Package schrodinger :: Package application :: Package msv :: Package io :: Module structure_model :: Class AbstractStructureModel

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Class AbstractStructureModel

       object --+            
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sip.simplewrapper --+        
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          sip.wrapper --+    
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     PyQt5.QtCore.QObject --+
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                           AbstractStructureModel

Known Subclasses:

MaestroStructureModel

A StructureModel manages interaction between an alignment and a structural representation of the same collection of sequences.

Interactions include residue selection, insertion, mutation, and deletion. A structure model should also provide a color scheme matching the scheme currently shown in the view provided by the alternative representation.

Instance Methods

[hide private]

__init__(self, parent=None)
x.__init__(...) initializes x; see help(type(x)) for signature

dict (sequence, list)

getResidueColors(self, sequences)
Returns a dictionary mapping sequences to rgb code arrays.

setAlignment(self, aln=None)
Set the alignment on the instance, connect any signals required, disconnect from a previous alignment if necessary, and emit a notification with the alignment

schrodinger.application.msv.alignment.Alignment

getAlignment(self)
Returns an alignment containing sequences synchronized with their structural counterparts

alignmentResiduesChanged(self, seq, start, end)
Respond to residue changes in the alignment

syncStructureSequences(self, cts=None)
Inspect all the structural sequences and synchronize them with the counterpart sequences in the alignment, if allowed

setSyncable(self, seq, allow)
Set a sequence to be synchronizable with its structural counterpart

enableSynchronization(self, enable=True)
Allow or disallow synchronization for all sequences in the alignment

Inherited from PyQt5.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, event, eventFilter, findChild, findChildren, inherits, installEventFilter, isSignalConnected, isWidgetType, isWindowType, killTimer, metaObject, moveToThread, objectName, objectNameChanged, parent, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setParent, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr

Inherited from sip.simplewrapper: __new__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

Inherited from PyQt5.QtCore.QObject: staticMetaObject

Instance Variables

[hide private]

requestUndoStackClear(...)
Signal emitted when synchronization with the structural representation makes undo impossible

alignmentChanged(...)
Signal emitted with the new alignment when it changes

structureViewInclusionChanged(...)
Signal emitted when the workspace ct changes

QtCore.pyqtSignal

structureViewVisibilityChanged
Signal emitted when the workspace ct visibility changes

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, parent=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

getResidueColors(self, sequences)

Returns a dictionary mapping sequences to rgb code arrays.

The rgb code arrays specify the color of the residues in the corresponding sequence on the structure model

Parameters:

sequences - An iterable of schrodinger.application.msv.sequence.ProteinSequence

Returns: dict (sequence, list)

A mapping of sequences to rgb code arrays

setAlignment(self, aln=None)

Set the alignment on the instance, connect any signals required, disconnect from a previous alignment if necessary, and emit a notification with the alignment

If the aln is None, we initialize an alignment

Parameters:

aln (schrodinger.application.msv.domain.ProteinAlignment) - An alignment to set on the instance, or None

alignmentResiduesChanged(self, seq, start, end)

Respond to residue changes in the alignment

Parameters:

seq (schrodinger.application.msv.domain.sequence .ProteinSequence) - The sequence in which residues have changed
start (int) - The start of the change
end (int) - The end of the change

syncStructureSequences(self, cts=None)

Inspect all the structural sequences and synchronize them with the counterpart sequences in the alignment, if allowed

Parameters:

cts (list
Note that the alignment can contain other non-project table sequences, which are unaffected by synchronization.
) - The cts to inspect or None, to inspect all available

setSyncable(self, seq, allow)

Set a sequence to be synchronizable with its structural counterpart

Parameters:

seq (schrodinger.application.msv.domain.Sequence) - The sequence to set synchronization state for
allow (bool) - Whether the sequence should sync with its structural counterpart

Class AbstractStructureModel

__init__(self, parent=None) (Constructor)

getResidueColors(self, sequences)

setAlignment(self, aln=None)

alignmentResiduesChanged(self, seq, start, end)

syncStructureSequences(self, cts=None)

setSyncable(self, seq, allow)

init(self, parent=None)
(Constructor)