Index

Symbols

$c2_session (global variable or constant) $c2_session.password ($c2_session attribute) $c2_session.server.create_session() ($c2_session.server method) $c2_session.server.delete_session() ($c2_session.server method) $c2_session.server.init() ($c2_session.server method) $c2_session.server.list_sessions() ($c2_session.server method)

$c2_session.server.url ($c2_session.server attribute) $c2_session.session ($c2_session attribute) $c2_session.session_list ($c2_session attribute) $c2_session.ui_init() ($c2_session method) $c2_session.user ($c2_session attribute)

A

activate() (Bindings method) activate_trigger() (TriggerSet method) add() (BBox method) add_atoms() (Atoms method) add_bbox() (BBox method) add_command() (Commands method) add_cylinder (C++ function) add_dependency() (TriggerSet method) add_drawing() (Drawing method) add_handler() (TriggerSet method) add_model() (Models method) add_models() (Models method) add_molecules() (Atoms method) add_new_frame_callback() (View method) add_overlay() (View method) add_rendered_frame_callback() (View method) add_sphere (C++ function) add_trigger() (TriggerSet method) all_atoms() (Models method) all_drawings() (Drawing method) ALL_EDGES_DISPLAY_MASK (Drawing attribute) all_geometries() (Drawing method) ambient_reflectivity (Material attribute) ambient_texture (Drawing attribute) ambient_texture_transform (Drawing attribute)

any_part_selected() (Drawing method) AppDirs::form_path (C++ function) application (Session attribute) apply_without_translation() (Place method) at_quit() (Session method) atom_count() (Molecule method) atom_names() (Atoms method) atom_subset() (Molecule method) AtomBlob (class in structaccess) Atoms (class in hydra.molecule.molecule) atoms (StructBlob attribute) atoms() (Molecule method) atoms_bonds (StructBlob attribute) attenuate (MotionBlur attribute) AttributeInfo (C++ type) AttributeInfo::count (C++ member) AttributeInfo::data_id (C++ member) AttributeInfo::name (C++ member) AttributeInfo::normalized (C++ member) AttributeInfo::offset (C++ member) AttributeInfo::stride (C++ member) AttributeInfo::type (C++ member) AttributeInfos (C++ type) axes() (Place method) axis_center_angle_shift() (Place method)

B

background_color (View attribute) BBox (class in chimera2.math3d) bin_dir (Session attribute) bind_shader_variable() (Bindings method) bind_texture() (Texture method) Bindings (class in hydra.graphics.opengl) block() (TriggerSet method) block_trigger() (TriggerSet method)

bond_templates (Session attribute) bounds() (Drawing method) Buffer (class in hydra.graphics.opengl) Buffer_Type (class in hydra.graphics.opengl) BufferTarget (C++ type) bulk_add() (BBox method) Bytes (C++ type)

C

Camera (class in hydra.graphics.camera) camera (View attribute) camera_framing_models() (in module hydra.graphics.camera) camera_orientation() (in module chimera2.math3d) center() (BBox method) center_of_rotation_needs_update() (View method) chain_ids (ResBlob attribute) chains() (Atoms method) child_drawings() (Drawing method) chimera2.io.formats.bild (module) chimera2.io.formats.stl (module) chimera2.math3d (module) chimera2.qtutils (module) chimera2.scene (module) chimera2.triggerset (module) CIFFile (C++ class), [1] CIFFile::block_code (C++ function), [1] CIFFile::category (C++ function), [1] CIFFile::data_block (C++ function), [1] CIFFile::error (C++ function), [1] CIFFile::finished_parse (C++ function), [1] CIFFile::get_column (C++ function), [1] CIFFile::global_block (C++ function), [1] CIFFile::parse (C++ function), [1] CIFFile::parse_file (C++ function), [1] CIFFile::parse_row (C++ function), [1] CIFFile::ParseCategory (C++ type), [1] CIFFile::ParseValue (C++ type), [1] CIFFile::ParseValues (C++ type), [1] CIFFile::PDB_fixed_columns (C++ function), [1] CIFFile::PDB_style (C++ function), [1] CIFFile::register_category (C++ function), [1] CIFFile::reset_parse (C++ function), [1] CIFFile::save_frame (C++ function), [1] CIFFile::set_PDB_fixed_columns (C++ function), [1] CIFFile::set_PDB_style (C++ function), [1]

