schrodinger.application.bioluminate.patch_utils.patch_finder module

schrodinger.application.bioluminate.patch_utils.patch_finder.read_asl_file(basename)
schrodinger.application.bioluminate.patch_utils.patch_finder.write_asl_file(basename, asl)
schrodinger.application.bioluminate.patch_utils.patch_finder.get_connected_components(st)

Determine all covalently connected components of st (i.e. unbroken chain segments).

Returns:A tuple of: - A list of list of residue names (str). Each list of residue names
represents a single covalently connected component.
schrodinger.application.bioluminate.patch_utils.patch_finder.calc_agg_scores(patches, res_lists)

Calculate Aggregation propensity scores for each residue.

Parameters:
  • patches (list of Patch objects) – List of patches from which to read the residues.
  • res_lists (list of lists of str) – Each list of residues represents a single covalently connected component/sequence. Each residue is in format “A:123i”.
schrodinger.application.bioluminate.patch_utils.patch_finder.triangle_area(coords)

Calculate the area of a triangle defined by three vertices

Parameters:coords (list) – A list of (x, y, z) coordinates for each vertex of the triangle, where each coordinate is a numpy array.
Returns:The area of the specified triangle
Return type:float
Note:The formula used here is taken from http://mathworld.wolfram.com/TriangleArea.html
class schrodinger.application.bioluminate.patch_utils.patch_finder.Patch(vertices, patch_type, vertex_coords, all_smoothed, neighboring_triangles, neighboring_vertices, nearest_atom_indices, patch_color)

Bases: object

Data about a single patch.

RES_TYPES = {'Arginine': 'ARG', 'Cysteine': 'CYS', 'Tryptophan': 'TRP', 'Tyrosine': 'TYR'}
__init__(vertices, patch_type, vertex_coords, all_smoothed, neighboring_triangles, neighboring_vertices, nearest_atom_indices, patch_color)
Parameters:
  • vertices (set) – A set of all vertices that belong to this patch
  • patch_type (settings.PatchType) – The type of patch this is
  • vertex_coords (list) – The (x, y, z) coordinates for each surface vertex
  • all_smoothed (list) – The smoothed value for each vertex
  • neighboring_triangles (list) – A list of neighboring triangles for each vertex, where each triangle is represented as a frozenset of three vertex indices.
  • neighboring_vertices (list) – A list of neighboring vertices for each vertex. Neighbors are given as a set.
  • nearest_atom_indices (list) – A list of the nearest atom index for each vertex.

@patch_color: color of the patch (r,g,b)

__getstate__()
__eq__(other)

Return self==value.

detailsData()

Generate a list describing the details of this patch

Returns:A list of details for the patch, where each detail is a list of [group, category, patch details for that category]
Return type:list
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n Data about a single patch.\n ', 'RES_TYPES': OrderedDict([('Arginine', 'ARG'), ('Cysteine', 'CYS'), ('Tryptophan', 'TRP'), ('Tyrosine', 'TYR')]), '__init__': <function Patch.__init__>, '_calcSize': <function Patch._calcSize>, '_calcLabelVertex': <function Patch._calcLabelVertex>, '_calcSmoothedStats': <function Patch._calcSmoothedStats>, '__getstate__': <function Patch.__getstate__>, '__eq__': <function Patch.__eq__>, 'detailsData': <function Patch.detailsData>, '_resListText': <function Patch._resListText>, '__dict__': <attribute '__dict__' of 'Patch' objects>, '__weakref__': <attribute '__weakref__' of 'Patch' objects>, '__hash__': None})
__dir__() → list

default dir() implementation

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__ = None
__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.patch_finder'
__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.patch_finder.ResInfo(res, zyggregator=None, aggrescan=None, aggscore=0.0)

Bases: object

Data about a single residue. Includes aggregation, surface area, and reactive residue grouping data.

__init__(res, zyggregator=None, aggrescan=None, aggscore=0.0)
Parameters:
  • res (schrodinger.structure._Residue) – The residue that this aggregation data describes
  • zyggregator (float) – The Zyggregator score for the residue
  • aggrescan (float) – The Aggrescan score for the residue
fullname

The full residue name, formatted similar to A:TYR100.

getIdStr()

Return a string ID for this residue, e.g. “A:2b” - same format as structure._Residue.___str__() return value.

__eq__(other)

Return self==value.

__lt__(other)

Return self<value.

__hash__()

Return hash(self).

