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.

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.

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)¶: Initialize self. See help(type(self)) for accurate signature.

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

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

addRule()¶

append()¶: appends another ‘this’ object

applyScheme()¶

clearRules()¶

deleteFile()¶

disown()¶: releases ownership of the pointer

getDescription()¶

getFileName()¶

getLongName()¶

getOriginalName()¶

getRules()¶

getShortName()¶

next()¶: returns the next ‘this’ object

own()¶: returns/sets ownership of the pointer

readRulesFromFile()¶

setDescription()¶

setFileName()¶

setLongName()¶

setOriginalName()¶

setRules()¶

setShortName()¶

this¶

thisown¶

writeFile()¶

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')¶

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

__init__(min_value=0, max_value=100)¶

Parameters:	min_value (int) – The value corresponding to red. max_value (int) – The value corresponding to purple.

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

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