RecentColorSubMenu
A submenu that shows the most recently chosen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

RecentCarbonColorSubMenu
A submenu that shows the most recently chosen carbon colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

RecentHydrogenColorSubMenu
A submenu that shows the most recently chosen hydrogen colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

RecentObjectColorSubMenu
A submenu that shows the most recently chosen object colors - these color choices are updated each time the menu shows to reflect the most recently chosen colors at the top.

ColorByElementSubMenu
The Color by Element submenu

ColorChainSubMenu
The ColorChainSubMenu menu

ColorSpectrumSubMenu
The ColorSpectrumSubMenu menu

CustomRecentColor

ColorBySubstructure

ColorSubstructureSubMenu
The ColorSubstructureSubMenu menu

AutoCycleColor

AutoCycleCarbonColor

AutoColorObjects

AutoColorCarbons

AutoColorSubMenu
The Color menu

ColorMenu
The Color menu

ToggleState
A MAction that toggles the enabled/disabled state of an object

ToggleVisibleObjectsState
A MAction that toggles the enabled/disabled state of Visible objects

DeleteAll

Reinitialize

Quit

Select

Disable

CreateEntry

GeneralContextSubMenu
The submenu that contains all the main actions used for most context menus

SubstructureContextSubMenu
The GeneralContextSubMenu for a right-click that is on an atom

ObjectFreeContextSubMenu
The GeneralContextSubMenu for a right-click that is not on an object

ToggleStateSubMenu
The submenu that allows the user to enable/disable individual objects

SelectedAtomContextActionSubMenu
The submenu that allows the user to enable/disable individual objects

SelectedAtomContextMenu
The context menu for right-clicks on selected atoms

AtomContextMenu
The context menu for right-clicks on non-selected atoms

SpaceContextMenu
The context menu for right-clicks in space

Functions

[hide private]

set_wait_cursor()
Set the cursor to a wait cursor if the toggle_table widget is defined

restore_cursor()
Restore the cursor to its nomral state if the toggle_table widget is defined

start_progress(maximum)
Show and restart the progress bar on the Toggle Table if the TT is defined

update_progress(inc=1, total=None)
Show the current progress on the progress bar on the Toggle Table if the TT is defined

end_progress()
Finish the progress bar and hide it

show_result(msg)

maestro_command(command)
A wrapper that handles exceptions from Maestro commands

tuple

get_matching_ws_atoms(asl, extract=False)
Get the atoms in the workspace structure that match the given asl

list or None

get_matching_ws_entries(owner, asl)
Get the entries in the workspace structure are affected by the given asl

list

get_visible_ws_atoms()
Return list of the the Visible workspace atoms

str

get_visible_ws_asl()
Return an ASL that represents the Visible workspace atoms

str

join_asls(asl1, asl2, joiner='AND')
Joins 2 asls with the given joiner (default is AND)

str

mod_asl(modifier, asl)
Puts a modifier in front of asl - which it protects in ()'s to make sure the modifier applies to the whole asl

iterable

get_surfaces(entry)
Get the surfaces associated with entry_id entry

display_atoms_as(asl, atoms, bonds=None, owner=None)
Display atoms and bonds with the given style, and turn off ribbons and surfaces

display_atoms(asl, atoms, bonds=None, owner=None)
Display atoms and bonds with the given style, leaving ribbons as is

display_ribbons(asl, style, hideatoms=False, scheme='calphaatom')
Show ribbons

rock_workspace(interval=1, amount=1, span=25)
Rotate the workspace back and forth smoothly by small degree increments over a span of degrees range.

stop_rocking()
Stop any rocking currently happening

_do_rocking()
Callback used to rock the workspace

_rocker_recall()
Removes the Maestro rocker callback

display_image(image_file)
Tries to display the image file in the default image viewer

str or None

ensure_proper_extension(filename, extensions)
Ensure that filename ends with the proper extension

create_surface(entry, asl, name, transparency=0, quality=0, style='solid', viewasl=None, viewdistance='3', scheme='"Atom Color"')
Create a surface

create_show_menu(menu, owner)

create_show_substructure_menu(menu, owner)

create_show_organic_menu(menu, owner)

list

find_all_entries(owner=None, asl=None)
Find all the entries specified by the given owner or asl

list

find_center_of_atoms(struct)
Finds the x,y,z coordinates of the center of the atoms

create_modify_menu(menu)
Creates a Modify menu for selections

find_polar_contacts(asl1, asl2=None)
Finds all polar contacts (hydrogen bonds) between asl1 and asl2.