__getstate__()
asl()

Return the ASL for finding this residue by chain/resnum/inscode.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n Data about a single residue. Includes aggregation, surface area, and\n reactive residue grouping data.\n ', '__init__': <function ResInfo.__init__>, 'fullname': <property object>, 'getIdStr': <function ResInfo.getIdStr>, '__eq__': <function ResInfo.__eq__>, '__lt__': <function ResInfo.__lt__>, '__hash__': <function ResInfo.__hash__>, '__getstate__': <function ResInfo.__getstate__>, 'asl': <function ResInfo.asl>, '__dict__': <attribute '__dict__' of 'ResInfo' objects>, '__weakref__': <attribute '__weakref__' of 'ResInfo' objects>, '__gt__': <function _gt_from_lt>, '__le__': <function _le_from_lt>, '__ge__': <function _ge_from_lt>})
__dir__() → list

default dir() implementation

__format__()

default object formatter

__ge__(other, NotImplemented=NotImplemented)

Return a >= b. Computed by @total_ordering from (not a < b).

__getattribute__

Return getattr(self, name).

__gt__(other, NotImplemented=NotImplemented)

Return a > b. Computed by @total_ordering from (not a < b) and (a != b).

__init_subclass__()

This method is called when a class is subclassed.

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

__le__(other, NotImplemented=NotImplemented)

Return a <= b. Computed by @total_ordering from (a < b) or (a == b).

__module__ = 'schrodinger.application.bioluminate.patch_utils.patch_finder'
__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)

schrodinger.application.bioluminate.patch_utils.patch_finder.ResData

alias of schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo

class schrodinger.application.bioluminate.patch_utils.patch_finder.ResPatchData(patch, res_info, contribution)

Bases: object

This class represents a residue’s contribution to a patch.

__init__(patch, res_info, contribution)

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

asl()

Return the ASL for finding this patch’s residue by chain/resnum/inscode.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': "\n This class represents a residue's contribution to a patch.\n ", '__init__': <function ResPatchData.__init__>, 'asl': <function ResPatchData.asl>, '__dict__': <attribute '__dict__' of 'ResPatchData' objects>, '__weakref__': <attribute '__weakref__' of 'ResPatchData' 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.patch_finder'
__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.patch_finder.ProteinProperties(struc, asa_by_atom)

Bases: object

Calculates protein properties for display on the Properties tab

Variables:KYTE_DOOLITTLE_SCALE (dict) – A hydrophobicity scale taken from A simple method for displaying the hydropathic character of a protein. J. Kyte, R.F. Doolittle, J Mol Biol. 1982 May 5;157(1):105-32.
KYTE_DOOLITTLE_SCALE = {'ALA': 1.8, 'ARG': -4.5, 'ASN': -3.5, 'ASP': -3.5, 'CYS': 2.5, 'GLN': -3.5, 'GLU': -3.5, 'GLY': -0.4, 'HID': -3.2, 'HIE': -3.2, 'HIP': -3.2, 'HIS': -3.2, 'ILE': 4.5, 'LEU': 3.8, 'LYS': -3.9, 'MET': 1.9, 'PHE': 2.8, 'PRO': -1.6, 'SER': -0.8, 'THR': -0.7, 'TRP': -0.9, 'TYR': -1.3, 'VAL': 4.2}
__init__(struc, asa_by_atom)
Parameters:
  • struc (schrodinger.structure.Structure) – The structure to calculate the properties of
  • asa_by_atom (OneIndexedList) – The accessible surface area of each atom
__getstate__()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n Calculates protein properties for display on the Properties tab\n\n :cvar KYTE_DOOLITTLE_SCALE: A hydrophobicity scale taken from\n A simple method for displaying the hydropathic character of a protein.\n J. Kyte, R.F. Doolittle, J Mol Biol. 1982 May 5;157(1):105-32.\n :vartype KYTE_DOOLITTLE_SCALE: dict\n ', 'KYTE_DOOLITTLE_SCALE': {'ALA': 1.8, 'CYS': 2.5, 'ASP': -3.5, 'GLU': -3.5, 'PHE': 2.8, 'GLY': -0.4, 'HIS': -3.2, 'HIP': -3.2, 'HIE': -3.2, 'HID': -3.2, 'ILE': 4.5, 'LYS': -3.9, 'LEU': 3.8, 'MET': 1.9, 'ASN': -3.5, 'PRO': -1.6, 'GLN': -3.5, 'ARG': -4.5, 'SER': -0.8, 'THR': -0.7, 'VAL': 4.2, 'TRP': -0.9, 'TYR': -1.3}, '__init__': <function ProteinProperties.__init__>, '_calcHydrophobicMoment': <function ProteinProperties._calcHydrophobicMoment>, '_calcPosNegSurfaceArea': <function ProteinProperties._calcPosNegSurfaceArea>, '_calcHBondSurfaceArea': <function ProteinProperties._calcHBondSurfaceArea>, '__getstate__': <function ProteinProperties.__getstate__>, '__dict__': <attribute '__dict__' of 'ProteinProperties' objects>, '__weakref__': <attribute '__weakref__' of 'ProteinProperties' 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.patch_finder'
__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.patch_finder.PatchAnalysis(st, surf, asl, clogp_smoothed, partial_charge_smoothed, neighboring_vertices, neighboring_triangles, res_data_by_vertex, prot_properties)

