Index

Symbols | _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Z

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)

_

__and__() (Collection method)
__getitem__() (Collection method)
__iter__() (Collection method)
__len__() (Collection method)
__or__() (Collection method)
__sub__() (Collection method)

A

activate_trigger() (TriggerSet method)
add() (LRUSetHistory method)
(Tasks method)
(Tools method)
add_2d_overlay() (View method)
add_atom() (Residue method)
add_callback() (View method)
add_dependency() (TriggerSet method)
add_drawing() (Drawing method)
add_handler() (TriggerSet method)
add_keyword_arguments() (in module chimera.core.commands.cli)
add_log() (Logger method)
add_overlay() (View method)
add_to() (Aggregate method)
add_tool_info() (Toolshed method)
add_trigger() (TriggerSet method)
Aggregate (class in chimera.core.commands.cli)
Alias (class in chimera.core.commands.cli)
alias() (in module chimera.core.commands.cli)
all_atomic_structures() (in module chimera.core.atomic.structure)
all_atoms() (in module chimera.core.atomic.structure)
all_drawings() (Drawing method)
ALL_EDGES_DISPLAY_MASK (Drawing attribute)
all_geometries() (Drawing method)
all_models() (Model method)
ALWAYS_DISPLAY (Bond attribute)
(Pseudobond attribute)
ambient_texture (Drawing attribute)
ambient_texture_transform (Drawing attribute)
Annotation (class in chimera.core.commands.cli)
AnnotationError
any_drawing_selected() (View method)
any_part_selected() (Drawing method)
AppDirs::form_path (C++ function)
apply_without_translation() (Place method)
Atom (class in chimera.core.atomic.molobject)
atom_count (MolecularSurface attribute)
AtomicStructure (class in chimera.core.atomic.structure)
AtomicStructureData (class in chimera.core.atomic.molobject)
AtomicStructureDatas (class in chimera.core.atomic.molarray)
AtomicStructuresArg (class in chimera.core.commands.cli)
atoms (AtomicStructure attribute)
(AtomicStructureData attribute)
(AtomicStructureDatas attribute)
(Bond attribute)
(Bonds attribute)
Atoms (class in chimera.core.atomic.molarray)
atoms (Pseudobond attribute)
(Pseudobonds attribute)
(Residue attribute)
(Residues attribute)
AtomsArg (class in chimera.core.commands.cli)
attenuate (MotionBlur attribute)
autostart() (Tools method)
axes() (Place method)
axis_center_angle_shift() (Place method)
AxisArg (class in chimera.core.commands.cli)

B

background_color (View attribute)
BALL_STYLE (Atom attribute)
bfactor (Atom attribute)
bind_texture() (Texture method)
block() (TriggerSet method)
block_trigger() (TriggerSet method)
Bond (class in chimera.core.atomic.molobject)
bonded_atoms (Atom attribute)
bonds (Atom attribute)
(AtomicStructureData attribute)
(AtomicStructureDatas attribute)
Bonds (class in chimera.core.atomic.molarray)
BoolArg (class in chimera.core.commands.cli)
boundary_edges() (in module chimera.core.surface._surface)
boundary_loops() (in module chimera.core.surface._surface)
Bounded (class in chimera.core.commands.cli)
bounds() (Drawing method)
buriedarea() (in module chimera.core.commands.buriedarea)
by_chain (Atoms attribute)
by_structure (Atoms attribute)