create_action_menu(menu, owner)

hide_atoms(asl)
Hide the atoms given by asl

hide_ribbons(asl)
Hide ribbons

hide_surface(entry_id)
Hide a surface

hide_labels(asl)
Hide the labels

hide_everything(asl, entry_id=None)
Hide atoms, ribbons and surfaces

create_hide_menu(menu, owner)
Create the Hide menu

clear_labels(asl)
Maestro doesn't seem to clear labels correctly, so we have to turn them off manually.

create_label_menu(menu, owner)
Put all the menu items in the Label menu

tuple

get_color()
Get a user-specified color from the list of known Maestro colors

color_atoms(color_name, asl)
Colors the specified atoms with the given color

color_atoms_rgb(red, green, blue, asl)
Colors the specified atoms with the given RGB colors

str

make_color_asl_for_element(asl, element)
Form an ASL that restricts the given ASL to those atoms of a specific element

color_by_element(base_asl, hydrogen='white', carbon='green', nitrogen='user27', oxygen='red', sulfur='orange')
Color H, C, N, O and S by colors

save_new_color(color_name, rgba, mytype)
The user has selected a new (or re-selected an existing custom set) - add it to the list of custom sets (or move it to the end) so it ends up at the top of the menu

str

get_asl_chain_name(cname)
Maestro doesn't like blank chain names in ASL without quotes so add the quotes if necessary

float or None

atom_b_factor(atom, zeros=True)
Returns the atom B-factor

list

bin_b_factors(struct, atoms, groups)
Divide atoms up into bins based on their B-factor (temperature factor).

color_chainbow_groups(asl, ribbons=None)
Color all the atoms (and sometimes the ribbons) as chainbows

create_colorbyele_menu(menu, owner, c_menu, h_menu)

add_common_context_items(menu, select=True)
Adds items common to many context menus

_color_key(item)
Sort colors in the order of magenta, blue, cyan, green, yellow, red, monochrome green, yellow, red, magenta, blue, cyan, monochrome

Variables

[hide private]

maestro = FakeMaestro()

TRIGGERED = '2triggered()'

DISULFIDE = '(fillres /S0-S0/) AND atom.ptype CA,CB,SG'

BACKBONE = 'backbone'

SIDECHAIN = 'sidechain'

POLYMER = '(backbone) or (sidechain)'

SOLVENT = 'water'

INORGANIC = 'not atom.ele H,C,N,O,F,P,S,Cl,Br,I'

PROT_AND_DNA_SELE = '(res. ALA,CYS,CYX,ASP,GLU,PHE,GLY,HIS,HID...

PYMOL_IONS = 'atom.ele Ca, Hg, K, Na, Zn, Mg, Cl'

SOLVENT_AND_IONS = '(water) OR atom.ele Ca, Hg, K, Na, Zn, Mg,...

WATER = 'water'

RIBBON_STYLE = 'calphatube'

THIN_TRACE = 'calphaline'

CALPHA_SCHEME = 'calphaatom'

CHAIN_SCHEME = 'chain'

POSITION_SCHEME = 'residueposition'

NONE = 'none'

TUBE = 'tube'

CARTOON = 'cartoon'

ATOM_NONE = 'none'

BOND_NONE = 'none'

CPK = 'cpk'

ATOM_WIRE = 'none'

BOND_WIRE = 'wire'

ATOM_BALLNSTICK = 'ballnstick'

BOND_BALLNSTICK = 'ballnstick'

MAESTRO_TO_STRUCT_STYLE = {None: 0, 'ballnstick': 3, 'cpk': 2,...

MMCT_TO_MAESTRO_RIBBON_STYLE = {0: 'none', 1: 'cartoon', 2: 'r...

