Index

A

addGenotype() (Population method) align_2seqs() (in module TEMPy.math.vector) altTorsion() (in module TEMPy.math.vector) anglar_sweep() (EnsembleGeneration method) angle_axis_to_quat() (in module TEMPy.assembly.gamma) apply_filter() (Filter static method)

apply_mask() (MapEdit method) arg() (Vector method) Assembly (class in TEMPy.assembly.assembly) avg_fitness() (Population method) axis_angle_to_euler() (in module TEMPy.math.vector) axis_angle_to_matrix() (in module TEMPy.math.vector)

B

BioPy_Structure (class in TEMPy.protein.prot_rep_biopy) BioPyAtom (class in TEMPy.protein.prot_rep_biopy) box_size() (Map method) (MapEdit method) box_transform() (MapEdit method)

break_into_segments() (BioPy_Structure method) breed() (Genotype method) breed_1child() (Population method) breedNewPop() (Population method) build_maps() (Assembly method) butterworth_lowpass() (Filter method)

C

calc_moc() (ScoringFunctions method) calc_SA() (PDBParser static method) calcMtrx() (in module TEMPy.math.vector) calculate_centre_of_mass() (BioPy_Structure method) calculate_centroid() (BioPy_Structure method) calculate_map_contour() (MapEdit method) calculate_map_threshold() (ScoringFunctions method) CCC() (ScoringFunctions method) CCC_chimera() (ScoringFunctions method) CCC_map() (ScoringFunctions method) centre() (Map method) chamfer_distance() (ScoringFunctions method) change_init_position() (BioPy_Structure method) (BioPyAtom method) change_origin() (Map method) check_for_mutations() (QuaternionGene method) (VectorGene method) close() (MapEdit method) Cluster (class in TEMPy.math.cluster) cluster_fit_ensemble_top_fit() (Cluster method) cmp_Rainbow() (Plot method) combine_maps() (Assembly method)

combine_SSE_structures() (BioPy_Structure method) combine_structs() (Assembly method) combine_structures() (BioPy_Structure method) compare_tuple() (MapEdit static method) compute_Hs() (in module TEMPy.protein.scoring_functions) conjuate() (Quaternion method) Consensus (class in TEMPy.math.consensus) copy() (BioPy_Structure method) (BioPyAtom method) (Filter method) (Genotype method) (Map method) (MapEdit method) (Population method) (Quaternion method) (QuaternionGene method) (Vector method) (VectorGene method) cps() (in module TEMPy.math.vector) crop_box() (MapEdit method) cross() (Vector method) crossover() (QuaternionGene method) (VectorGene method)

D

data_copy() (MapEdit method) dist() (Vector method) distance_from_atom() (BioPyAtom method) distance_from_init_position() (BioPyAtom method)

dot() (Vector method) dot_product() (QuaternionGene method) downsample_apix() (MapEdit method) downsample_map() (Map method)

E

EnsembleGeneration (class in TEMPy.optimisation.ensemble_generation) envelope_score() (ScoringFunctions method)

envelope_score_map() (ScoringFunctions method) euler_to_matrix() (in module TEMPy.math.vector)

F

fancy_index_as_slices() (MapEdit static method) fetch_mmCIF() (mmCIFParser static method) fetch_PDB() (PDBParser static method) fetch_PDB_BioPy() (PDBParser static method) Filter (class in TEMPy.map_process.map_filters)

find_level() (MapEdit method) find_same_atom() (BioPy_Structure method) fourier_filter() (Filter method) fourier_transform() (Filter method) (Map method)

G

GA (class in TEMPy.assembly.gamma) gauss_bandpass() (Filter method) gauss_lowpass() (Filter method) gaussian_blur() (StructureBlurrer method) gaussian_blur_box() (StructureBlurrer method) gaussian_blur_real_space() (StructureBlurrer method) gaussian_blur_real_space_Bfac() (StructureBlurrer method) gaussian_blur_real_space_box() (StructureBlurrer method) generate_args() (TempyParser method) Genotype (class in TEMPy.assembly.gamma) get_atom() (BioPy_Structure method) get_atom_list() (BioPy_Structure method) get_backbone() (BioPy_Structure method) get_CAonly() (BioPy_Structure method) get_chain() (BioPy_Structure method) get_chain_ca() (BioPy_Structure method) get_chain_list() (BioPy_Structure method) get_clash_map() (ScoringFunctions method) get_com() (Map method) get_coordinates() (StructureBlurrer method) get_dict_str() (BioPy_Structure method) get_endian() (MapParser static method) get_extreme_values() (BioPy_Structure method) get_fitness() (Genotype method) get_ga_pool() (GA method) get_gene_list() (VectorGene method) get_id_no() (BioPyAtom method) get_indices() (StructureBlurrer method) get_interpolated_quat() (QuaternionGene method) get_line_between_points() (Map method) get_mass() (BioPyAtom method) get_name() (BioPyAtom method) get_normal_vector() (Map method) get_overlay_comp_maplist() (ScoringFunctions method)