C

cache_data() (ToolInfo method)
calculate_surface_geometry() (MolecularSurface method)
calculate_vertex_normals() (in module chimera.core.surface._surface)
Camera (class in chimera.core.graphics.camera)
camera (View attribute)
camera() (in module chimera.core.commands.camera)
camera_framing_drawings() (in module chimera.core.graphics.camera)
categorized_formats() (in module chimera.core.io)
category (PseudobondGroupData attribute)
category() (in module chimera.core.io)
Chain (class in chimera.core.atomic.molobject)
chain_id (Atom attribute)
(Chain attribute)
(Residue attribute)
chain_ids (Chains attribute)
(Residues attribute)
chains (AtomicStructureData attribute)
(AtomicStructureDatas attribute)
Chains (class in chimera.core.atomic.molarray)
check() (Postcondition method)
check_remote() (Toolshed method)
child_drawings() (Drawing method)
child_models() (Model method)
ChildToolWindow (class in chimera.core.ui.gui)
chimera.core.atomic.molarray (module)
chimera.core.atomic.molobject (module)
chimera.core.atomic.molsurf (module)
chimera.core.atomic.pbgroup (module)
chimera.core.atomic.pdbio (module)
chimera.core.atomic.structure (module)
chimera.core.commands.cli (module)
chimera.core.configfile (module)
chimera.core.data_events (module)
chimera.core.geometry.place (module)
chimera.core.geometry.vector (module)
chimera.core.graphics.camera (module)
chimera.core.graphics.drawing (module)
chimera.core.graphics.view (module)
chimera.core.history (module)
chimera.core.io (module)
chimera.core.logger (module)
chimera.core.map.data.griddata (module)
chimera.core.map.filter.vopcommand (module)
chimera.core.map.series.vseries_command (module)
chimera.core.map.volume (module)
chimera.core.models (module)
chimera.core.orderedset (module)
chimera.core.safesave (module)
chimera.core.scripting (module)
chimera.core.serialize (module)
chimera.core.session (module)
chimera.core.settings (module)
chimera.core.surface._surface (module)
chimera.core.surface.area (module)
chimera.core.surface.dust (module)
chimera.core.surface.gaussian (module)
chimera.core.surface.gridsurf (module)
chimera.core.surface.sasa (module)
chimera.core.surface.shapes (module)
chimera.core.tasks (module)
chimera.core.tools (module)
chimera.core.toolshed (module)
chimera.core.triggerset (module)
chimera.core.ui.gui (module)
chimera.core.utils (module)
chimera.movie.moviecmd (module)
chimera.toolshed.cmd (module)
CIFFile (C++ class)
CIFFile::block_code (C++ function)
CIFFile::category (C++ function)
CIFFile::data_block (C++ function)
CIFFile::error (C++ function)
CIFFile::finished_parse (C++ function)
CIFFile::get_column (C++ function)
CIFFile::global_block (C++ function)
CIFFile::parse (C++ function)
CIFFile::parse_file (C++ function)
CIFFile::parse_row (C++ function)
CIFFile::ParseCategory (C++ type)
CIFFile::ParseValue (C++ type)
CIFFile::ParseValues (C++ type)
CIFFile::PDB_fixed_columns (C++ function)
CIFFile::PDB_style (C++ function)
CIFFile::register_category (C++ function)
CIFFile::reset_parse (C++ function)
CIFFile::save_frame (C++ function)
CIFFile::set_PDB_fixed_columns (C++ function)
CIFFile::set_PDB_style (C++ function)
CIFFile::tags (C++ function)
CIFFile::version (C++ function)
class_name_of_unique_id() (Session method)
class_of_unique_id() (Session method)
cleanup() (ToolWindow method)
clear() (FIFOHistory method)
(Logger method)
clear_selection() (Drawing method)
clear_selection_promotion_history() (Drawing method)
clip_plane_points() (Camera method)
(View method)
close() (in module chimera.core.commands.close)
(SaveFile method)
close_destroys (ToolWindow attribute)
cmd_desc() (Alias method)
CmdDesc (class in chimera.core.commands.cli)
CollatingLog (class in chimera.core.logger)
Collator (class in chimera.core.logger)
Collection (class in chimera.core.atomic.molarray)
color (Atom attribute)
(Bond attribute)
(Drawing attribute)
(Pseudobond attribute)
color() (in module chimera.core.commands.color)
colordef() (in module chimera.core.commands.color)
colors (Atoms attribute)
(Bonds attribute)
(Drawing attribute)
(Pseudobonds attribute)
combine_rendered_camera_views() (Camera method)
Command (class in chimera.core.commands.cli)
command_function() (in module chimera.core.commands.cli)
command_line_hide() (in module chimera.cmd_line.cmd)
command_line_show() (in module chimera.cmd_line.cmd)
command_url() (in module chimera.core.commands.cli)
commas() (in module chimera.core.commands.cli)
common_startup() (in module chimera.core.session)
concatenate() (in module chimera.core.atomic.molarray)
ConfigFile (class in chimera.core.configfile)
connect_structure (C++ function)
connected_pieces() (in module chimera.core.surface._surface)
connected_triangles() (in module chimera.core.surface._surface)
connects_to() (Atom method)
constructor (DottedTupleOf attribute)
(ListOf attribute)
(SetOf attribute)
(TupleOf attribute)
contacts() (in module chimera.contacts.cmd)
coord (Atom attribute)
coords (Atoms attribute)
copy() (AtomicStructure method)
(CmdDesc method)
create_child_window() (MainToolWindow method)
cross_product() (in module chimera.core.geometry.place)
(in module chimera.core.geometry.vector)
CrossFade (class in chimera.core.graphics.crossfade)
crossfade() (in module chimera.core.commands.crossfade)
crosslinks() (in module chimera.core.commands.crosslinks)
cylinder_geometry() (in module chimera.core.surface.shapes)