DARK_BLUE = 'user2'

BLUE = 'user27'

CYAN = 'user4'

SEAFOAM = 'userM'

DARK_GREEN = 'user3'

LIME = 'user19'

DEEPTEAL = 'user59'

HOTPINK = 'userN'

YELLOWORANGE = 'userT'

SLATE = 'blue14'

YELLOW = 'user16'

LIGHTBLUE = 'blue9'

GREEN = 'green'

RED = 'red'

WHITE = 'white'

ORANGE = 'orange'

PINK = 'pink'

MAGENTA = 'purple'

DEEPRED = 'brown'

OLIVE = 'olive'

GREY = 'gray'

ATOM_RAINBOW_COLORS = ['user27', 'blue9', 'userM', 'user19', '...

RIBBON_RAINBOW_COLORS = ['blue', 'lightblue', 'turquoise', 'sp...

PYMOL_COLOR_CYCLE = ['green', 'user4', 'purple', 'user16', 'pi...

object_color_cycles = {}

RT_COLOR_LABEL_START = '<span style="background-color:black;fo...

RT_COLOR_LABEL_END = '</span>'

RT_TO_MAESTRO_COLORS = {'cyan': 'user4', 'lime': 'green', 'mag...

PARTIAL_CHARGE_4D = '1charge - b'

SURFACE_AREA_CUTOFF = 10.0

PML_SURFACE = 'BL_Surface'

PML_PRESET_SURFACE = 'BL_Preset_Surface'

DAVE_DEBUG = False

results_window = None
hash(x)

toggle_table = None
The parent Toggle Table widget

rock_data = RockData(interval= 1, amount= 1, span= 25)

mmshare_data = '/nfs/builds/objects/OB/alpaca/Linux-x86_64/bui...

colorpath = '/nfs/builds/objects/OB/alpaca/Linux-x86_64/build2...

colorfile = open(colorpath, 'r')

color_dict = OrderedDict([((191, 0, 191), 'userQ'), ((225, 30,...

HYDROGEN_COLOR = 'hydrogen'

CARBON_COLOR = 'carbon'

OBJECT_COLOR = 'object'

MAX_RECENT_COLORS = 12

pref_dir = None
hash(x)

color_path = None
hash(x)

custom_color_dicts = {'carbon': OrderedDict(), 'hydrogen': Ord...

color_file = open(color_path, 'r')

__package__ = 'schrodinger.application.bioluminate'

line = ''

rgb = (0, 0, 0)

tokens = ['256', '0', '0', '0', 'user160']

Function Details

[hide private]

start_progress(maximum)

Show and restart the progress bar on the Toggle Table if the TT is defined

Parameters:

maximum (int) - The maximum value of the progress bar

update_progress(inc=1, total=None)

Show the current progress on the progress bar on the Toggle Table if the TT is defined

Parameters:

inc (int) - The amount to increment the progress bar value
total (int) - The absolute value to set the progress bar to

get_matching_ws_atoms(asl, extract=False)

Get the atoms in the workspace structure that match the given asl

Parameters:

asl (str) - the asl this action will apply to
extract (bool) - True if a structure containing the matching atoms should be extracted and returned, False if not

Returns: tuple

workspace structure (schrodinger.Structure), list of matching atom indicies, matching structure (or None)

get_matching_ws_entries(owner, asl)

Get the entries in the workspace structure are affected by the given asl

Parameters:

owner (ToggleTableObject) - the object this command will operate on
asl (str) - the asl this action will apply to

Returns: list or None

Each item of the list is a workspace entry (Structure) that is affected by asl. In case of error - normally caused by multiple Scratch entries - None is returned. An empty list is returned if ASL does not affect any workspace entries.

get_visible_ws_atoms()

Return list of the the Visible workspace atoms

Returns: list: list of atom indexes of visible workspace atoms

get_visible_ws_asl()

Return an ASL that represents the Visible workspace atoms

Returns: str: an ASL expression that represents the Visible workspace objects, or None if no atoms are visible

join_asls(asl1, asl2, joiner=`'AND'`)

Joins 2 asls with the given joiner (default is AND)

Parameters:

asl1 (str) - the first asl
asl2 (str) - the second asl
joiner (str) - the linking logic (AND, AND NOT, OR...)

