schrodinger.structutils.color module

An interface to the Maestro color palette and color schemes.

Color schemes are read from maestro-v<version>/data/res/scheme.res.

Copyright Schrodinger, LLC. All rights reserved.

schrodinger.structutils.color.get_rgb_from_color_index(index)

A convenience function for getting the rgb value for a color index.

Parameters

index – an integer specifying the color index

Return r,g,b

a tuple of 3 integer values for the red, green, blue values. Range from 0 to 255.

schrodinger.structutils.color.rgb_to_hex(rgb)
Parameters

rgb (Tuple(int, int, int)) – 0-255 based RGB tuple

Returns

Hex value for color

Return type

str

class schrodinger.structutils.color.Color(color)

Bases: object

Represent a color as either an integer (colormap index), string (color name or hex “RRGGBB” value), or an RGB value (tuple/list of 3 ints, values 0-255).

Provides the following properties and methods:
  • Color.index = int(Color) - mmcolor index of the closest color

  • Color.name = str(Color) - mmcolor name of the closest color

  • Color.rgb - (tuple of 0-255 ints)

  • equal = (col1 == col2)

When object is initialized from the RGB value, the Color.index and Color.name attributes are set to the closest color in the mmcolor palette.

__init__(color)
property rgb_float

Returns a tuple of (R, G, B) for this color, each ranging from 0.0 to 1.0.

property hex_string

Returns the color as string of hex RGB values (RRGGBB). For example, pure red will be returned as “FF0000”.

class schrodinger.structutils.color.ColorScheme(name='element', color_asl_list=[])

Bases: colorscheme.MM_CScheme

Define a Maestro color scheme.

This class provides the following functionality:

colorscheme.apply(st, [atoms])
for color, asl in colorscheme:
    <do>
__init__(name='element', color_asl_list=[])

Create ColorScheme object

Parameters
  • name (str) – Name of ColorScheme

  • color_asl_list (asl patterns) – List of asl patterns in ColorScheme

add(color_str, asl, rule_description='')

Add another set of rules to this color scheme.

Parameters
  • color – color string

  • asl – what to apply the color to

__len__()

Return the number of rules in the scheme

copy()

Return a copy of this scheme.

apply(st, atoms=None)

Applies the scheme to the specified Structure <st>.

Parameters

atoms – Optionally specify which atoms to apply the scheme to in format. Can be a list atom atom indices, or a Bitset instance.

writeSchemeFile(filename)

Write the scheme to the specified .sch file.

Parameters

filename (str) – filelocation to save scheme file to

acquire()

acquires ownership of the pointer

addDefaultColorRule(self, long_name)
addRule(self, rule)
append()

appends another ‘this’ object

applyScheme(self, ct, bs) MMcolor_status
clearRules(self)
copySchemeColors(self, src_scheme, default_color)
deleteDefaultColorRule(self)
deleteFile(self)
disown()

releases ownership of the pointer

getColorSchemesDirPath(self) boost::filesystem::path
getDescription(self) std::string
getFileName(self) std::string
getLongName(self) std::string
getOriginalName(self) std::string
getRules(self) MMcscheme_rule_list
getShortName(self) std::string
next()

returns the next ‘this’ object

own()

returns/sets ownership of the pointer

readRulesFromFile(self, file_name, read_description, is_sub_cscheme=False, is_absolute_file=False) MMcolor_status
setDescription(self, description)
setFileName(self, file_name)
setLongName(self, long_name)
setOriginalName(self, original_name)
setRules(self, rules)
setShortName(self, short_name)
this
thisown
writeFile(self)
class schrodinger.structutils.color.ColorRamp(colors=('white', 'blue'), values=(0, 100))

Bases: object

An object for calculating colors on a customizable color ramp.

Coloring atoms according to a calculated property that ranges from 0 to 10:

color_ramp = ColorRamp(colors=("white", "blue"), values=(0,10))
for atom in st.atom:
    property = calc_property(atom)
    r, g, b  = color_ramp.getRGB(property)
    atom.setColorRGB(r, g, b)

Coloring atoms according to a calculated property that ranges from -10 to 10 using blues for negative values and reds for positive values:

color_ramp = ColorRamp(colors=("blue", "white", "red"),
                       values=(-10, 0, 10))
for atom in st.atom:
    property = calc_property(atom)
    color = color_ramp.getRGB(property)
    atom.setColorRGB(*color)
__init__(colors=('white', 'blue'), values=(0, 100))

Initialize a ColorRamp object where the specified values correspond to the given colors

Parameters
  • colors (list or tuple) – The list of colors. Any color description that is recognized by Color may be used (a color name or colormap index).

  • values (list or tuple) – The list of numerical values. This list must be the same length as colors, all values must be unique, and the list must be sorted in either ascending or descending order.

getRGB(value)

Determine the color that corresponds to the specified value

Parameters

value (int or float) – The value to calculate the color for

Returns

The color corresponding to the specified value, where the color is a represented by a list of (red, green, blue) integers in the 0-255 range.

Return type

list

class schrodinger.structutils.color.RainbowColorRamp(min_value=0, max_value=100)

Bases: schrodinger.structutils.color.ColorRamp

COLORS = ('red1', 'user10', 'user12', 'user14', 'user15', 'user16', 'user17', 'user18', 'user19', 'user20', 'user21', 'green', 'user53', 'user54', 'user55', 'user56', 'user57', 'user58', 'user59', 'user60', 'user26', 'user28', 'user30', 'user32', 'user61', 'user62', 'purple')
__init__(min_value=0, max_value=100)
Parameters
  • min_value (int) – The value corresponding to red.

  • max_value (int) – The value corresponding to purple.

getRGB(value)

Determine the color that corresponds to the specified value

Parameters

value (int or float) – The value to calculate the color for

Returns

The color corresponding to the specified value, where the color is a represented by a list of (red, green, blue) integers in the 0-255 range.

Return type

list

schrodinger.structutils.color.available_color_schemes()

Return a list of available color schemes (list of names). Raises RuntimeError if Maestro installation is not available. Raises IOError if scheme.res file could not be found

schrodinger.structutils.color.get_color_scheme(name)

Return a ColorScheme object for scheme <name>. Raises ValueError if such scheme does not exist. Raises RuntimeError if Maestro installation is not available. Raises IOError if scheme.res file could not be found

schrodinger.structutils.color.apply_color_scheme(st, scheme, atom_list=None)

Applies the scheme to the specified Structure <st>. Optionally a list of atom indecies may be specified.

scheme

One of the names returned by available_color_schemes() or a ColorScheme object returned by get_color_scheme().

atom_list

A list of atom indices to apply color scheme to (default all atoms).

Raises ValueError if such scheme does not exist. Raises RuntimeError if Maestro installation is not available. Raises IOError if scheme.res file could not be found