Package schrodinger :: Package application :: Package matsci :: Module amorphous

Module amorphous

Classes

Box
Class that defines the region a new structure may be placed in

Scaffold
A Scaffold is a structure that occupies space in a cluster of molecules but is not considered part of the system itself.

BuilderWithClashDetection
The base class for the amorphous builder classes

AmorphousCellBuilder
Builder for an amorphous cell

Functions

[hide private]

tuple

get_color(index)
Get the next color in the color list - after the defined colors, a random color is returned if index > color list length

random_rotation(struct, max_rotation=TWO_PI)
Randomly rotate struct in 3 dimensions

vector_to_string(vector, format_string='%.6f')
Convert a vector to a space delimited string of numbers

Variables

[hide private]

__doc__ = ...

COLOR_BY_MOLECULE = 'molecule'

GREEN = 30, 225, 30

RED = 225, 30, 30

CYAN = 0, 255, 255

MAGENTA = 225, 30, 225

YELLOW = 255, 240, 0

BLUE = 30, 30, 225

PINK = 255, 152, 163

SLATE = 111, 111, 255

ORANGE = 234, 130, 50

LIME = 153, 255, 0

HOTPINK = 255, 0, 159

YELLOWORANGE = 255, 191, 51

DEEPTEAL = 0, 102, 255

DARKBLUE = 0, 0, 128

SEAFOAM = 0, 191, 127

DARKGREEN = 34, 139, 34

GREY = 160, 160, 160

LIGHTBLUE = 71, 71, 255

DEEPRED = 165, 42, 42

OLIVE = 107, 142, 35

COLOR_CYCLE = [GREEN, CYAN, RED, MAGENTA, YELLOW, BLUE, PINK, ...

TWO_PI = 2.0* numpy.pi

OBEY_DENSITY = 'density'

OBEY_CLASH = 'clash'

OBEY_BOTH = 'both'

SCAFFOLD_ATOM_PROP = 'b_matsci_scaffold_atom'

OPLS2005 = mm.mmffld_get_ffld_name(14)

Function Details

[hide private]

get_color(index)

Get the next color in the color list - after the defined colors, a random color is returned if index > color list length

Parameters:

index (int) - The index of the color to return

Returns: tuple

(R, G, B) color tuple

random_rotation(struct, max_rotation=TWO_PI)

Randomly rotate struct in 3 dimensions

Parameters:

struct (schrodinger.structure.Structure) - The structure to rotate
max_rotation (float) - The maximum rotation to perform

Variables Details

[hide private]

doc

Value:

"""
Builder classes for making amorphous cells

Copyright Schrodinger, LLC. All rights reserved.
"""

COLOR_CYCLE

Value:

[GREEN, CYAN, RED, MAGENTA, YELLOW, BLUE, PINK, SLATE, ORANGE, DARKGRE
EN, LIME, HOTPINK, YELLOWORANGE, DEEPTEAL, DARKBLUE, SEAFOAM, GREY, DE
EPRED, LIGHTBLUE, OLIVE]