get_partial_DLSF() (ScoringFunctions method) get_point_map() (Map method) get_pos() (Map method) get_pos_mass() (BioPyAtom method) get_pos_mass_list() (BioPy_Structure method) get_pos_vector() (BioPyAtom method) get_primary_boundary() (Map method) get_prot_mass_from_atoms() (BioPy_Structure method) get_prot_mass_from_res() (BioPy_Structure method) get_raps() (Filter method) get_res() (BioPyAtom method) get_res_no() (BioPyAtom method) get_residue() (BioPy_Structure method) get_rgyration() (BioPy_Structure method) get_rigid_body_str_instances() (RBParser static method) get_sccc() (ScoringFunctions method) get_second_boundary() (Map method) get_selection() (BioPy_Structure method) get_selection_less_than() (BioPy_Structure method) get_selection_more_than() (BioPy_Structure method) get_sigma_map() (MapEdit method) get_significant_points() (Map method) get_sm_score() (ScoringFunctions method) get_torsion_angles() (BioPy_Structure method) get_vector_list() (BioPy_Structure method) get_vectors() (Map method) get_vectors_a() (Map method) get_VQ_points() (in module TEMPy.math.vq) get_x() (BioPyAtom method) get_y() (BioPyAtom method) get_z() (BioPyAtom method) getBestScores() (Population method) getMap() (Map method) grid_footprint() (MapEdit method)

H

hard_sphere() (StructureBlurrer method)

hard_sphere_box() (StructureBlurrer method) header_to_binary() (Map method)

I

interpolate_to_grid() (MapEdit method)

inv_fourier_transform() (Filter method)

L

label_patches() (Filter method) laplace_CCC() (ScoringFunctions method) laplace_filtered() (Map method) lineplot() (Plot method) LJ_() (in module TEMPy.protein.scoring_functions)

LJ_score() (in module TEMPy.protein.scoring_functions) LJ_score_VC() (in module TEMPy.protein.scoring_functions) load_matrix() (TransformParser method) loadEnsemble() (EnsembleGeneration method) local_select() (Selection method) LSF() (ScoringFunctions method)

M

mag() (Quaternion method) make_atom_overlay_map() (StructureBlurrer method) make_atom_overlay_map1() (StructureBlurrer method) make_atom_overlay_mapB() (StructureBlurrer method) make_bin_map() (Map method) make_fourier_shell() (Filter method) make_model_grid() (StructureBlurrer method) make_spherical_footprint() (MapEdit method) make_vq_points() (Assembly method) makeKDTree() (Map method) Map (class in TEMPy.maps.em_map) map_digitize() (MapEdit method) map_grid_position() (BioPyAtom method) map_points() (in module TEMPy.math.vq) map_rotate_by_axis_angle() (Map method) map_size() (Map method) mapComparison() (ScoringFunctions method) MapEdit (class in TEMPy.map_process.process) mapfunc() (in module TEMPy.assembly.gamma) mapGridPosition() (StructureBlurrer method) mapGridPositions() (StructureBlurrer method) mapGridPositions_vdw() (StructureBlurrer method) MapParser (class in TEMPy.maps.map_parser) MapTransformationScore (class in TEMPy.maps.map_transform_score) maptree() (StructureBlurrer method) matrix_transform() (BioPy_Structure method) (BioPyAtom method) (Map method) (Vector method) max() (Map method) (MapEdit method) max_fitness() (Population method) mean() (Map method) median() (Map method) MI() (ScoringFunctions method) MI_full() (in module TEMPy.protein.scoring_functions) MI_histo() (in module TEMPy.protein.scoring_functions) migration_select() (Selection method) min() (Map method) (MapEdit method) min_fitness() (Population method) mmCIFParser (class in TEMPy.protein.structure_parser) mod() (Vector method)

