Index

Symbols

--gamma-gof TEMPy.gamma command line option --gamma-mut-rate TEMPy.gamma command line option --gamma-num-cpus TEMPy.gamma command line option --gamma-num-gas TEMPy.gamma command line option --gamma-num-gens TEMPy.gamma command line option --gamma-offset-mag TEMPy.gamma command line option --gamma-pop-size TEMPy.gamma command line option --gamma-seed-file TEMPy.gamma command line option --gamma-xover-rate TEMPy.gamma command line option --half-map-1 TEMPy.loqfit command line option --half-map-2 TEMPy.loqfit command line option --help TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option --map TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option --max-loqfit-score TEMPy.loqfit command line option --model-colors TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option --model-names TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option --models TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option --output-dir TEMPy.gamma command line option --output-file TEMPy.gamma command line option --output-format TEMPy.loqfit command line option TEMPy.smoc command line option

--output-pdbsnap TEMPy.gamma command line option --output-prefix TEMPy.loqfit command line option TEMPy.smoc command line option --plot-bands TEMPy.loqfit command line option TEMPy.smoc command line option --plot-normalize TEMPy.loqfit command line option TEMPy.smoc command line option --plot-residue-range TEMPy.loqfit command line option TEMPy.smoc command line option --plot-type TEMPy.loqfit command line option TEMPy.smoc command line option --plot-unmodelled TEMPy.loqfit command line option TEMPy.smoc command line option --resolution TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option --smoc-method TEMPy.smoc command line option --smoc-window TEMPy.smoc command line option -h TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option -hm1 TEMPy.loqfit command line option -hm2 TEMPy.loqfit command line option -m TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option -p TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option -r TEMPy.gamma command line option TEMPy.loqfit command line option TEMPy.smoc command line option

_

__init__() (TEMPy.protein.scoring_functions.FastSCCC method) (TEMPy.protein.scoring_functions.FastSMOC method) (TEMPy.protein.scoring_functions.LocalMI method)

A

add_structure() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method)

add_structure_instance() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) Atom (class in TEMPy.protein.prot_rep_biopy)

B

BioPy_Structure (class in TEMPy.protein.prot_rep_biopy)

box_size() (TEMPy.maps.em_map.Map method) break_into_segments() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

C

calculate_centre_of_mass() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) calculate_centroid() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) centre() (TEMPy.maps.em_map.Map method) change_init_position() (TEMPy.protein.prot_rep_biopy.Atom method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) change_origin() (TEMPy.maps.em_map.Map method)

combine_SSE_structures() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) combine_structures() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) copy() (TEMPy.maps.em_map.Map method) (TEMPy.protein.prot_rep_biopy.Atom method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) (TEMPy.protein.prot_rep_biopy.gemmi_Structure method)

D

distance_from_atom() (TEMPy.protein.prot_rep_biopy.Atom method)

distance_from_init_position() (TEMPy.protein.prot_rep_biopy.Atom method)

F

FastSCCC (class in TEMPy.protein.scoring_functions) FastSMOC (class in TEMPy.protein.scoring_functions) fetch_mmCIF() (TEMPy.protein.structure_parser.mmCIFParser static method)

fetch_PDB() (TEMPy.protein.structure_parser.PDBParser static method) find_same_atom() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) fourier_transform() (TEMPy.maps.em_map.Map method)

G

gaussian_blur() (TEMPy.protein.structure_blurrer.StructureBlurrer method) gaussian_blur_box() (TEMPy.protein.structure_blurrer.StructureBlurrer method) gaussian_blur_real_space() (TEMPy.protein.structure_blurrer.StructureBlurrer method) gaussian_blur_real_space_box() (TEMPy.protein.structure_blurrer.StructureBlurrer method) gemmi_Structure (class in TEMPy.protein.prot_rep_biopy) gemmiAtom (class in TEMPy.protein.prot_rep_biopy) get_atom() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_atom_list() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_atom_vals() (TEMPy.protein.prot_rep_biopy.gemmiAtom method) get_atoms_in_chains() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_backbone() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_CAonly() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_chain() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) get_chain_list() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_col_labels() (TEMPy.protein.prot_rep_biopy.gemmiAtom method) get_com() (TEMPy.maps.em_map.Map method) get_coordinates() (TEMPy.protein.structure_blurrer.StructureBlurrer method) get_cropped_box() (TEMPy.maps.em_map.Map method) get_cropped_box_around_atom() (TEMPy.maps.em_map.Map method) get_endian() (TEMPy.maps.map_parser.old_MapParser static method) get_extreme_values() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_global_score() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) get_id_no() (TEMPy.protein.prot_rep_biopy.Atom method) get_indices() (TEMPy.protein.structure_blurrer.StructureBlurrer method) get_indices_aj() (TEMPy.protein.structure_blurrer.StructureBlurrer method) get_line_between_points() (TEMPy.maps.em_map.Map method) get_mass() (TEMPy.protein.prot_rep_biopy.Atom method)