D

dangerous() (in module chimera.core.io)
dashed_cylinder_geometry() (in module chimera.core.surface.shapes)
decay_factor (MotionBlur attribute)
deduce_format() (in module chimera.core.io)
delay_registration() (in module chimera.core.commands.cli)
delete() (AtomicStructure method)
(AtomicStructureData method)
(Atoms method)
(Drawing method)
(Scenes method)
(ToolInstance method)
(in module chimera.core.commands.delete)
delete_handler() (TriggerSet method)
delete_trigger() (TriggerSet method)
demote_selection() (Drawing method)
depth_cue_enabled() (View method)
dequeue() (FIFOHistory method)
deregister() (in module chimera.core.commands.cli)
deregister_commands() (ToolInfo method)
deregister_for_keystrokes() (UI method)
deregister_handler() (Server method)
description() (Pick method)
(Place method)
deserialize() (in module chimera.core.serialize)
destroy() (ToolWindow method)
determinant() (Place method)
discard_article() (in module chimera.core.commands.cli)
display (Atom attribute)
(Bond attribute)
(Drawing attribute)
(Pseudobond attribute)
display() (in module chimera.core.commands.display)
(ToolInstance method)
display_name() (Task method)
display_positions (Drawing attribute)
display_style (Drawing attribute)
displays (Atoms attribute)
(Bonds attribute)
(Pseudobonds attribute)
distance() (in module chimera.core.geometry.vector)
distribution() (ToolInfo method)
Dot (Drawing attribute)
DottedTupleOf (class in chimera.core.commands.cli)
draw() (Drawing method)
(View method)
draw_2d_overlays() (in module chimera.core.graphics.drawing)
draw_depth() (in module chimera.core.graphics.drawing)
draw_drawings() (in module chimera.core.graphics.drawing)
draw_mode (Atom attribute)
draw_modes (Atoms attribute)
draw_new_frame() (View method)
draw_outline() (in module chimera.core.graphics.drawing)
draw_overlays() (in module chimera.core.graphics.drawing)
draw_self() (Drawing method)
Drawing (class in chimera.core.graphics.drawing)
drawing() (Pick method)
drawing_bounds() (View method)
drawing_lineage (Drawing attribute)
dump() (in module chimera.core.session)

E

echo() (in module chimera.core.commands.echo)
edge_mask (Drawing attribute)
Element (class in chimera.core.atomic.molobject)
element_name (Atom attribute)
element_names (Atoms attribute)
element_number (Atom attribute)
element_numbers (Atoms attribute)
empty_drawing() (Drawing method)
EmptyArg (class in chimera.core.commands.cli)
enable_depth_cue() (View method)
enclosed_volume() (in module chimera.core.surface._surface)
(in module chimera.core.surface.area)
enqueue() (FIFOHistory method)
EnumOf (class in chimera.core.commands.cli)
environment variable
USERNAME
error() (Logger method)
error_check() (Command method)
error_message() (Postcondition method)
estimate_surface_area_of_spheres() (in module chimera.core.surface._surface)
execute() (Command method)
exit() (in module chimera.core.commands.exit)
exited_normally() (Job method)
export() (in module chimera.core.commands.export)
export_function() (in module chimera.core.io)
extend() (FIFOHistory method)
extensions() (in module chimera.core.io)
eye_separation_pixels (StereoCameraMode attribute)
eye_separation_scene (StereoCameraMode attribute)

F

fetch_function() (in module chimera.core.io)
field_of_view (Camera attribute)
FIFOHistory (class in chimera.core.history)
filename (ConfigFile attribute)
filename() (in module chimera.core.history)
fill_context_menu() (ToolWindow method)
filter() (Collection method)
find_by_class() (Tasks method)
(Tools method)
find_by_id() (Tasks method)
(Tools method)
find_tool() (Toolshed method)
finish_rendering() (View method)
first_intercept() (Drawing method)
(View method)
fitmap() (in module chimera.core.map.fit.fitcmd)
flattened() (in module chimera.core.utils)
FloatArg (class in chimera.core.commands.cli)
format_names() (in module chimera.core.io)
formats() (in module chimera.core.io)
forward_keystroke() (UI method)
frame_buffer_rgba() (View method)
frustum() (in module chimera.core.graphics.camera)
fully_selected() (Drawing method)

