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

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Class MaestroStructureModel

       object --+                
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sip.simplewrapper --+            
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          sip.wrapper --+        
                        |        
     PyQt4.QtCore.QObject --+    
                            |    
       AbstractStructureModel --+
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                               MaestroStructureModel

Instance Methods

[hide private]

dict (sequence, list)

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

str

_getSequenceASL(self, seq, residues)
Inspects a sequence and residues and formulates a reasonable asl query for them

setResidueSelection(self, selection_info)
Sets selection in workspace using specified selection info

_emitSelection(self)

workspaceChanged(self, what_changed)

list of schrodinger.applicaiton.msv.alignment.Alignment

getAlignment(self)
See AbstractStructureModel for documentation.

bool

_isPolypeptide(self, chain)
Helper method to determine whether a chain is a valid polypeptide.

getSequenceStructurePairs(self, sequences)
Pairs sequences in msv with sequences in the structure model.

updateProjectEntries(self, sequences)
Updates structures in Maestro project after MSV modified the structure.

Inherited from AbstractStructureModel: __init__, structureModelChanged, structureSelectionChanged

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

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

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

Overrides: AbstractStructureModel.getResidueColors

(inherited documentation)

_getSequenceASL(self, seq, residues)

Inspects a sequence and residues and formulates a reasonable asl query for them

Parameters:

seq (schrodinger.application.msv.domain.ProteinSequence) - The sequence containing the residues
residues (list of schrodinger.application.msv.domain.residue .Residue) - The residues for which to formulate an asl

Returns: str

An asl matching the residues

setResidueSelection(self, selection_info)

Sets selection in workspace using specified selection info

Parameters:

selection_info - A dictionary mapping sequences to selected residues

Overrides: AbstractStructureModel.setResidueSelection

(inherited documentation)

workspaceChanged(self, what_changed)

Parameters:

what_changed (str
Examines a workspace change and emits appropriate signals
) - constant describing workspace change

getAlignment(self)

See AbstractStructureModel for documentation.

TODO: We'll also need to handle the all_rows case, and not just the included rows. I'm not adding it as a parameter at the moment because we should think more about how we want to handle the interface in general.

TODO: We need to return the appropriate alignment (protein, not protein)

Returns: list of schrodinger.applicaiton.msv.alignment.Alignment
Overrides: AbstractStructureModel.getAlignment

_isPolypeptide(self, chain)

Helper method to determine whether a chain is a valid polypeptide. The sole criterion is whether the chain contains a single standard residue.

TODO: Change this to test if the structure's residues contain a peptidic backbone (C-alpha, and C, N, O backbone atoms).

Parameters:

chain - The chain to inspect

Returns: bool

Whether the chain is a valid polypeptide

getSequenceStructurePairs(self, sequences)

Pairs sequences in msv with sequences in the structure model.

Parameters:

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

Returns:

A list of (sequence, chain) tuples

updateProjectEntries(self, sequences)

Updates structures in Maestro project after MSV modified the structure.

Parameters:

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