get_name() (TEMPy.protein.prot_rep_biopy.Atom method) get_next_chain_id() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_normal_vector() (TEMPy.maps.em_map.Map method) get_point_map() (TEMPy.maps.em_map.Map method) get_pos() (TEMPy.maps.em_map.Map method) get_pos_mass() (TEMPy.protein.prot_rep_biopy.Atom method) get_pos_mass_list() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_pos_vector() (TEMPy.protein.prot_rep_biopy.Atom method) get_primary_boundary() (TEMPy.maps.em_map.Map method) get_prot_mass_from_atoms() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_prot_mass_from_res() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_res() (TEMPy.protein.prot_rep_biopy.Atom method) get_res_no() (TEMPy.protein.prot_rep_biopy.Atom method) get_residue() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_residue_indexes() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_second_boundary() (TEMPy.maps.em_map.Map method) get_selection() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_selection_less_than() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_selection_more_than() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_significant_points() (TEMPy.maps.em_map.Map method) get_str_atom_vals() (TEMPy.protein.prot_rep_biopy.gemmiAtom method) get_torsion_angles() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_vector_list() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) get_vectors() (TEMPy.maps.em_map.Map method) get_x() (TEMPy.protein.prot_rep_biopy.Atom method) get_y() (TEMPy.protein.prot_rep_biopy.Atom method) get_z() (TEMPy.protein.prot_rep_biopy.Atom method) getMap() (TEMPy.maps.em_map.Map method) gridpoints_around_atom() (TEMPy.protein.prot_rep_biopy.Atom method)

H

hard_sphere() (TEMPy.protein.structure_blurrer.StructureBlurrer method)

hard_sphere_box() (TEMPy.protein.structure_blurrer.StructureBlurrer method)

I

iter_asym_id() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

L

laplace_filtered() (TEMPy.maps.em_map.Map method)

LocalMI (class in TEMPy.protein.scoring_functions)

M

make_atom_overlay_map() (TEMPy.protein.structure_blurrer.StructureBlurrer method) make_atom_overlay_map1() (TEMPy.protein.structure_blurrer.StructureBlurrer method) make_atom_overlay_mapB() (TEMPy.protein.structure_blurrer.StructureBlurrer method) make_bin_map() (TEMPy.maps.em_map.Map method) makeKDTree() (TEMPy.maps.em_map.Map method) Map (class in TEMPy.maps.em_map) map_grid_position() (TEMPy.protein.prot_rep_biopy.Atom method) map_rotate_by_axis_angle() (TEMPy.maps.em_map.Map method) map_size() (TEMPy.maps.em_map.Map method) mapGridPosition() (TEMPy.protein.structure_blurrer.StructureBlurrer method) mapGridPositions() (TEMPy.protein.structure_blurrer.StructureBlurrer method) mapGridPositions_vdw() (TEMPy.protein.structure_blurrer.StructureBlurrer method) maptree() (TEMPy.protein.structure_blurrer.StructureBlurrer method) matrix_transform() (TEMPy.maps.em_map.Map method) (TEMPy.protein.prot_rep_biopy.Atom method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

max() (TEMPy.maps.em_map.Map method) mean() (TEMPy.maps.em_map.Map method) median() (TEMPy.maps.em_map.Map method) min() (TEMPy.maps.em_map.Map method) mmCIFParser (class in TEMPy.protein.structure_parser) model_tree() (TEMPy.protein.structure_blurrer.StructureBlurrer method) module TEMPy.maps.em_map TEMPy.maps.map_parser TEMPy.protein, [1] TEMPy.protein.prot_rep_biopy TEMPy.protein.structure_blurrer TEMPy.protein.structure_parser TEMPy.script.gamma TEMPy.script.loqfit TEMPy.script.smoc

N

no_of_chains() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) (TEMPy.protein.prot_rep_biopy.gemmi_Structure method)

normalise() (TEMPy.maps.em_map.Map method) normalise_to_1_minus1() (TEMPy.maps.em_map.Map method) number_of_residues() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

O

old_get_indices() (TEMPy.protein.structure_blurrer.StructureBlurrer method) old_MapParser (class in TEMPy.maps.map_parser)

old_write_to_MRC_file() (TEMPy.maps.em_map.Map method) origin_change_maps() (TEMPy.maps.em_map.Map method)