G

gaussian_surface() (in module chimera.core.surface.gaussian)
geometry (Drawing attribute)
get_class() (ToolInfo method)
get_group() (PseudobondManager method)
get_polymer_spline() (Residues method)
Grid_Data (class in chimera.core.map.data.griddata)

H

halfbond (Bond attribute)
(Pseudobond attribute)
halfbonds (Bonds attribute)
(Pseudobonds attribute)
has_handlers() (TriggerSet method)
has_trigger() (TriggerSet method)
help() (in module chimera.core.commands.help)
hide (Atom attribute)
(Bond attribute)
hide() (MolecularSurface method)
HIDE_RIBBON (Atom attribute)
(Bond attribute)
html_to_plain() (in module chimera.core.logger)
html_usage() (in module chimera.core.commands.cli)
html_user_agent() (in module chimera.core.utils)
HtmlLog (class in chimera.core.logger)

I

id_string() (Pick method)
identity() (in module chimera.core.geometry.place)
ijk_to_xyz() (Grid_Data method)
image() (View method)
in_chain (Atom attribute)
in_chains (Atoms attribute)
index() (Collection method)
info() (Logger method)
init() (in module chimera.core.toolshed)
initial_camera_view() (View method)
initialize_thresholds() (Volume method)
initialize_view() (Camera method)
inner_product() (in module chimera.core.geometry.vector)
inner_product_64() (in module chimera.core.geometry.vector)
install_tool() (Toolshed method)
IntArg (class in chimera.core.commands.cli)
interpolate() (Place method)
intersect() (Collection method)
intersects() (Collection method)
intersects_each() (Collection method)
inverse() (Place method)
invert_vertex_normals() (in module chimera.core.surface._surface)
is_backbone (Atom attribute)
is_helix (Residue attribute)
(Residues attribute)
is_identity() (Place method)
is_metal (Element attribute)
is_not_whitespace (C++ function)
is_python_keyword() (in module chimera.core.commands.cli)
is_sheet (Residue attribute)
(Residues attribute)
is_trigger_blocked() (TriggerSet method)
is_whitespace (C++ function)

J

Job (class in chimera.core.tasks)
JobError
JobLaunchError
JobMonitorError

K

ks() (in module chimera.shortcuts.shortcuts)

L

largest_blobs_triangle_mask() (in module chimera.core.surface.dust)
launch() (Job method)
length (Pseudobond attribute)
Lighting (class in chimera.core.graphics.opengl)
lighting() (in module chimera.core.commands.lighting)
(View method)
Limited (class in chimera.core.commands.cli)
list() (in module chimera.core.commands.list)
(Tasks method)
(Tools method)
ListOf (class in chimera.core.commands.cli)
load() (ObjectCache method)
Log (class in chimera.core.logger)
log() (HtmlLog method)
(Log method)
(PlainTextLog method)
(in module chimera.log.cmd)
Logger (class in chimera.core.logger)
LRUSetHistory (class in chimera.core.history)

M

MainToolWindow (class in chimera.core.ui.gui)
make_current() (OpenGLContext method)
manage() (ToolWindow method)
mask() (Collection method)
mass (Element attribute)
Material (class in chimera.core.graphics.opengl)
material() (in module chimera.core.commands.material)
(View method)
matrix (Place attribute)
matrix() (Grid_Data method)
merge() (Collection method)
Mesh (Drawing attribute)
metadata (AtomicStructureData attribute)
(AtomicStructureDatas attribute)
(Session attribute)
metadata() (Scenes method)
migrate_from() (ConfigFile method)
migrate_value() (ConfigFile method)
mime_types() (in module chimera.core.io)
mode (Camera attribute)
Model (class in chimera.core.models)
MolecularSurface (class in chimera.core.atomic.molsurf)
molmap() (in module chimera.core.map.molmap)
monitor() (Job method)
MotionBlur (class in chimera.core.graphics.crossfade)
mousemodes_hide() (in module chimera.mouse_modes.cmd)
mousemodes_show() (in module chimera.mouse_modes.cmd)
move() (in module chimera.core.commands.move)
(Place method)
(View method)
moved() (Place method)
movie_abort() (in module chimera.movie.moviecmd)
movie_crossfade() (in module chimera.movie.moviecmd)
movie_duplicate() (in module chimera.movie.moviecmd)
movie_encode() (in module chimera.movie.moviecmd)
movie_formats() (in module chimera.movie.moviecmd)
movie_ignore() (in module chimera.movie.moviecmd)
movie_record() (in module chimera.movie.moviecmd)
movie_reset() (in module chimera.movie.moviecmd)
movie_status() (in module chimera.movie.moviecmd)
movie_stop() (in module chimera.movie.moviecmd)

