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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                           AbstractStructureModel
Known Subclasses:

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 PyQt4.QtCore.QObject: __getattr__, blockSignals, childEvent, children, connect, connectNotify, customEvent, deleteLater, destroyed, disconnect, disconnectNotify, dumpObjectInfo, dumpObjectTree, dynamicPropertyNames, emit, 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:

alignmentResiduesChanged(self, seq, start, end)

 

Respond to residue changes in the alignment

Parameters:

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