Returns: str

the two asls joined by the joiner

mod_asl(modifier, asl)

Puts a modifier in front of asl - which it protects in ()'s to make sure the modifier applies to the whole asl

Parameters:

modifier (str) - the modifier to prepend to the asl (NOT, FILLRES, FILLMOL)
asl (str) - the asl

Returns: str

the modified asl with the modifier prepended to it

get_surfaces(entry)

Get the surfaces associated with entry_id entry

Parameters:

entry (str) - The entry_id of the entry of interest

Returns: iterable

iterable object containing surfaces associated with this entry

display_atoms_as(asl, atoms, bonds=None, owner=None)

Display atoms and bonds with the given style, and turn off ribbons and surfaces

Parameters:

asl (str) - the asl this action will apply to
atoms (str) - atom display style
bonds (str) - bond display style
owner (ToggleTableObject) - the object this command will operate on - used to see if the atoms should be made visible or not

display_atoms(asl, atoms, bonds=None, owner=None)

Display atoms and bonds with the given style, leaving ribbons as is

Parameters:

asl (str) - the asl this action will apply to
atoms (str) - atom display style
bonds (str) - bond display style
owner (ToggleTableObject) - the object this command will operate on - used to see if the atoms should be made visible or not

display_ribbons(asl, style, hideatoms=False, scheme=`'calphaatom'`)

Show ribbons

Parameters:

asl (str) - the asl this action will apply to
style (str) - the ribbon style
hideatoms (bool) - True if atoms should be hidden, False if not

rock_workspace(interval=1, amount=1, span=25)

Rotate the workspace back and forth smoothly by small degree increments over a span of degrees range. If called when rocking is currently occuring, will stop the rocking.

Parameters:

interval (int) - in units of ~1/20 second, the frequency at which the rocking movement should be made
amount (int) - The number of degrees the workspace should be rotated each rocking movement
span (int) - The amount to rotate in one direction (past 0) before reversing

display_image(image_file)

Tries to display the image file in the default image viewer

Parameters:

image_file (str) - The path to the image to be displayed

ensure_proper_extension(filename, extensions)

Ensure that filename ends with the proper extension

Parameters:

filename (str) - the filename to check
extensions (str or list) - a list of valid extensions or a single extension. Extensions should include the '.'

Returns: str or None

either

filename if filename has a valid extension
filename + ext if filename has no extension, ext is the value of, or the first item in extensions,
None if filename has an extension not given by extensions

create_surface(entry, asl, name, transparency=0, quality=0, style=`'solid'`, viewasl=None, viewdistance=`'3'`, scheme=`'"Atom Color"'`)

Create a surface

Parameters:

entry (str) - The entry id to create the surface for
asl (str) - The ASL defining the atoms to create the surface for
name (str) - The name given to the created surface
style (str or None) - One of the following values
- 'solid' (default)
- 'mesh'
- 'dots'
quality (int) - The quality of the displayed surface.
- 1 is medium quality (default)
- 2 is high quality
transparancy (int) - transparancy % of the surface. Default is 0 (solid), max is 100.
viewasl (str) - The ASL that defines the portion of the surface to view - default is to view the entire surface
viewdistance (str) - A string representation of a number that defines how close the suface needs to be to the set of viewasl atoms to be shown. Default is 3 Angstroms.
scheme (str) - The coloring scheme for the surface (default is Atom Color)

create_show_menu(menu, owner)

Parameters:

menu (QMenu) - the QMenu that owns this action
owner (ToggleTableObject) - the object this Menu will operate on

create_show_substructure_menu(menu, owner)

Parameters:

menu (QMenu) - the QMenu that owns this action
owner (ToggleTableObject) - the object this Menu will operate on

create_show_organic_menu(menu, owner)

Parameters:

menu (QMenu) - the QMenu that owns this action
owner (ToggleTableObject) - the object this Menu will operate on

find_all_entries(owner=None, asl=None)

Find all the entries specified by the given owner or asl

Parameters:

owner (ToggleTableObject) - The ToggleTableObject this function applies to, if None and asl is None,(the default), then all included entry id's are returned
asl (str) - The asl to find entries for

Returns: list

list of entry ID's the asl spans

find_center_of_atoms(struct)

Finds the x,y,z coordinates of the center of the atoms

Parameters:

struct (schrodinger.Structure object) - structure containing the atoms

Returns: list

[x, y, z] specifying the center of the atoms

find_polar_contacts(asl1, asl2=None)

Finds all polar contacts (hydrogen bonds) between asl1 and asl2.