N

name (Annotation attribute)
(Atom attribute)
(AtomicStructureData attribute)
(Drawing attribute)
(Element attribute)
(Residue attribute)
names (AtomicStructureDatas attribute)
(Atoms attribute)
(Residues attribute)
names() (Scenes method)
NEVER_DISPLAY (Bond attribute)
(Pseudobond attribute)
new_atom() (AtomicStructureData method)
new_bond() (AtomicStructureData method)
new_drawing() (Drawing method)
new_parameters() (MolecularSurface method)
new_pseudobond() (PseudobondGroupData method)
new_region() (Volume method)
new_residue() (AtomicStructureData method)
newer_than() (ToolInfo method)
next_token() (in module chimera.core.commands.cli)
NoArg (class in chimera.core.commands.cli)
norm() (in module chimera.core.geometry.vector)
normalize_vector() (in module chimera.core.geometry.vector)
normalize_vectors() (in module chimera.core.geometry.vector)
normals (Drawing attribute)
num_atoms (AtomicStructureData attribute)
(AtomicStructureDatas attribute)
(Residue attribute)
(Residues attribute)
num_bonds (Atom attribute)
(AtomicStructureData attribute)
(AtomicStructureDatas attribute)
num_chains (AtomicStructureData attribute)
(AtomicStructureDatas attribute)
num_coord_sets (AtomicStructureData attribute)
num_pseudobonds (PseudobondGroupData attribute)
num_residues (AtomicStructureData attribute)
(AtomicStructureDatas attribute)
(Chain attribute)
(Chains attribute)
num_selected (Atoms attribute)
number (Element attribute)
(Residue attribute)
number_of_positions() (Drawing method)
number_of_triangles() (Drawing method)
number_of_views() (Camera method)
(StereoCameraMode method)
numbers (Residues attribute)

O

ObjectCache (class in chimera.core.history)
oculus() (in module chimera.core.devices.oculus.oculuscmd)
on_disk() (ConfigFile method)
on_finish() (Task method)
OPAQUE_DRAW_PASS (Drawing attribute)
opaque_texture (Drawing attribute)
open() (in module chimera.core.commands.open)
open_ch() (in module chimera.core.scripting)
open_data() (in module chimera.core.io)
open_function() (in module chimera.core.io)
open_map() (in module chimera.core.map.volume)
open_multiple_data() (in module chimera.core.io)
open_py() (in module chimera.core.scripting)
opengl_matrices() (Places method)
opengl_matrix() (Place method)
opengl_version() (View method)
OpenGLContext (class in chimera.core.graphics.view)
Or (class in chimera.core.commands.cli)
OrderedSet (class in chimera.core.orderedset)
OrderedWeakrefSet (class in chimera.core.orderedset)
origin() (Place method)
ortho() (in module chimera.core.graphics.camera)
orthonormal_frame() (in module chimera.core.geometry.place)
other_atom() (Bond method)
overlays() (View method)

P

parse() (Annotation static method)
parse_stl() (in module chimera.core.surface._surface)
parse_text() (Command method)
pbg_map (AtomicStructureData attribute)
pbg_maps (AtomicStructureDatas attribute)
pdbimages() (in module chimera.core.commands.pdbimages)
perframe() (in module chimera.core.commands.perframe)
Pick (class in chimera.core.graphics.drawing)
pixel_shift (Camera attribute)
pixel_shift() (StereoCameraMode method)
pixel_size() (Camera method)
(View method)
Place (class in chimera.core.geometry.place)
placements (ToolWindow attribute)
Places (class in chimera.core.geometry.place)
PlainTextLog (class in chimera.core.logger)
polymers() (AtomicStructureData method)
position (Camera attribute)
(Drawing attribute)
positions (Drawing attribute)
Postcondition (class in chimera.core.commands.cli)
prefixes() (in module chimera.core.io)
product() (in module chimera.core.geometry.place)
projection_matrix() (Camera method)
promote_selection() (Drawing method)
Pseudobond (class in chimera.core.atomic.molobject)
pseudobond_group() (AtomicStructureData method)
pseudobond_groups (AtomicStructure attribute)
PseudobondGroup (class in chimera.core.atomic.pbgroup)
PseudobondGroupData (class in chimera.core.atomic.molobject)
PseudobondManager (class in chimera.core.atomic.molobject)
Pseudobonds (class in chimera.core.atomic.molarray)
pseudobonds (PseudobondGroupData attribute)
pwd() (in module chimera.core.commands.pwd)
Python Enhancement Proposals
PEP 8

