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

Module amorphous

Builder classes for making amorphous cells

Classes

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

BoxWithInnerHull
A cubic Box object that contains an inner non-cubic region that limits the valid volume for the components to be placed in.

ScaffoldError
Class for errors involving the scaffold input

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]

float

get_maximum_vdw_radius(struct)
Find the maximum VDW radius of any atom in the structure

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=6.28318530718)
Randomly rotate struct in 3 dimensions

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 = [(30, 225, 30), (0, 255, 255), (225, 30, 30), (2...

TWO_PI = 6.28318530718

OBEY_DENSITY = 'density'

OBEY_CLASH = 'clash'

OBEY_BOTH = 'both'

SCAFFOLD_ATOM_PROP = 'b_matsci_scaffold_atom'

OPLS2005 = 'OPLS_2005'

AMCELL_NO_SYSTEM_OUT = '-amcell.maegz'

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

get_maximum_vdw_radius(struct)

Find the maximum VDW radius of any atom in the structure

Parameters:

struct (schrodinger.structure.Structure) - The structure to check

Returns: float

The maximum VDW radius of any atom

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=6.28318530718)

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:

[(30, 225, 30),
 (0, 255, 255),
 (225, 30, 30),
 (225, 30, 225),
 (255, 240, 0),
 (30, 30, 225),
 (255, 152, 163),
 (111, 111, 255),
...