Bases: object

Object representing a pre-analysis instance, which is saved by the backend and loaded into the GUI. It is also saved/restored when panel state is saved and restored.

__init__(st, surf, asl, clogp_smoothed, partial_charge_smoothed, neighboring_vertices, neighboring_triangles, res_data_by_vertex, prot_properties)
Parameters:
  • st (structure.Structure) – Analyzed structure.
  • surf (schrodinger.surface.Surface) – The surface to find patches on
  • asl (str) – Asl for atoms that were analyzed
  • clogp_smoothed (list) – The cLogP (hydrophobicity) values smoothed over the surface. This list contains the smoothed value at each surface vertex.
  • partial_charge_smoothed (list) – The partial charge values smoothed over the surface. This list contains the smoothed value at each surface vertex.
  • neighboring_vertices (list) – A list of neighboring vertices for each vertex.
  • neighboring_triangles (list) – A list of neighboring triangles for each vertex, where each triangle is represented as a frozenset of three vertex indices.
  • res_data_by_vertex (list) – A list of residue data for each vertex. The ResInfo object is given for the residue closest to the vertex.
  • prot_properties (ProteinProperties) – The protein properties to be loaded into the Properties tab.
write(basename)
classmethod read(basename)

Read the PreAnalyzer data from the specified basename and use it to create a PatchFinder object.

Parameters:basename (str) – The basename for the PreAnalyzer output files
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n Object representing a pre-analysis instance, which is saved by the backend\n and loaded into the GUI. It is also saved/restored when panel state is\n saved and restored.\n ', '__init__': <function PatchAnalysis.__init__>, 'write': <function PatchAnalysis.write>, 'read': <classmethod object>, '__dict__': <attribute '__dict__' of 'PatchAnalysis' objects>, '__weakref__': <attribute '__weakref__' of 'PatchAnalysis' 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.patch_finder'
__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.patch_finder.PreAnalyzer(struc, asl)

Bases: object

Perform patch finding calculations that only need to be done once per structure. This class is intended to be run under job control.

__init__(struc, asl)
Parameters:
classmethod readAndRun(basename)

Read a structure and ASL from the specified files and run the analysis.

Parameters:basename (str) – The full path to the file to analyzes except the “.maegz” and “.txt” extensions
Returns:The completed pre-analysis
Return type:PreAnalyzer
run()

Perform the pre-analysis. The results will be stored in instance attributes and can be written to a pickle file using write.

write(basename)

Write out the surface and all calculated values

Parameters:basename (str) – The filename to write the output to. The surface will be written to basename.vis and the calculated values will be written to basename.pkl.
getAnalysis()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n Perform patch finding calculations that only need to be done once per\n structure. This class is intended to be run under job control.\n ', '__init__': <function PreAnalyzer.__init__>, 'readAndRun': <classmethod object>, 'run': <function PreAnalyzer.run>, '_prepareStructure': <function PreAnalyzer._prepareStructure>, '_calcCLogP': <function PreAnalyzer._calcCLogP>, '_calcPartialCharges': <function PreAnalyzer._calcPartialCharges>, '_prepareSurface': <function PreAnalyzer._prepareSurface>, '_calculateSurfaceNeighbors': <function PreAnalyzer._calculateSurfaceNeighbors>, '_calcSmoothedValues': <function PreAnalyzer._calcSmoothedValues>, '_preCalcResData': <function PreAnalyzer._preCalcResData>, '_calcAggregation': <function PreAnalyzer._calcAggregation>, '_resDataByVertex': <function PreAnalyzer._resDataByVertex>, '_calcZyggregator': <function PreAnalyzer._calcZyggregator>, '_calcAggrescan': <function PreAnalyzer._calcAggrescan>, '_calcSasa': <function PreAnalyzer._calcSasa>, '_calcAccessibility': <function PreAnalyzer._calcAccessibility>, '_calcReactiveResidues': <function PreAnalyzer._calcReactiveResidues>, '_genSeqDictsForReactiveResiduesSearch': <function PreAnalyzer._genSeqDictsForReactiveResiduesSearch>, '_calcDisulfides': <function PreAnalyzer._calcDisulfides>, '_resHasDisulfide': <function PreAnalyzer._resHasDisulfide>, '_calcAntibodyTopography': <function PreAnalyzer._calcAntibodyTopography>, 'write': <function PreAnalyzer.write>, 'getAnalysis': <function PreAnalyzer.getAnalysis>, '__dict__': <attribute '__dict__' of 'PreAnalyzer' objects>, '__weakref__': <attribute '__weakref__' of 'PreAnalyzer' 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.patch_finder'
__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.patch_finder.PatchFinder(analysis)