P

pad_map() (TEMPy.maps.em_map.Map method) PDBParser (class in TEMPy.protein.structure_parser)

pixel_centre() (TEMPy.maps.em_map.Map method) protMap() (TEMPy.protein.structure_blurrer.StructureBlurrer method) protMapBox() (TEMPy.protein.structure_blurrer.StructureBlurrer method)

R

randomise_position() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) read_mmCIF_file() (TEMPy.protein.structure_parser.mmCIFParser static method) read_PDB_file() (TEMPy.protein.structure_parser.PDBParser static method) readMRC() (TEMPy.maps.map_parser.old_MapParser static method) readMRCHeader() (TEMPy.maps.map_parser.old_MapParser static method) rename_asym_labels() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) rename_chains() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) rename_entity_labels() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) renumber_atoms() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) renumber_residues() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) reorder_residues() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

represent_normal_vectors() (TEMPy.maps.em_map.Map method) resample_by_apix() (TEMPy.maps.em_map.Map method) resample_by_box_size() (TEMPy.maps.em_map.Map method) reset_position() (TEMPy.protein.prot_rep_biopy.Atom method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) resize_map() (TEMPy.maps.em_map.Map method) RMSD_from_init_position() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) RMSD_from_same_structure() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) rotate_by_axis_angle() (TEMPy.maps.em_map.Map method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) rotate_by_euler() (TEMPy.maps.em_map.Map method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) rotate_by_matrix() (TEMPy.maps.em_map.Map method)

S

scale_map() (TEMPy.maps.em_map.Map method) set_atom_labels() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) set_global_score() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) set_local_score() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) set_x() (TEMPy.protein.prot_rep_biopy.Atom method) set_y() (TEMPy.protein.prot_rep_biopy.Atom method)

set_z() (TEMPy.protein.prot_rep_biopy.Atom method) shift_origin() (TEMPy.maps.em_map.Map method) SMOC() (TEMPy.protein.scoring_functions.ScoringFunctions method) split_into_chains() (TEMPy.protein.prot_rep_biopy.BioPy_Structure method) (TEMPy.protein.prot_rep_biopy.gemmi_Structure method) std() (TEMPy.maps.em_map.Map method) StructureBlurrer (class in TEMPy.protein.structure_blurrer)

T

TEMPy.gamma command line option --gamma-gof --gamma-mut-rate --gamma-num-cpus --gamma-num-gas --gamma-num-gens --gamma-offset-mag --gamma-pop-size --gamma-seed-file --gamma-xover-rate --help --map --model-colors --model-names --models --output-dir --output-file --output-pdbsnap --resolution -h -m -p -r TEMPy.loqfit command line option --half-map-1 --half-map-2 --help --map --max-loqfit-score --model-colors --model-names --models --output-format --output-prefix --plot-bands --plot-normalize --plot-residue-range --plot-type --plot-unmodelled --resolution -h -hm1 -hm2 -m -p -r

TEMPy.maps.em_map module TEMPy.maps.map_parser module TEMPy.protein module, [1] TEMPy.protein.prot_rep_biopy module TEMPy.protein.structure_blurrer module TEMPy.protein.structure_parser module TEMPy.script.gamma module TEMPy.script.loqfit module TEMPy.script.smoc module TEMPy.smoc command line option --help --map --model-colors --model-names --models --output-format --output-prefix --plot-bands --plot-normalize --plot-residue-range --plot-type --plot-unmodelled --resolution --smoc-method --smoc-window -h -m -p -r threshold_map() (TEMPy.maps.em_map.Map method) translate() (TEMPy.maps.em_map.Map method) (TEMPy.protein.prot_rep_biopy.Atom method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

U

update_header() (TEMPy.maps.em_map.Map method)

V

vectorise_point() (TEMPy.maps.em_map.Map method)

W

write_sasd_to_pdb() (TEMPy.protein.structure_parser.PDBParser static method) write_sasd_to_txt() (TEMPy.protein.structure_parser.PDBParser static method) write_to_mmcif() (TEMPy.protein.prot_rep_biopy.gemmi_Structure method)

write_to_MRC_file() (TEMPy.maps.em_map.Map method) write_to_PDB() (TEMPy.protein.prot_rep_biopy.Atom method) (TEMPy.protein.prot_rep_biopy.BioPy_Structure method)

X

x_origin() (TEMPy.maps.em_map.Map method)

x_size() (TEMPy.maps.em_map.Map method)

Y

y_origin() (TEMPy.maps.em_map.Map method)

y_size() (TEMPy.maps.em_map.Map method)

Z

z_origin() (TEMPy.maps.em_map.Map method)

z_size() (TEMPy.maps.em_map.Map method)