cadnano.oligo.oligo module¶

class Oligo(part, color=None)¶

Bases: cadnano.cnobject.CNObject

Oligo is a group of Strands that are connected via 5’ and/or 3’ connections. It corresponds to the physical DNA strand, and is thus used tracking and storing properties that are common to a single strand, such as its color.

Commands that affect Strands (e.g. create, remove, merge, split) are also responsible for updating the affected Oligos.

Parameters:	part (Part) – the model `Part` color (str) – optional, color property of the `Oligo`

addToPart(part)¶

applyAbstractSequences()¶

applyColor(color, use_undostack=True)¶

applySequence(sequence, use_undostack=True)¶

applySequenceCMD(sequence)¶

clearAbstractSequences()¶

destroy()¶

displayAbstractSequences()¶

dump()¶

Return dictionary of this oligo and its properties. It’s expected that caller will copy the properties if mutating

Returns:	dict

editable_properties = ['name', 'color']¶

getColor()¶

getModelProperties()¶

Return a reference to the property dictionary

Returns:	dict

getName()¶

getOutlineProperties()¶

Convenience method for the outline view

Returns:	tuple – (<name>, <color>, <is_visible>)

getProperty(key)¶

isLoop()¶

length()¶

locString()¶

oligoPropertyChangedSignal = <cadnano.cnproxy.DummySignal object>¶: self, property_name, new_value

oligoRemovedSignal = <cadnano.cnproxy.DummySignal object>¶: part, self

oligoSequenceAddedSignal = <cadnano.cnproxy.DummySignal object>¶: self

oligoSequenceClearedSignal = <cadnano.cnproxy.DummySignal object>¶: self

part()¶

refreshLength()¶

remove(use_undostack=True)¶

removeFromPart()¶

This method merely disconnects the object from the model. It still lives on in the undoStack until clobbered

Note: don’t set self._part = None because we need to continue passing the same reference around.

sequence()¶

Get the sequence applied to this Oligo

Returns:	str or None

sequenceExport(output)¶

Iterative appending to argument output which is a dictionary of lists

Parameters:	output (dict) – dictionary with keys given in NucleicAcidPart.getSequences
Returns:	dict

setPart(part)¶

setProperty(key, value, use_undostack=True)¶

setStrand5p(strand)¶

shallowCopy()¶

shouldHighlight()¶

strand3p()¶

strand5p()¶

undoStack()¶