model_tree() (StructureBlurrer method) module TEMPy TEMPy.assembly TEMPy.assembly.assembly TEMPy.assembly.gamma TEMPy.cli TEMPy.cli.class_arg TEMPy.graphics TEMPy.graphics.show_plot TEMPy.map_process TEMPy.map_process.map_filters TEMPy.map_process.process TEMPy.maps TEMPy.maps.em_map TEMPy.maps.map_parser TEMPy.maps.map_transform_score TEMPy.math TEMPy.math.cluster TEMPy.math.consensus TEMPy.math.quaternion TEMPy.math.transform_parser TEMPy.math.vector TEMPy.math.vq TEMPy.optimisation TEMPy.optimisation.ensemble_generation TEMPy.protein TEMPy.protein.prot_rep_biopy TEMPy.protein.rigid_body_parser TEMPy.protein.scoring_functions TEMPy.protein.structure_blurrer TEMPy.protein.structure_parser move_assembly_components() (in module TEMPy.assembly.gamma) move_map_and_prot_by_aa() (Assembly method) move_map_and_prot_by_euler() (Assembly method) move_map_and_prot_by_mat() (Assembly method) move_map_and_prot_by_quat() (Assembly method) move_map_prot() (in module TEMPy.assembly.gamma) move_struct_quat() (in module TEMPy.assembly.gamma) muate() (QuaternionGene method) multi_diff() (in module TEMPy.protein.scoring_functions) multiply_3() (Quaternion method) mutate() (VectorGene method)

N

NMI_histo() (in module TEMPy.protein.scoring_functions) no_of_chains() (BioPy_Structure method)

normal_vector_score() (ScoringFunctions method) normalise() (Map method) (Quaternion method)

O

optimise_EM_g() (in module TEMPy.assembly.gamma)

origin_change_maps() (Map method)

P

pad_map() (Map method) (MapEdit method) PDBParser (class in TEMPy.protein.structure_parser) peak_density() (MapEdit method) pickBest() (Population method) pickSetOfBest() (Population method) pickSetOfWorst() (Population method) pickWorst() (Population method)

pixel_centre() (Map method) Plot (class in TEMPy.graphics.show_plot) plot_raps() (Filter method) Population (class in TEMPy.assembly.gamma) PrintOutChimeraAttributeFileSCCC_Score() (Plot method) PrintOutChimeraCmdClusterAnalysis() (Plot method) PrintOutClusterAnalysis() (Plot method) protMap() (StructureBlurrer method) protMapBox() (StructureBlurrer method)

Q

Quaternion (class in TEMPy.math.quaternion)

quaternion_align_vectors() (in module TEMPy.assembly.gamma) QuaternionGene (class in TEMPy.assembly.gamma)

R

rand_quat_vec() (in module TEMPy.assembly.gamma) random() (in module TEMPy.assembly.gamma) random_vector() (in module TEMPy.math.vector) random_vector2() (in module TEMPy.math.vector) randomise_position() (BioPy_Structure method) randomise_structs() (Assembly method) (EnsembleGeneration method) randomise_structs_and_maps() (Assembly method) rank_fit_ensemble() (Cluster method) RBfileToRBlist() (RBParser static method) RBParser (class in TEMPy.protein.rigid_body_parser) read_FlexEM_RIBFIND_files() (RBParser static method) read_mmCIF_file() (mmCIFParser static method) read_PDB_file() (PDBParser static method) read_PDB_file_BioPy() (PDBParser static method) read_rigid_body_file() (RBParser static method) read_rigid_body_file_as_dict() (RBParser static method) readMRC() (MapParser static method) readMRCHeader() (MapParser static method) refine_Bfac() (StructureBlurrer method) reinitialize() (MapEdit method) reinitialize_data() (MapEdit method) reinitialize_header() (MapEdit method) rename_chains() (BioPy_Structure method) renumber_atoms() (BioPy_Structure method)

renumber_residues() (BioPy_Structure method) reorder_residues() (BioPy_Structure method) represent_normal_vectors() (Map method) resample_by_apix() (Map method) resample_by_box_size() (Map method) reset_all() (Assembly method) reset_maps() (Assembly method) reset_position() (BioPy_Structure method) (BioPyAtom method) reset_structs() (Assembly method) resize_map() (Map method) restricted_rand_q() (in module TEMPy.assembly.gamma) reverse() (Vector method) RMSD_ensemble() (Cluster method) RMSD_from_init_position() (BioPy_Structure method) RMSD_from_same_structure() (BioPy_Structure method) rotate_by_axis_angle() (BioPy_Structure method) (Map method) rotate_by_euler() (BioPy_Structure method) (Map method) rotate_by_matrix() (Map method) rotate_by_quaternion() (BioPy_Structure method) (BioPyAtom method) roulette_wheel() (Selection method) run() (GA method)