CIFFile::tags (C++ function), [1] CIFFile::version (C++ function), [1] clear_all (C++ function) clear_buffers (C++ function) clear_matrices (C++ function) clear_objects (C++ function) clear_primitives (C++ function) clear_programs (C++ function) clear_selection() (Drawing method) clear_selection_promotion_history() (Drawing method) clip_plane_points() (Camera method) (View method) close() (Point method) (Vector method) close_all_models() (Models method) close_models() (Models method) color (Drawing attribute) color_atoms() (Atoms method) color_ribbon() (Atoms method) (Molecule method) colors (Drawing attribute) colors() (Atoms method) combine_rendered_camera_views() (Camera method) Commands (class in hydra.commands.commands) commands (Session attribute) connect_structure (C++ function) coordinates() (Atoms method) coords (AtomBlob attribute) count() (Atoms method) create_buffer (C++ function) create_form() (in module chimera2.qtutils) create_matrix (C++ function) create_object (C++ function) create_program (C++ function) create_singleton (C++ function) cross() (in module chimera2.math3d) cross_product() (in module hydra.geometry.place) (in module hydra.geometry.vector) CrossFade (class in hydra.graphics.crossfade)

D

databases (Session attribute) DataType (C++ type) decay_factor (MotionBlur attribute) delete() (Drawing method) delete_buffer (C++ function) delete_buffer() (Buffer method) delete_handler() (TriggerSet method) delete_matrix (C++ function) delete_object (C++ function) delete_program (C++ function) delete_trigger() (TriggerSet method) demote_selection() (Drawing method) depth_cue_enabled() (View method) description() (Pick method) (Place method) determinant() (Place method) diffuse_reflectivity (Material attribute) display (Drawing attribute)

display_positions (Drawing attribute) display_style (Drawing attribute) distance() (in module hydra.geometry.vector) Dot (Drawing attribute) draw() (Drawing method) (Molecule method) (View method) draw_background() (Render method) draw_depth() (in module hydra.graphics.drawing) draw_drawings() (in module hydra.graphics.drawing) draw_elements() (Buffer method) draw_if_changed() (View method) draw_outline() (in module hydra.graphics.drawing) draw_overlays() (in module hydra.graphics.drawing) draw_self() (Drawing method) draw_transparent() (Render method) Drawing (class in hydra.graphics.drawing) drawing() (Pick method)

E

edge_mask (Drawing attribute) element_names (AtomBlob attribute) element_numbers (AtomBlob attribute) element_numbers() (Atoms method) empty_drawing() (Drawing method) enable_blending() (Render method) enable_depth_cue() (View method)

enable_depth_test() (Render method) enable_shortcuts() (Main_Window method) environment variable USERNAME exclude_water() (Atoms method) extend_to_chains() (Atoms method) eye_separation_pixels (Camera attribute) eye_separation_scene (Camera attribute)

F

fetch_eds_map() (in module hydra.map.fetch_eds) fetch_emdb_map() (in module hydra.map.fetch_emdb) fetch_file() (in module hydra.files.fetch) fetch_from_database() (in module hydra.files.fetch) fetch_mmcif() (in module hydra.molecule.fetch_pdb) fetch_pdb() (in module hydra.molecule.fetch_pdb) field_of_view (Camera attribute) file_history (Session attribute) file_readers (Session attribute)

file_readers() (in module hydra.files.opensave) finish_rendering() (View method) first_intercept() (Drawing method) (View method) fit_list (Session attribute) frame_buffer_image() (Render method) frame_buffer_rgba() (View method) Framebuffer (class in hydra.graphics.opengl) frustum() (in module chimera2.math3d) (in module hydra.graphics.camera) fully_selected() (Drawing method)

G

geometry (Drawing attribute)

Grid_Data (class in hydra.map.data.griddata)

H

has_handlers() (TriggerSet method) hide_atoms() (Atoms method) hide_objects (C++ function) hide_ribbon() (Atoms method) hydra.commands.commands (module) hydra.commands.shortcuts (module) hydra.files.fetch (module) hydra.files.history (module) hydra.files.opensave (module) hydra.files.read_apr (module) hydra.files.read_stl (module) hydra.files.read_swc (module) hydra.files.session_file (module) hydra.geometry.place (module) hydra.geometry.vector (module) hydra.graphics.camera (module)

hydra.graphics.drawing (module) hydra.graphics.opengl (module) hydra.graphics.view (module) hydra.map.data.griddata (module) hydra.map.fetch_eds (module) hydra.map.fetch_emdb (module) hydra.map.fit.fitmap (module) hydra.map.volume (module) hydra.models (module) hydra.molecule.fetch_pdb (module) hydra.molecule.molecule (module) hydra.molecule.pdb (module) hydra.session (module) hydra.surface.gridsurf (module) hydra.surface.sasa (module) hydra.ui.qt.gui (module)

