Documentation for TEMPy
The TEMPy documentation is broken into a few different categories below.
- Quick start
- Guides
- TEMPy Tutorials
- Python API Reference
- TEMPy.protein.structure_blurrer
- Note on real space blurring:
StructureBlurrerStructureBlurrer.gaussian_blur()StructureBlurrer.gaussian_blur_box()StructureBlurrer.gaussian_blur_real_space()StructureBlurrer.gaussian_blur_real_space_box()StructureBlurrer.get_coordinates()StructureBlurrer.get_indices()StructureBlurrer.get_indices_aj()StructureBlurrer.hard_sphere()StructureBlurrer.hard_sphere_box()StructureBlurrer.make_atom_overlay_map()StructureBlurrer.make_atom_overlay_map1()StructureBlurrer.make_atom_overlay_mapB()StructureBlurrer.mapGridPosition()StructureBlurrer.mapGridPositions()StructureBlurrer.mapGridPositions_vdw()StructureBlurrer.maptree()StructureBlurrer.model_tree()StructureBlurrer.old_get_indices()StructureBlurrer.protMap()StructureBlurrer.protMapBox()
- TEMPy.protein.scoring_functions
- TEMPy.protein.structure_parser
- TEMPy.protein.prot_rep_biopy
AtomAtom.change_init_position()Atom.copy()Atom.distance_from_atom()Atom.distance_from_init_position()Atom.get_id_no()Atom.get_mass()Atom.get_name()Atom.get_pos_mass()Atom.get_pos_vector()Atom.get_res()Atom.get_res_no()Atom.get_x()Atom.get_y()Atom.get_z()Atom.gridpoints_around_atom()Atom.map_grid_position()Atom.matrix_transform()Atom.reset_position()Atom.set_x()Atom.set_y()Atom.set_z()Atom.translate()Atom.write_to_PDB()
BioPy_StructureBioPy_Structure.RMSD_from_init_position()BioPy_Structure.RMSD_from_same_structure()BioPy_Structure.break_into_segments()BioPy_Structure.calculate_centre_of_mass()BioPy_Structure.calculate_centroid()BioPy_Structure.change_init_position()BioPy_Structure.combine_SSE_structures()BioPy_Structure.combine_structures()BioPy_Structure.copy()BioPy_Structure.find_same_atom()BioPy_Structure.get_CAonly()BioPy_Structure.get_atom()BioPy_Structure.get_atom_list()BioPy_Structure.get_atoms_in_chains()BioPy_Structure.get_backbone()BioPy_Structure.get_chain()BioPy_Structure.get_chain_list()BioPy_Structure.get_extreme_values()BioPy_Structure.get_next_chain_id()BioPy_Structure.get_pos_mass_list()BioPy_Structure.get_prot_mass_from_atoms()BioPy_Structure.get_prot_mass_from_res()BioPy_Structure.get_residue()BioPy_Structure.get_residue_indexes()BioPy_Structure.get_selection()BioPy_Structure.get_selection_less_than()BioPy_Structure.get_selection_more_than()BioPy_Structure.get_torsion_angles()BioPy_Structure.get_vector_list()BioPy_Structure.iter_asym_id()BioPy_Structure.matrix_transform()BioPy_Structure.no_of_chains()BioPy_Structure.number_of_residues()BioPy_Structure.randomise_position()BioPy_Structure.rename_chains()BioPy_Structure.renumber_atoms()BioPy_Structure.renumber_residues()BioPy_Structure.reorder_residues()BioPy_Structure.reset_position()BioPy_Structure.rotate_by_axis_angle()BioPy_Structure.rotate_by_euler()BioPy_Structure.split_into_chains()BioPy_Structure.translate()BioPy_Structure.write_to_PDB()
gemmiAtomgemmi_Structuregemmi_Structure.add_structure()gemmi_Structure.add_structure_instance()gemmi_Structure.combine_structures()gemmi_Structure.copy()gemmi_Structure.get_chain()gemmi_Structure.get_global_score()gemmi_Structure.no_of_chains()gemmi_Structure.rename_asym_labels()gemmi_Structure.rename_chains()gemmi_Structure.rename_entity_labels()gemmi_Structure.set_atom_labels()gemmi_Structure.set_global_score()gemmi_Structure.set_local_score()gemmi_Structure.split_into_chains()gemmi_Structure.write_to_mmcif()
- TEMPy.maps.em_map
MapMap.box_size()Map.centre()Map.change_origin()Map.copy()Map.fourier_transform()Map.getMap()Map.get_com()Map.get_cropped_box()Map.get_cropped_box_around_atom()Map.get_line_between_points()Map.get_normal_vector()Map.get_point_map()Map.get_pos()Map.get_primary_boundary()Map.get_second_boundary()Map.get_significant_points()Map.get_vectors()Map.laplace_filtered()Map.makeKDTree()Map.make_bin_map()Map.map_rotate_by_axis_angle()Map.map_size()Map.matrix_transform()Map.max()Map.mean()Map.median()Map.min()Map.normalise()Map.normalise_to_1_minus1()Map.old_write_to_MRC_file()Map.origin_change_maps()Map.pad_map()Map.pixel_centre()Map.represent_normal_vectors()Map.resample_by_apix()Map.resample_by_box_size()Map.resize_map()Map.rotate_by_axis_angle()Map.rotate_by_euler()Map.rotate_by_matrix()Map.scale_map()Map.shift_origin()Map.std()Map.threshold_map()Map.translate()Map.update_header()Map.vectorise_point()Map.write_to_MRC_file()Map.x_origin()Map.x_size()Map.y_origin()Map.y_size()Map.z_origin()Map.z_size()
- TEMPy.maps.map_parser