S

save_npy_matrix() (TransformParser method) save_npz_matrix() (TransformParser method) scale_map() (Map method) scale_median() (ScoringFunctions method) SCCC() (ScoringFunctions method) SCCC_LAP() (ScoringFunctions method) SCCC_MI() (ScoringFunctions method) SCCCHeatMap_fromSCCCfiles() (Plot method) SCCCHeatMap_fromSCCCList() (Plot method) score_pop_segment_CCC() (in module TEMPy.assembly.gamma) score_pop_segment_MI() (in module TEMPy.assembly.gamma) score_population() (GA method) ScoringFunctions (class in TEMPy.protein.scoring_functions) Selection (class in TEMPy.assembly.gamma) set_apix_as_tuple() (MapEdit method) set_apix_dim() (MapEdit method) set_apix_tempy() (MapEdit method) set_data_header() (MapEdit method) set_dim_apix() (MapEdit method) set_newmap_data_header() (MapEdit method)

set_score_as_bfactor() (ScoringFunctions method) set_x() (BioPyAtom method) set_y() (BioPyAtom method) set_z() (BioPyAtom method) shift_density() (MapEdit method) shift_origin() (Map method) ShowGeneralMatrix() (Plot method) ShowHierarchicalClusterings() (Plot method) ShowRMSDmatrix() (Plot method) size() (Population method) size_patches() (MapEdit method) SMOC() (ScoringFunctions method) spiral_sweep() (EnsembleGeneration method) split_into_chains() (BioPy_Structure method) std() (Map method) (MapEdit method) std_fitness() (Population method) StructureBlurrer (class in TEMPy.protein.structure_blurrer) SUS() (Selection method) swap() (Genotype method)

T

tanh_bandpass() (Filter method) tanh_lowpass() (Filter method) TEMPy module TEMPy.assembly module TEMPy.assembly.assembly module TEMPy.assembly.gamma module TEMPy.cli module TEMPy.cli.class_arg module TEMPy.graphics module TEMPy.graphics.show_plot module TEMPy.map_process module TEMPy.map_process.map_filters module TEMPy.map_process.process module TEMPy.maps module TEMPy.maps.em_map module TEMPy.maps.map_parser module TEMPy.maps.map_transform_score module TEMPy.math module TEMPy.math.cluster module TEMPy.math.consensus module TEMPy.math.quaternion module

TEMPy.math.transform_parser module TEMPy.math.vector module TEMPy.math.vq module TEMPy.optimisation module TEMPy.optimisation.ensemble_generation module TEMPy.protein module TEMPy.protein.prot_rep_biopy module TEMPy.protein.rigid_body_parser module TEMPy.protein.scoring_functions module TEMPy.protein.structure_blurrer module TEMPy.protein.structure_parser module TEMPycheck() (in module TEMPy.map_process.process) TEMPyException TempyParser (class in TEMPy.cli.class_arg) threshold_map() (Map method) (MapEdit method) times() (Vector method) to_atom() (Vector method) to_rotation_matrix() (Quaternion method) (QuaternionGene method) torsion() (in module TEMPy.math.vector) totalFitnessScore() (Population method) tournament() (Selection method) transform_map() (MapTransformationScore method) TransformParser (class in TEMPy.math.transform_parser) translate() (BioPy_Structure method) (BioPyAtom method) (Map method) (Vector method)

U

uniform_crossover() (Genotype method) unit() (Vector method) unit_quat() (Quaternion method) update_data() (MapEdit method)

update_header() (Map method) (MapEdit method) update_newmap_data() (MapEdit method) update_newmap_header() (MapEdit method)

V

Vector (class in TEMPy.math.vector) VectorGene (class in TEMPy.assembly.gamma) vectorise() (BioPy_Structure method) vectorise_point() (Map method)

vote() (Consensus method) vote_list() (Consensus method) vote_mode() (Consensus method) vprint() (in module TEMPy.assembly.gamma) VQ() (in module TEMPy.math.vq)

W

which_chain() (in module TEMPy.assembly.gamma) write_all_to_files() (Assembly method) write_sasd_to_pdb() (PDBParser static method) write_sasd_to_txt() (PDBParser static method)

write_to_MRC_file() (Map method) write_to_PDB() (BioPy_Structure method) (BioPyAtom method) write_to_pdb() (in module TEMPy.math.vq)

X

x_origin() (Map method) (MapEdit method)

x_size() (Map method) (MapEdit method)

Y

y_origin() (Map method) (MapEdit method)

y_size() (Map method) (MapEdit method)

Z

z_origin() (Map method) (MapEdit method)

z_size() (Map method) (MapEdit method)