I

Id (C++ type) id_string() (Pick method) Identity() (in module chimera2.math3d) identity() (in module hydra.geometry.place) ijk_to_xyz() (Grid_Data method) image() (View method) initial_camera_view() (View method) initialize_opengl() (Render method) initialize_thresholds() (Volume method)

initialize_view() (Camera method) inner_product() (in module hydra.geometry.vector) inner_product_64() (in module hydra.geometry.vector) interpolate() (Place method) inverse() (Place method) is_identity() (Place method) is_not_whitespace (C++ function), [1] is_trigger_blocked() (TriggerSet method) is_whitespace (C++ function), [1]

K

Keyboard_Shortcuts (class in hydra.commands.shortcuts)

keyboard_shortcuts (Session attribute)

L

last_session_path (Session attribute) length() (Vector method) Lighting (class in hydra.graphics.opengl) lighting() (View method)

llb (BBox attribute) load_pdb_local() (in module hydra.molecule.pdb) log (Session attribute) look_at() (in module chimera2.math3d)

M

Main_Window (class in hydra.ui.qt.gui) main_window (Session attribute) make_orthonormal() (Xform method) maps() (Models method) Material (class in hydra.graphics.opengl) material() (View method) matrix (Place attribute) matrix() (Grid_Data method) Mesh (Drawing attribute) mode (Camera attribute) Model (class in hydra.models)

model_count() (Models method) model_list() (Models method) Models (class in hydra.models) Molecule (class in hydra.molecule.molecule) molecules() (Atoms method) (Models method) motion_to_maximum() (in module hydra.map.fit.fitmap) MotionBlur (class in hydra.graphics.crossfade) move() (Place method) (View method) move_atoms() (Atoms method) move_atoms_to_maximum() (in module hydra.map.fit.fitmap) moved() (Place method)

N

name (Drawing attribute) names (AtomBlob attribute) (ResBlob attribute) names() (Atoms method) new_drawing() (Drawing method) new_region() (Volume method) norm() (in module hydra.geometry.vector) normalize() (Vector method)

normalize_vector() (in module hydra.geometry.vector) normalize_vectors() (in module hydra.geometry.vector) normals (Drawing attribute) number_of_positions() (Drawing method) number_of_triangles() (Drawing method) number_of_views() (Camera method) numbers (ResBlob attribute)

O

Objects (C++ type) oculus (Session attribute) oculus_centering_shift (Camera attribute) opaque (C++ function) OPAQUE_DRAW_PASS (Drawing attribute) opaque_texture (Drawing attribute) open() (in module chimera2.io.formats.bild) (in module chimera2.io.formats.stl) open_autopack_results() (in module hydra.files.read_apr) open_files() (in module hydra.files.opensave) open_map() (in module hydra.files.opensave)

open_pdb_file() (in module hydra.molecule.pdb) open_session() (in module hydra.files.opensave) opengl_matrices() (Places method) opengl_matrix() (Place method) opengl_version() (Render method) (View method) OpenGLWidget (class in chimera2.qtutils) ortho() (in module chimera2.math3d) orthonormal_frame() (in module hydra.geometry.place) overlays() (View method)

P

parse_mmCIF_file() (in module pdbio) pdbio (module) perspective() (in module chimera2.math3d) Pick (class in hydra.graphics.drawing) pixel_shift (Camera attribute) pixel_size() (Camera method) (View method) place (Camera attribute) Place (class in hydra.geometry.place) place_inverse (Camera attribute)

Places (class in hydra.geometry.place) Point (class in chimera2.math3d) position (Drawing attribute) position() (Camera method) positions (Drawing attribute) PrimitiveType (C++ type) projection_matrix() (Camera method) promote_selection() (Drawing method) Python Enhancement Proposals PEP 8

R

radii() (Atoms method) read_matrix() (Grid_Data method) read_pdb_file() (in module pdbio) read_python() (in module hydra.files.opensave) read_stl() (in module hydra.files.read_stl) read_swc() (in module hydra.files.read_swc) redraw_needed (Camera attribute) (Drawing attribute) register_commands() (in module hydra.commands.commands) register_fetch_database() (in module hydra.files.fetch) register_shortcuts() (in module hydra.commands.shortcuts) release() (TriggerSet method) release_trigger() (TriggerSet method) reload_texture() (Texture method) remove_all_drawings() (Drawing method) remove_drawing() (Drawing method) remove_drawings() (Drawing method) remove_duplicates() (Atoms method) remove_new_frame_callback() (View method)

remove_overlays() (View method) remove_rendered_frame_callback() (View method) render (C++ function) Render (class in hydra.graphics.opengl) report_framerate() (View method) ResBlob (class in structaccess) residue_names() (Atoms method) residue_numbers() (Atoms method) residues (AtomBlob attribute) (StructBlob attribute) resize() (View method) restore_session() (in module hydra.files.session_file) reverse_order_children (Drawing attribute) rgba_drawing() (in module hydra.graphics.drawing) rotate() (View method) (Xform method) Rotation() (in module chimera2.math3d) rotation() (in module hydra.geometry.place) rotation_angle() (Place method) run_command() (Commands method)