Parameters:

asl1 (str) - ASL defining one set of atoms to find H-bonds between. If asl2 is defined, then H-bonds are found between the two sets, but not within. If asl2 is not defined, then H-bonds are found within asl1.
asl2 (str) - ASL defining one set of atoms to find H-bonds between. If asl2 is defined, then H-bonds are found between asl1 and asl2, but not within. If asl2 is not defined, then H-bonds are found within asl1.

create_action_menu(menu, owner)

Parameters:

menu (QMenu) - the QMenu that owns this action
owner (ToggleTableObject) - the object this Menu will operate on

hide_atoms(asl)

Hide the atoms given by asl

Parameters:

asl (str) - the asl this action will apply to

hide_ribbons(asl)

Hide ribbons

Parameters:

asl (str) - the asl this action will apply to

hide_surface(entry_id)

Hide a surface

Parameters:

entry_id (str) - the entry_id this action will apply to

hide_labels(asl)

Hide the labels

Parameters:

asl (str) - The ASL defining the atoms whose labels will be hidden

hide_everything(asl, entry_id=None)

Hide atoms, ribbons and surfaces

Parameters:

asl (str) - the asl this action will apply to
entry_id (str) - the entry_id this action will apply to

create_hide_menu(menu, owner)

Create the Hide menu

Parameters:

menu (QMenu) - the QMenu that owns this action
owner (ToggleTableObject) - the object this Menu will operate on

clear_labels(asl)

Maestro doesn't seem to clear labels correctly, so we have to turn them off manually. They disappear from the screen, but will show up the next time labels are added. So you end up with a long string of labels.

Parameters:

asl (str) - the asl this action will apply to

get_color()

Get a user-specified color from the list of known Maestro colors

Returns: tuple: (Maestro color name, (R, G, B, Alpha)) or (None, None) if the user cancels the window.

color_atoms(color_name, asl)

Colors the specified atoms with the given color

Parameters:

color_name (str) - a Maestro-recognized color name, found in mmshare/data/colors.res
asl (str) - The ASL specifying the atoms to color

color_atoms_rgb(red, green, blue, asl)

Colors the specified atoms with the given RGB colors

Parameters:

red (int) - integer between 0 and 255
green (int) - integer between 0 and 255
blue (int) - integer between 0 and 255
asl (str) - The ASL specifying the atoms to color

make_color_asl_for_element(asl, element)

Form an ASL that restricts the given ASL to those atoms of a specific element

Parameters:

asl (str) - The general asl to make element specific
element (str) - an atomic symbol to restrict the ASL to

Returns: str

color_by_element(base_asl, hydrogen=`'white'`, carbon=`'green'`, nitrogen=`'user27'`, oxygen=`'red'`, sulfur=`'orange'`)

Color H, C, N, O and S by colors

Parameters:

base_asl (str) - asl defining the group of atoms to color
hydrogen (str) - the Maestro color string defining the color for H atoms
carbon (str) - the Maestro color string defining the color for C atoms
nitrogen (str) - the Maestro color string defining the color for N atoms
oxygen (str) - the Maestro color string defining the color for O atoms
sulfur (str) - the Maestro color string defining the color for S atoms

save_new_color(color_name, rgba, mytype)

The user has selected a new (or re-selected an existing custom set) - add it to the list of custom sets (or move it to the end) so it ends up at the top of the menu

