schrodinger.application.bioluminate.patch_utils.patch_finder module¶
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schrodinger.application.bioluminate.patch_utils.patch_finder.
read_asl_file
(basename)¶
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schrodinger.application.bioluminate.patch_utils.patch_finder.
write_asl_file
(basename, asl)¶
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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.- A list of list of
schrodinger.structure._Residue
objects. This object mirrors the structure of the list of list of residue names.
- A list of list of
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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”.
- patches (list of
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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
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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.
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RES_TYPES
= {'Arginine': 'ARG', 'Cysteine': 'CYS', 'Tryptophan': 'TRP', 'Tyrosine': 'TYR'}¶
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__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)
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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
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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.
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__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
- res (
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fullname
¶ The full residue name, formatted similar to A:TYR100.
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getIdStr
()¶ Return a string ID for this residue, e.g. “A:2b” - same format as structure._Residue.___str__() return value.
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getAsl
()¶ Return the ASL for finding this residue by chain/resnum/inscode.
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schrodinger.application.bioluminate.patch_utils.patch_finder.
ResData
¶ alias of
schrodinger.application.bioluminate.patch_utils.patch_finder.ResInfo
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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.
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__init__
(patch, res_info, contribution)¶ Initialize self. See help(type(self)) for accurate signature.
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getAsl
()¶ Return the ASL for finding this patch’s residue by chain/resnum/inscode.
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class
schrodinger.application.bioluminate.patch_utils.patch_finder.
ProteinProperties
(struc, asa_by_atom)¶ Bases:
object
Calculates protein-level properties. Properties will be stored at the ct-level and returned 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}¶
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__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
- struc (
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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.
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__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.
- st (
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write
(basename)¶
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classmethod
read
(basename)¶ Read the
PreAnalyzer
data from the specified basename and use it to create aPatchFinder
object.Parameters: basename (str) – The basename for the PreAnalyzer
output files
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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.
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__init__
(struc, asl)¶ Parameters: - struc (
schrodinger.structure.Structure
) – The structure to analyze - asl (str) – An ASL describing atoms of
struc
to analyze
- struc (
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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
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run
()¶ Perform the pre-analysis. The results will be stored in instance attributes and can be written to a pickle file using
write
.
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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.
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getAnalysis
()¶
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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
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classmethod
read
(basename)¶ Read the
PreAnalyzer
data from the specified basename and use it to create aPatchFinder
object.Parameters: basename (str) – The basename for the PreAnalyzer
output files
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write
(basename)¶
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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 calculationsReturns: A tuple of: - the calculated patches as a list of Patch
objects - the residue aggregation data as a list of {ResidueAggData} objectsReturn type: tuple
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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)
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colorSurfByPatches
(surf, patches, psettings)¶
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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 thePatchFinder
analysis completes. Emits all return values ofPatchFinder.calculate
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patchesFound
¶
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__init__
(finder, settings)¶ Initialize self. See help(type(self)) for accurate signature.
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blockSignals
(self, bool) → bool¶
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childEvent
(self, QChildEvent)¶
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children
(self) → object¶
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connectNotify
(self, QMetaMethod)¶
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customEvent
(self, QEvent)¶
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deleteLater
(self)¶
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destroyed
¶ destroyed(self, QObject = None) [signal]
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disconnect
(self)¶
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disconnectNotify
(self, QMetaMethod)¶
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dumpObjectInfo
(self)¶
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dumpObjectTree
(self)¶
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dynamicPropertyNames
(self) → object¶
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event
(self, QEvent) → bool¶
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eventFilter
(self, QObject, QEvent) → bool¶
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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
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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]
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inherits
(self, str) → bool¶
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installEventFilter
(self, QObject)¶
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isSignalConnected
(self, QMetaMethod) → bool¶
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isWidgetType
(self) → bool¶
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isWindowType
(self) → bool¶
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killTimer
(self, int)¶
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metaObject
(self) → QMetaObject¶
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moveToThread
(self, QThread)¶
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objectName
(self) → str¶
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objectNameChanged
¶ objectNameChanged(self, str) [signal]
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parent
(self) → QObject¶
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property
(self, str) → Any¶
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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.
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receivers
(self, PYQT_SIGNAL) → int¶
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removeEventFilter
(self, QObject)¶
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run
()¶ Run the
PatchFinder
analysis and emitpatchesFound
when complete.
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sender
(self) → QObject¶
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senderSignalIndex
(self) → int¶
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setObjectName
(self, str)¶
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setParent
(self, QObject)¶
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setProperty
(self, str, Any) → bool¶
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signalsBlocked
(self) → bool¶
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startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
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staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
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thread
(self) → QThread¶
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timerEvent
(self, QTimerEvent)¶
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tr
(self, str, disambiguation: str = None, n: int = -1) → str¶
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