R

radii (Atoms attribute)
(Bonds attribute)
(Pseudobonds attribute)
radius (Atom attribute)
(Bond attribute)
(Pseudobond attribute)
rcolor() (in module chimera.core.commands.color)
read_matrix() (Grid_Data method)
read_metadata() (Session method)
read_pdb_file() (in module chimera.core.atomic.pdbio)
redraw_needed (Camera attribute)
redraw_needed() (Drawing method)
register() (in module chimera.core.commands.cli)
register_commands() (ToolInfo method)
register_fetch() (in module chimera.core.io)
register_for_keystrokes() (UI method)
register_format() (in module chimera.core.io)
register_handler() (Server method)
register_open() (in module chimera.core.io)
registered_commands() (in module chimera.core.commands.cli)
release() (TriggerSet method)
release_trigger() (TriggerSet method)
reload() (Toolshed method)
reload_texture() (Texture method)
remove() (Tasks method)
(Tools method)
remove_2d_overlays() (View method)
remove_all_drawings() (Drawing method)
remove_callback() (View method)
remove_drawing() (Drawing method)
remove_drawings() (Drawing method)
remove_log() (Logger method)
remove_overlays() (View method)
remove_solvent_ligands_ions() (in module chimera.core.atomic.molsurf)
replace() (FIFOHistory method)
replace_attribute() (Session method)
replace_state_manager() (Session method)
report_framerate() (View method)
requires_filename() (in module chimera.core.io)
reset() (ConfigFile method)
(Session method)
reset_state() (Tasks method)
(Tools method)
(View method)
residue (Atom attribute)
Residue (class in chimera.core.atomic.molobject)
residues (AtomicStructureData attribute)
(AtomicStructureDatas attribute)
(Atoms attribute)
(Chain attribute)
(Chains attribute)
Residues (class in chimera.core.atomic.molarray)
resize() (View method)
restore() (Scenes method)
(Session method)
restore_snapshot() (Tasks method)
(Tools method)
restore_unique_id() (Session method)
retrieve_cached_url() (in module chimera.core.utils)
reverse_order_children (Drawing attribute)
rgba_drawing() (in module chimera.core.graphics.drawing)
ribbon() (in module chimera.core.commands.ribbon)
ribbon_color (Residue attribute)
ribbon_colors (Residues attribute)
ribbon_display (Residue attribute)
ribbon_displays (Residues attribute)
roll() (in module chimera.core.commands.roll)
rotate() (View method)
rotation() (in module chimera.core.geometry.place)
rotation_angle() (Place method)
rotation_axis_and_angle() (Place method)
run() (in module chimera.core.commands.run)
(Job method)
(Server method)
(Task method)
running() (Job method)