Parameters:

color_name (str) - the Maestro color name of the color to save
rgba (4-tuple or None) - tuple of (red, blue, green, alpha) if this is a new color, or None if this is already an existing color
mytype (str) - the type of color this is (HYDROGEN_COLOR, CARBON_COLOR, OBJECT_COLOR)

get_asl_chain_name(cname)

Maestro doesn't like blank chain names in ASL without quotes so add the quotes if necessary

Parameters:

cname (str) - the chain name

Returns: str

cname if cname is not blank, otherwise a double-quoted space

atom_b_factor(atom, zeros=True)

Returns the atom B-factor

Parameters:

atom (schrodinger._Atom) - atom object to return the B-factor for
zeros (bool) - True if atoms with No B-factor should return 0.0, False if it should return None

Returns: float or None

the B-factor of the given atom

bin_b_factors(struct, atoms, groups)

Divide atoms up into bins based on their B-factor (temperature factor). The groups are determined to span equal ranges of b-factor (some groups may therefore contain no atoms).

Parameters:

atoms (list) - list of atom indexes to bin
groups (int) - The number of bins to create
struct (schrodinger.structure.Structure)

Returns: list

List of binned atom indexes - each item of the list is a list containing the atom indexes for that bin. Item 0 are the lowest B-Factors.

color_chainbow_groups(asl, ribbons=None)

Color all the atoms (and sometimes the ribbons) as chainbows

Parameters:

asl (str) - the asl this action will apply to
ribbons (str) - The type of ribbons to create with these colorings. The default is not to create ribbons.
Color each chain like a rainbow! Each group of atoms within a chain gets different colors. Groups are created to (roughly) equal number of atoms in each group, and all the atoms in a residue are given the same color (if the residue != UNK).

create_colorbyele_menu(menu, owner, c_menu, h_menu)

Parameters:

menu (QMenu) - the QMenu that owns this action
owner (ToggleTableObject) - the object this Menu will operate on
c_menu (QMenu) - Submenu for recent custom carbon colors
h_menu (QMenu) - Submenu for recent custom hydrogen colors

add_common_context_items(menu, select=True)

Adds items common to many context menus

Parameters:

menu (PMLMenu) - the menu to add items to
select (bool) - True if Select is on the menu, False if not

Variables Details

[hide private]

PROT_AND_DNA_SELE

Value:

'(res. ALA,CYS,CYX,ASP,GLU,PHE,GLY,HIS,HID,HIE,HIP,HISE,HISD,HISP,ILE,
LYS,LEU,MET,MSE,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR,A,C,T,G,U)'

SOLVENT_AND_IONS

Value:

'(water) OR atom.ele Ca, Hg, K, Na, Zn, Mg, Cl'

MAESTRO_TO_STRUCT_STYLE

Value:

{None: 0, 'ballnstick': 3, 'cpk': 2, 'none': 0, 'tube': 2, 'wire': 1}

MMCT_TO_MAESTRO_RIBBON_STYLE

Value:

{0: 'none',
 1: 'cartoon',
 2: 'ribbon',
 3: 'tube',
 4: 'thintube',
 5: 'curvedline',
 6: 'calphaline',
 7: 'calphatube'}

ATOM_RAINBOW_COLORS

Value:

['user27',
 'blue9',
 'userM',
 'user19',
 'user3',
 'green',
 'olive',
 'user16',
...

RIBBON_RAINBOW_COLORS

Value:

['blue',
 'lightblue',
 'turquoise',
 'springgreen',
 'darkgreen',
 'green',
 'yellowgreen',
 'yellow',
...

PYMOL_COLOR_CYCLE

Value:

['green',
 'user4',
 'purple',
 'user16',
 'pink',
 'white',
 'blue14',
 'orange',
...

