class method), [1], [2], [3] (csa_config.ExtractionConfig method), [1], [2]

G

geometry_utils module

get_refcode_families_df() (csd_operations.CSDOperations method), [1], [2], [3] get_unique_structures() (csd_operations.CSDOperations method), [1], [2], [3]

H

h5_in (data_reader.RawDataReader attribute), [1] h5_out (data_writer.ComputedDataWriter attribute), [1] (data_writer.RawDataWriter attribute), [1] hdf5_path (structure_data_extractor.StructureDataExtractor attribute), [1], [2]

hdf5_utils module hydrogen_atom (structure_post_extraction_processor.InterHBParams attribute), [1] hydrogen_atom_frac_coords (structure_post_extraction_processor.InterHBParams attribute), [1] hydrogen_atom_idx (structure_post_extraction_processor.InterHBParams attribute), [1]

I

identify_rigid_fragments_batch() (in module fragment_utils), [1], [2] ignore_bond_types (csd_operations.SimilaritySettings attribute), [1] ignore_hydrogen_counts (csd_operations.SimilaritySettings attribute), [1] ignore_hydrogen_positions (csd_operations.SimilaritySettings attribute), [1] ignore_spacegroup (csd_operations.SimilaritySettings attribute), [1] in_los (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] index() (structure_post_extraction_processor.AtomParams method), [1], [2] (structure_post_extraction_processor.BondParams method), [1], [2] (structure_post_extraction_processor.CrystalParams method), [1], [2] (structure_post_extraction_processor.InterCCParams method) (structure_post_extraction_processor.InterHBParams method)

initialize_hdf5_file() (in module hdf5_utils), [1] InterCCParams (class in structure_post_extraction_processor) InterHBParams (class in structure_post_extraction_processor) invert_sym_op() (in module symmetry_utils), [1] is_cyclic (structure_post_extraction_processor.BondParams attribute), [1], [2], [3], [4], [5] is_rotatable_raw (structure_post_extraction_processor.BondParams attribute), [1], [2], [3], [4], [5] is_valid (csd_structure_validator.StructureValidationResult attribute), [1]

L

labels (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] lengths (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1]

load_config() (in module csa_config), [1], [2]

M

main() (in module csa_main), [1] mask (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] (structure_post_extraction_processor.BondParams attribute), [1], [2], [3], [4], [5] module cell_utils contact_utils crystal_analyzer csa_config csa_main csd_operations data_reader data_writer dimension_scanner fragment_utils geometry_utils hdf5_utils structure_data_extractor structure_post_extraction_processor symmetry_utils

N

normalise_unit_cell (csd_operations.SimilaritySettings attribute), [1]

P

packing_shell_size (csd_operations.SimilaritySettings attribute), [1] parse_args() (in module csa_main), [1]

parse_sym_op() (in module symmetry_utils), [1] post_extraction_batch_size (csa_config.ExtractionConfig attribute), [1], [2] prepare_fragments_batch() (in module fragment_utils), [1]

R

RawDataReader (class in data_reader), [1] RawDataWriter (class in data_writer), [1] read_atoms() (data_reader.RawDataReader method), [1], [2], [3], [4] read_bonds() (data_reader.RawDataReader method), [1], [2], [3], [4] read_crystal_parameters() (data_reader.RawDataReader method), [1], [2], [3], [4] read_intermolecular_contacts() (data_reader.RawDataReader method), [1], [2], [3], [4] read_intermolecular_hbonds() (data_reader.RawDataReader method), [1], [2], [3], [4]

read_intramolecular_contacts() (data_reader.RawDataReader method), [1], [2], [3], [4] read_intramolecular_hbonds() (data_reader.RawDataReader method), [1], [2], [3], [4] reader (csd_operations.CSDOperations attribute), [1], [2] (structure_data_extractor.StructureDataExtractor attribute), [1], [2] run() (structure_data_extractor.StructureDataExtractor method), [1], [2], [3] (structure_post_extraction_processor.StructurePostExtractionProcessor method), [1], [2], [3] run_extraction() (in module csa_main), [1]

S

save_refcode_families_csv() (csd_operations.CSDOperations method), [1], [2], [3] scan_max_dimensions() (in module dimension_scanner), [1] setup_logging() (in module csa_main), [1] similarity_engine (csd_operations.CSDOperations attribute), [1], [2] SimilaritySettings (class in csd_operations), [1] strengths (structure_post_extraction_processor.InterCCParams attribute), [1] structure_data_extractor module structure_post_extraction_processor module StructureDataExtractor (class in structure_data_extractor), [1], [2] StructurePostExtractionProcessor (class in structure_post_extraction_processor), [1], [2]

StructureValidationResult (class in csd_structure_validator) symbols (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] symmetry_A (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] symmetry_A_inv (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] symmetry_T (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] symmetry_T_inv (structure_post_extraction_processor.InterCCParams attribute), [1] (structure_post_extraction_processor.InterHBParams attribute), [1] symmetry_utils module

W

weights (structure_post_extraction_processor.AtomParams attribute), [1], [2], [3], [4], [5] write_computed_atom_data() (data_writer.ComputedDataWriter method), [1], [2], [3], [4] write_computed_bond_data() (data_writer.ComputedDataWriter method), [1], [2], [3], [4] write_computed_crystal_data() (data_writer.ComputedDataWriter method), [1], [2], [3], [4] write_computed_fragment_data() (data_writer.ComputedDataWriter method), [1], [2] write_computed_intermolecular_contact_data() (data_writer.ComputedDataWriter method), [1], [2], [3] write_computed_intermolecular_hbond_data() (data_writer.ComputedDataWriter method), [1], [2], [3]

write_computed_molecule_data() (data_writer.ComputedDataWriter method), [1], [2], [3], [4] write_raw_atom_data() (data_writer.RawDataWriter method), [1], [2], [3], [4] write_raw_bond_data() (data_writer.RawDataWriter method), [1], [2], [3], [4] write_raw_crystal_data() (data_writer.RawDataWriter method), [1], [2], [3], [4] write_raw_intramolecular_contact_data() (data_writer.RawDataWriter method), [1], [2], [3], [4] write_raw_intramolecular_hbond_data() (data_writer.RawDataWriter method), [1], [2], [3], [4] write_structure_group() (in module hdf5_utils), [1]