Bases: object

Find surface patches using the output of PreAnalyzer. This object is intended to run in a separate thread and therefore must not use mmlibs after initialization.

__init__(analysis)

Class for grouping patches from a PatchAnalysis object based on specific settings.

Parameters:analysis (PatchAnalysis) – Pre-analysis object
classmethod read(basename)

Read the PreAnalyzer data from the specified basename and use it to create a PatchFinder object.

Parameters:basename (str) – The basename for the PreAnalyzer output files
write(basename)
calculate(settings)

Calculate patches and residue aggregation data using the specified settings. # NOTE: This method runs from within a thread, so it should not access # any mmlibs code.

Parameters:settings (settings.PatchSettings) – The settings to use for the patch calculations
Returns:A tuple of: - the calculated patches as a list of Patch objects - the residue aggregation data as a list of {ResidueAggData} objects
Return type:tuple
getColorsForPatchVertices(patch, psettings)

Return colors for all vertices of the given patch.

Parameters:patch (patch_finder.Patch) – Patch to get colors for.
Returns:Colors for each vertex of the patch
Return type:list of (float, float, float)
colorSurfByPatches(surf, patches, psettings)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n Find surface patches using the output of `PreAnalyzer`. This object is\n intended to run in a separate thread and therefore must not use mmlibs after\n initialization.\n ', '__init__': <function PatchFinder.__init__>, 'read': <classmethod object>, 'write': <function PatchFinder.write>, 'calculate': <function PatchFinder.calculate>, '_calcPatches': <function PatchFinder._calcPatches>, '_calcPatchesFor': <function PatchFinder._calcPatchesFor>, '_findAllPatchVertices': <function PatchFinder._findAllPatchVertices>, '_calcResData': <function PatchFinder._calcResData>, 'getColorsForPatchVertices': <function PatchFinder.getColorsForPatchVertices>, 'colorSurfByPatches': <function PatchFinder.colorSurfByPatches>, '__dict__': <attribute '__dict__' of 'PatchFinder' objects>, '__weakref__': <attribute '__weakref__' of 'PatchFinder' 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.patch_finder'
__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.patch_finder.PatchFinderRunner(finder, settings)

Bases: PyQt5.QtCore.QObject

An object used to run the PatchFinder analysis in a separate thread.

Variables:patchesFound (QtCore.pyqtSignal) – A signal emitted when the PatchFinder analysis completes. Emits all return values of PatchFinder.calculate.
patchesFound
__init__(finder, settings)

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

run()

Run the PatchFinder analysis and emit patchesFound when complete.

__class__

alias of sip.wrappertype

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.patch_utils.patch_finder', '__doc__': '\n An object used to run the `PatchFinder` analysis in a separate thread.\n\n :cvar patchesFound: A signal emitted when the `PatchFinder` analysis\n completes. Emits all return values of `PatchFinder.calculate`.\n :vartype patchesFound: `QtCore.pyqtSignal`\n ', 'patchesFound': <unbound PYQT_SIGNAL PatchFinderRunner.patchesFound[list, list]>, '__init__': <function PatchFinderRunner.__init__>, 'run': <function PatchFinderRunner.run>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattr__(self, str) → object
__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.patch_finder'
__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)

blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject]

inherits(self, str) → bool
installEventFilter(self, QObject)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

parent(self) → QObject
property(self, str) → Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
tr(self, str, disambiguation: str = None, n: int = -1) → str
schrodinger.application.bioluminate.patch_utils.patch_finder.launch_pre_analysis(struc, asl)

Launch a pre-analysis job under job control. This method will return as soon as the job has been launched.

Parameters:
Returns:

A tuple of: - A job object for the running job (schrodinger.job.jobcontrol.Job) - The basename for the job output (str) - The job directory (str) - The job log file (str)
Return type:

tuple