S

same() (Place method)
SameSize (class in chimera.core.commands.cli)
sasa() (in module chimera.core.commands.sasa)
save() (ConfigFile method)
(FIFOHistory method)
(LRUSetHistory method)
(ObjectCache method)
(Scenes method)
(Session method)
(in module chimera.core.commands.save)
(in module chimera.core.session)
SaveBinaryFile (class in chimera.core.safesave)
SaveFile (class in chimera.core.safesave)
SaveTextFile (class in chimera.core.safesave)
scale() (in module chimera.core.geometry.place)
scene_coord (Atom attribute)
scene_coords (Atoms attribute)
Scenes (class in chimera.core.session)
scolor() (in module chimera.core.commands.scolor)
select() (Pick method)
select_atom() (AtomicStructure method)
select_atoms() (AtomicStructure method)
select_residue() (AtomicStructure method)
selected (Atom attribute)
(Atoms attribute)
(Drawing attribute)
selected_atoms() (in module chimera.core.atomic.structure)
selected_displayed_triangles_mask (Drawing attribute)
selected_positions (Drawing attribute)
selected_triangles_mask (Drawing attribute)
SELECTION_DRAW_PASS (Drawing attribute)
serialize() (in module chimera.core.serialize)
Server (class in webapp_server)
ses_surface_geometry() (in module chimera.core.surface.gridsurf)
Session (class in chimera.core.session)
session (Task attribute)
(ToolInstance attribute)
session_info() (AtomicStructureData method)
set() (in module chimera.core.commands.set)
set_default_parameters() (Lighting method)
(Material method)
set_field_of_view_from_view_width() (Camera method)
set_log() (Server method)
set_multishadow() (View method)
set_multishadow_map_size() (View method)
set_parameters() (Volume method)
set_render_target() (Camera method)
(StereoCameraMode method)
set_representation() (Volume method)
set_shadow_map_size() (View method)
SetOf (class in chimera.core.commands.cli)
Settings (class in chimera.core.settings)
shadows (View attribute)
sharp_edge_patches() (in module chimera.core.surface._surface)
shift_and_angle() (Place method)
show() (MolecularSurface method)
(Volume method)
show_outline_box() (Volume method)
showing_transparent() (Drawing method)
shown (ToolWindow attribute)
shown_atom_count() (AtomicStructure method)
shown_changed() (ToolWindow method)
skew_axes() (in module chimera.core.geometry.place)
SMART_DISPLAY (Bond attribute)
(Pseudobond attribute)
snav() (in module chimera.core.devices.spacenavigator.snav)
Solid (Drawing attribute)
sphere_geometry() (in module chimera.core.surface.shapes)
SPHERE_STYLE (Atom attribute)
spheres_surface_area() (in module chimera.core.surface.sasa)
split() (in module chimera.core.commands.split)
ss_id (Residue attribute)
(Residues attribute)
start() (Task method)
(ToolInfo method)
status() (Log method)
(Logger method)
StereoCameraMode (class in chimera.core.graphics.camera)
STICK_STYLE (Atom attribute)
stop() (in module chimera.core.commands.stop)
str (Residue attribute)
str_to_float (C++ function)
str_to_int (C++ function)
StringArg (class in chimera.core.commands.cli)
StringVector (C++ type)
strs (Residues attribute)
structure (Atom attribute)
(Chain attribute)
(Residue attribute)
structures (Atoms attribute)
(Chains attribute)
(Residues attribute)
style() (in module chimera.core.commands.style)
subdivide_mesh() (in module chimera.core.surface._surface)
subdivide_triangles() (in module chimera.core.surface._surface)
subtract() (Collection method)
surface() (in module chimera.core.commands.surface)
surface_area() (in module chimera.core.surface._surface)
(in module chimera.core.surface.area)
surface_area_of_spheres() (in module chimera.core.surface._surface)
surface_volume_and_area() (in module chimera.core.surface.area)
surfaces() (AtomicStructure method)
swap_buffers() (OpenGLContext method)
sym() (in module chimera.core.commands.sym)

T

take_snapshot() (Tasks method)
(Tools method)
Task (class in chimera.core.tasks)
Tasks (class in chimera.core.tasks)
terminate() (Server method)
(Task method)
terminated() (Task method)
terminating() (Task method)
Texture (class in chimera.core.graphics.opengl)
texture (Drawing attribute)
texture_coordinates (Drawing attribute)
texture_format() (Texture method)
thread_safe() (UI method)
title_change() (in module chimera.title.label)
title_create() (in module chimera.title.label)
title_delete() (in module chimera.title.label)
tool_info() (Toolshed method)
ToolInfo (class in chimera.core.toolshed)
ToolInstance (class in chimera.core.tools)
Tools (class in chimera.core.tools)
Toolshed (class in chimera.core.toolshed)
ToolshedError
ToolshedInstalledError
ToolshedUnavailableError
ToolshedUninstalledError
ToolWindow (class in chimera.core.ui.gui)
translate() (View method)
translation() (in module chimera.core.geometry.place)
(Place method)
TRANSPARENT_DEPTH_DRAW_PASS (Drawing attribute)
TRANSPARENT_DRAW_PASS (Drawing attribute)
transpose() (Place method)
triangle_mask (Drawing attribute)
triangle_vertices() (in module chimera.core.surface._surface)
TrianglePick (class in chimera.core.graphics.drawing)
triangles (Drawing attribute)
trigger_handlers() (TriggerSet method)
trigger_names() (TriggerSet method)
TriggerSet (class in chimera.core.triggerset)
ts_hide() (in module chimera.toolshed.cmd)
ts_install() (in module chimera.toolshed.cmd)
ts_list() (in module chimera.toolshed.cmd)
ts_refresh() (in module chimera.toolshed.cmd)
ts_remove() (in module chimera.toolshed.cmd)
ts_show() (in module chimera.toolshed.cmd)
ts_start() (in module chimera.toolshed.cmd)
ts_update() (in module chimera.toolshed.cmd)
tube_geometry() (in module chimera.core.surface._surface)
tube_geometry_colors() (in module chimera.core.surface._surface)
tube_triangle_mask() (in module chimera.core.surface._surface)
TupleOf (class in chimera.core.commands.cli)
turn() (in module chimera.core.commands.turn)
twod_overlays() (View method)