S

same() (Place method) save_image() (in module hydra.files.opensave) save_session() (in module hydra.files.opensave) (in module hydra.files.session_file) Scale() (in module chimera2.math3d) scale() (in module hydra.geometry.place) (Xform method) scale_atom_colors() (Atoms method) scenes (Session attribute) select() (Pick method) selected (Drawing attribute) selected_positions (Drawing attribute) selected_triangles_mask (Drawing attribute) selection_add (C++ function) selection_clear (C++ function) SELECTION_DRAW_PASS (Drawing attribute) selection_remove (C++ function) separate_chains() (Atoms method) separate_molecules() (Atoms method) sequence_numbers() (Atoms method) ses_surface_geometry() (in module hydra.surface.gridsurf) Session (class in hydra.session) session_state() (in module hydra.files.session_file) set_atom_style() (Atoms method) set_attribute_alias (C++ function) set_background_color() (Render method) set_camera_mode() (View method) set_clear_color (C++ function) set_default_parameters() (Lighting method) set_edge_mask() (Drawing method) set_framebuffer() (Camera method) set_model_matrix() (Render method) set_mono_buffer() (Render method) set_multishadow() (View method) set_parameters() (Volume method) set_projection_matrix() (Render method) set_representation() (Volume method) set_single_color() (Render method) set_stereo_buffer() (Render method) set_uniform (C++ function) set_view() (Camera method)

set_view_matrix() (Render method) set_viewport() (Render method) Shader (class in hydra.graphics.opengl) shader() (Render method) ShaderType (C++ type) shadows (View attribute) shift_and_angle() (Place method) show() (Volume method) show_atoms() (Atoms method) show_back_forward_buttons() (Main_Window method) show_info() (Session method) show_objects (C++ function) show_outline_box() (Volume method) show_ribbon() (Atoms method) show_status() (Main_Window method) (Session method) show_text() (Main_Window method) show_warning() (Session method) showing_transparent() (Drawing method) shown_atom_count() (Molecule method) size() (BBox method) skew_axes() (in module hydra.geometry.place) Solid (Drawing attribute) sort_atoms() (in module hydra.molecule.pdb) space_navigator (Session attribute) specular_exponent (Material attribute) specular_reflectivity (Material attribute) spheres_surface_area() (in module hydra.surface.sasa) sqlength() (Vector method) str_to_float (C++ function), [1] str_to_int (C++ function), [1] StringVector (C++ type), [1] structaccess (module) StructBlob (class in structaccess) structures (StructBlob attribute) subset() (Atoms method) support_stereo() (Render method) surface() (in module hydra.surface.gridsurf) surfaces() (Models method)

T

Texture (class in hydra.graphics.opengl) texture (Drawing attribute) texture_coordinates (Drawing attribute) texture_format() (Texture method) Texture_Window (class in hydra.graphics.opengl) transform() (in module chimera2.math3d) translate() (View method) (Xform method) Translation() (in module chimera2.math3d) translation() (in module hydra.geometry.place) (Place method) transparent (C++ function)

TRANSPARENT_DEPTH_DRAW_PASS (Drawing attribute) TRANSPARENT_DRAW_PASS (Drawing attribute) transpose() (Place method) triangle_and_edge_mask (Drawing attribute) TRIANGLE_DISPLAY_MASK (Drawing attribute) triangles (Drawing attribute) trigger_handlers() (TriggerSet method) trigger_names() (TriggerSet method) TriggerSet (class in chimera2.triggerset)

U

unbind_texture() (Texture method) update_buffer (C++ function) update_buffer_data() (Buffer method) update_center_of_rotation() (View method) update_level_of_detail() (View method)

urf (BBox attribute) use_lighting (Drawing attribute) use_shader() (Render method) USERNAME

V

Vector (class in chimera2.math3d) vector_rotation() (in module hydra.geometry.place) vector_sum() (in module hydra.geometry.vector) vertex_colors (Drawing attribute) vertices (Drawing attribute) View (class in hydra.graphics.view) view (Session attribute)

view() (Camera method) view_all() (Camera method) (View method) view_direction() (Camera method) view_inverse() (Camera method) view_width() (Camera method) Volume (class in hydra.map.volume) volume_defaults (Session attribute)

W

warp_window_size (Camera attribute) was_deleted (Drawing attribute)

weighted_point() (in module chimera2.math3d)

X

Xform (class in chimera2.math3d) xform() (BBox method)

xyz_to_ijk() (Grid_Data method)

Z

z_axis() (Place method)

zero_translation() (Place method)