RT_COLOR_LABEL_START

Value:

'<span style="background-color:black;font-size:16px">'

RT_TO_MAESTRO_COLORS

Value:

{'cyan': 'user4',
 'lime': 'green',
 'magenta': 'purple',
 'pink': 'pink',
 'red': 'red',
 'yellow': 'user16'}

mmshare_data

Value:

'/nfs/builds/objects/OB/alpaca/Linux-x86_64/build23/mmshare-v2.1/data'

colorpath

Value:

'/nfs/builds/objects/OB/alpaca/Linux-x86_64/build23/mmshare-v2.1/data/
colors.res'

color_dict

Value:

OrderedDict([((191, 0, 191), 'userQ'), ((225, 30, 225), 'purple'), ((2
34, 173, 234), 'plum'), ((216, 191, 216), 'thistle'), ((191, 159, 255)
, 'userH'), ((180, 0, 255), 'user62'), ((95, 63, 255), 'userR'), ((120
, 0, 255), 'user61'), ((90, 0, 255), 'user32'), ((75, 0, 255), 'user31
'), ((60, 0, 255), 'user30'), ((45, 0, 255), 'user29'), ((30, 0, 255),
 'user28'), ((15, 0, 255), 'user27'), ((0, 0, 38), 'user63'), ((0, 0, 
128), 'user2'), ((30, 30, 225), 'blue'), ((247, 247, 255), 'blue31'), 
((239, 239, 255), 'blue30'), ((231, 231, 255), 'blue29'), ((223, 223, 
...

custom_color_dicts

Value:

{'carbon': OrderedDict(),
 'hydrogen': OrderedDict(),
 'object': OrderedDict()}

Module pml_menus

start_progress(maximum)

update_progress(inc=1, total=None)

get_matching_ws_atoms(asl, extract=False)

get_matching_ws_entries(owner, asl)

get_visible_ws_atoms()

get_visible_ws_asl()

join_asls(asl1, asl2, joiner='AND')

mod_asl(modifier, asl)

get_surfaces(entry)

display_atoms_as(asl, atoms, bonds=None, owner=None)

display_atoms(asl, atoms, bonds=None, owner=None)

display_ribbons(asl, style, hideatoms=False, scheme='calphaatom')

rock_workspace(interval=1, amount=1, span=25)

display_image(image_file)

ensure_proper_extension(filename, extensions)

create_surface(entry, asl, name, transparency=0, quality=0, style='solid', viewasl=None, viewdistance='3', scheme='"Atom Color"')

create_show_menu(menu, owner)

create_show_substructure_menu(menu, owner)

create_show_organic_menu(menu, owner)

find_all_entries(owner=None, asl=None)

find_center_of_atoms(struct)

find_polar_contacts(asl1, asl2=None)

create_action_menu(menu, owner)

hide_atoms(asl)

hide_ribbons(asl)

hide_surface(entry_id)

hide_labels(asl)

hide_everything(asl, entry_id=None)

create_hide_menu(menu, owner)

clear_labels(asl)

get_color()

color_atoms(color_name, asl)

color_atoms_rgb(red, green, blue, asl)

make_color_asl_for_element(asl, element)

color_by_element(base_asl, hydrogen='white', carbon='green', nitrogen='user27', oxygen='red', sulfur='orange')

save_new_color(color_name, rgba, mytype)

get_asl_chain_name(cname)

atom_b_factor(atom, zeros=True)

bin_b_factors(struct, atoms, groups)

color_chainbow_groups(asl, ribbons=None)

create_colorbyele_menu(menu, owner, c_menu, h_menu)

add_common_context_items(menu, select=True)

PROT_AND_DNA_SELE

SOLVENT_AND_IONS

MAESTRO_TO_STRUCT_STYLE

MMCT_TO_MAESTRO_RIBBON_STYLE

ATOM_RAINBOW_COLORS

RIBBON_RAINBOW_COLORS

PYMOL_COLOR_CYCLE

RT_COLOR_LABEL_START

RT_TO_MAESTRO_COLORS

mmshare_data

colorpath

color_dict

custom_color_dicts

join_asls(asl1, asl2, joiner=`'AND'`)

display_ribbons(asl, style, hideatoms=False, scheme=`'calphaatom'`)

create_surface(entry, asl, name, transparency=0, quality=0, style=`'solid'`, viewasl=None, viewdistance=`'3'`, scheme=`'"Atom Color"'`)

color_by_element(base_asl, hydrogen=`'white'`, carbon=`'green'`, nitrogen=`'user27'`, oxygen=`'red'`, sulfur=`'orange'`)