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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     PyQt4.QtCore.QObject --+    
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            Qt.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 Qt.QtCore.QObject: connect, emit

Inherited from PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, event, eventFilter, findChild, findChildren, inherits, installEventFilter, isWidgetType, killTimer, metaObject, moveToThread, objectName, parent, property, pyqtConfigure, receivers, removeEventFilter, sender, senderSignalIndex, setObjectName, setParent, setProperty, signalsBlocked, startTimer, thread, timerEvent, tr, trUtf8

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 PyQt4.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

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.applicaiton.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.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)