schrodinger.application.bioluminate.patch_utils.settings module

Classes for storing panel settings.

class schrodinger.application.bioluminate.patch_utils.settings.PatchTypeSettings(size=10, threshold=None, color=None)

Bases: object

Settings for a single patch type (i.e. hydrophobic, positive, or negative).

__init__(size=10, threshold=None, color=None)
Parameters:
  • size (float) – The minimum size of a patch in Angstroms squared
  • threshold (float) – The minimum value for a vertex to be considered part of a patch
  • color (list or tuple) – What to color the patch in the workspace and panel tables, given as integer (r, g, b) values.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.settings', '__doc__': '\n Settings for a single patch type (i.e. hydrophobic, positive, or negative).\n ', '__init__': <function PatchTypeSettings.__init__>, '__dict__': <attribute '__dict__' of 'PatchTypeSettings' objects>, '__weakref__': <attribute '__weakref__' of 'PatchTypeSettings' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.patch_utils.settings'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.bioluminate.patch_utils.settings.PatchSettings

Bases: object

Settings for all patch types (i.e. hydrophobic, positive, and negative).

Variables:EP (float) – A very small value (i.e. epsilon) used for floating point comparisons in sameSizeAndThreshold.
DEFAULT_TRANSPARENCY = 15
EP = 1e-07
__init__()

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

color(patch_type)

Get the color for the specified patch type. If coloring by AggScore, then the user’s color for AggScore is always returned instead.

Parameters:patch_type (PatchType) – The patch type to get the color for
Returns:The requested color as a tuple of integer (r, g, b) values
Return type:tuple
getPatchColorRamp(patch_type)

Return the ColorRamp object for the given patch type. Used for coloring Workspace patch surface, as well as background column in tables. If coloring by AggScore, then color ramp for AggScore is always used.

Parameters:patch_type (PatchType) – The patch type to get the color ramp for
Returns:The requeted color ramp
Return type:color.ColorRamp
sameSizeAndThreshold(other)

Check to see if this object and other have the same patch size and patch threshold settings. Differences in color are ignored.

Parameters:other (PatchSettings) – The object to compare
Returns:True if these objects have the same size and threshold settings. False otherwise.
Return type:bool
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.settings', '__doc__': '\n Settings for all patch types (i.e. hydrophobic, positive, and negative).\n\n :cvar EP: A very small value (i.e. epsilon) used for floating point\n comparisons in `sameSizeAndThreshold`.\n :vartype EP: float\n ', 'DEFAULT_TRANSPARENCY': 15, 'EP': 1e-07, '__init__': <function PatchSettings.__init__>, 'color': <function PatchSettings.color>, 'getPatchColorRamp': <function PatchSettings.getPatchColorRamp>, 'sameSizeAndThreshold': <function PatchSettings.sameSizeAndThreshold>, '__dict__': <attribute '__dict__' of 'PatchSettings' objects>, '__weakref__': <attribute '__weakref__' of 'PatchSettings' objects>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.bioluminate.patch_utils.settings'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.bioluminate.patch_utils.settings.PatchType(long_name, short_name, unit)

Bases: enum.Enum

An enumeration.

positive = ('Positive', 'pos', 'eV')
negative = ('Negative', 'neg', 'eV')
hydrophobic = ('Hydrophobic', 'hyd', 'sLogP')
__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('positive', <PatchType.positive: ('Positive', 'pos', 'eV')>), ('negative', <PatchType.negative: ('Negative', 'neg', 'eV')>), ('hydrophobic', <PatchType.hydrophobic: ('Hydrophobic', 'hyd', 'sLogP')>)]))
__module__ = 'schrodinger.application.bioluminate.patch_utils.settings'