U

UI (class in chimera.core.ui.gui)
unalias() (in module chimera.core.commands.cli)
unbind_texture() (Texture method)
uncolordef() (in module chimera.core.commands.color)
undisplay() (in module chimera.core.commands.display)
unescape() (in module chimera.core.commands.cli)
unescape_with_index_map() (in module chimera.core.commands.cli)
uninstall_tool() (Toolshed method)
unique_chain_ids (Residues attribute)
unique_id() (Session method)
unique_ids (Residues attribute)
unique_obj() (Session method)
unique_residues (Atoms attribute)
unique_structures (Atoms attribute)
(Residues attribute)
unique_vertex_map() (in module chimera.core.surface._surface)
unribbon() (in module chimera.core.commands.ribbon)
update() (ConfigFile method)
update_state() (Tasks method)
url (Annotation attribute)
usage() (in module chimera.core.commands.cli)
use_lighting (Drawing attribute)
USERNAME

V

Value (class in chimera.core.configfile)
vector_rotation() (in module chimera.core.geometry.place)
vector_sum() (in module chimera.core.geometry.vector)
VERSION (in module chimera.core.serialize)
vertex_areas() (in module chimera.core.surface._surface)
vertex_colors (Drawing attribute)
vertex_to_atom_map() (MolecularSurface method)
vertices (Drawing attribute)
View (class in chimera.core.graphics.view)
view() (in module chimera.core.commands.view)
(StereoCameraMode method)
view_all() (Camera method)
(View method)
view_direction() (Camera method)
view_width() (Camera method)
visible (Atom attribute)
(Bond attribute)
visibles (Atoms attribute)
(Bonds attribute)
Volume (class in chimera.core.map.volume)
volume() (in module chimera.core.map.volumecommand)
vop_add() (in module chimera.core.map.filter.vopcommand)
vop_bin() (in module chimera.core.map.filter.vopcommand)
vop_boxes() (in module chimera.core.map.filter.vopcommand)
vop_cover() (in module chimera.core.map.filter.vopcommand)
vop_falloff() (in module chimera.core.map.filter.vopcommand)
vop_flatten() (in module chimera.core.map.filter.vopcommand)
vop_flip() (in module chimera.core.map.filter.vopcommand)
vop_fourier() (in module chimera.core.map.filter.vopcommand)
vop_gaussian() (in module chimera.core.map.filter.vopcommand)
vop_laplacian() (in module chimera.core.map.filter.vopcommand)
vop_local_correlation() (in module chimera.core.map.filter.vopcommand)
vop_maximum() (in module chimera.core.map.filter.vopcommand)
vop_median() (in module chimera.core.map.filter.vopcommand)
vop_morph() (in module chimera.core.map.filter.vopcommand)
vop_multiply() (in module chimera.core.map.filter.vopcommand)
vop_octant() (in module chimera.core.map.filter.vopcommand)
vop_octant_complement() (in module chimera.core.map.filter.vopcommand)
vop_permute_axes() (in module chimera.core.map.filter.vopcommand)
vop_resample() (in module chimera.core.map.filter.vopcommand)
vop_ridges() (in module chimera.core.map.filter.vopcommand)
vop_scale() (in module chimera.core.map.filter.vopcommand)
vop_subtract() (in module chimera.core.map.filter.vopcommand)
vop_threshold() (in module chimera.core.map.filter.vopcommand)
vop_tile() (in module chimera.core.map.filter.vopcommand)
vop_unbend() (in module chimera.core.map.filter.vopcommand)
vop_unroll() (in module chimera.core.map.filter.vopcommand)
vop_zone() (in module chimera.core.map.filter.vopcommand)
vseries_align() (in module chimera.core.map.series.vseries_command)
vseries_measure() (in module chimera.core.map.series.vseries_command)
vseries_play() (in module chimera.core.map.series.vseries_command)
vseries_save() (in module chimera.core.map.series.vseries_command)
vseries_slider() (in module chimera.core.map.series.vseries_command)
vseries_stop() (in module chimera.core.map.series.vseries_command)

W

wait() (in module chimera.core.commands.wait)
warning() (Logger method)
was_deleted (Drawing attribute)
webapp_server (module)
writable() (SaveFile method)
write() (SaveFile method)
writelines() (SaveFile method)

X

xyz_to_ijk() (Grid_Data method)

Z

z_axis() (Place method)
zero_translation() (Place method)