Welcome to cadnano’s documentation!

cadnano is a computer-aided design tool for creating DNA nanostructures.

Warning

These docs are under development as part of the upcoming cadnano 2.5 release. Some information, such as installation steps, may not be useful prior to the official release.

Quickstart

Installation

Install Python 3.5 , followed by cadnano.

Usage

To launch the cadnano GUI from the command line:

python3 cadnano

To import cadnano as a Python module and work without a GUI:

import cadnano

Installation

Install Python 3.5

There are many ways to get Python on your system.

• If you prefer the complete “batteries included” option, Anaconda Python is available for Mac, Windows or Linux.
• On Mac, Homebrew is a great way to install Python.
• If you just want a clean Python install and nothing else, installers from python.org work great too.

Cadnano will run on Python 3.3, 3.4 and 3.5, but we only support 3.5. We do not support Python 2.X.

Install cadnano

pip3 install cadnano

Advanced: Building from scratch

Should the above not work for you:

1. Let us know
2. The requirements PyQt5 and SIP are available from Riverbank Computing Limited at:

• Qt5
• PyQt5 downloads
• SIP downloads

Windows

Instructions to come.

Mac and Linux

These instructions can work 10.10 Yosemite and 10.11 El Capitan under Xcode 7.0.1 and 6.5. It has also been tested on Debian 7.9 Wheezy Please provide feedback if you have problems running this in issues.

You can run the included pyqt5_check.py which will grab, build and install Qt5, SIP and PyQt5 in your python environment. It is cleanest using virtualenv and virtualenvwrapper creating a virtualenv with:

mkvirtualenv --always-copy <myvenv>
python pyqttools/install_pyqt_from_src.py

and then running the script, but you can definitely install in your system python if you run:

sudo python pyqttools/install_pyqt_from_src.py

This script only builds required parts of Qt5 and PyQt5 in the interest of time.

Manual installation of PyQt5 is fine too, but you’ll need to trouble shoot on your own

1. Install Qt5. download the online installer
2. Build sip and PyQt5 against this Qt5

Of course there are many ways to accomplish this feat, but needless to say OS X and Linux installs of PyQt5 can be painful for some people.

Tutorial

We have planned to create some new tutorials to add here. In the meantime, you can start by checking out the original tutorials that were released for the original version of cadnano.

	Tutorial 1: How DNA geometry relates to building 3D shapes with a honeycomb lattice
	Tutorial 2: How to create a basic shape in cadnano export the DNA staple sequences

Understanding the interface

The basic knowledge of DNA geometry necessary to understand the interface is covered by Tutorial 1. The new tutorial planned for this section will explain the latest version of the GUI interface in that context, and walk through what each of the tools do.

Creating a new design

We are also planning an updated version of Tutorial 2, which will be a step-by-step design, start to finish.

API

Packages

cadnano.decorators package

Submodules

cadnano.decorators.insertion module

class Insertion(index, length)

Bases: object

Insertions do affect an applied sequence and do not store a sequence themselves. They are a skip if the length is less than 0

Parameters:

• index (int) – the index into the StrandSet the Insertion occurs at
• length (int) – length of Insertion

idx()

Returns:int – the index into the StrandSet the Insertion occurs at

isSkip()

Returns:bool – True is is a skip, False otherwise

length()

This is the length of a sequence that is immutable by the strand

Returns:int – length of Insertion

setLength(length)

Setter for the length

Parameters:length (int) –

updateIdx(delta)

Increment the index by delta

Parameters:delta (int) – can be negative

Module contents

cadnano.docmodscmd module

class AddModCommand(document, params, mid)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

class ModifyModCommand(document, params, mid)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

class RemoveModCommand(document, mid)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.fileio package

Submodules

cadnano.fileio.c25decode module

cadnano.fileio.lattice module

class HoneycombDnaPart

Bases: object

SCAF_LOW = [[1, 11], [8, 18], [4, 15]] SCAF_HIGH = [[2, 12], [9, 19], [5, 16]] STAP_LOW = [[6, 16], [3, 13], [10, 20]] STAP_HIGH = [[7, 17], [4, 14], [0, 11]]

# from 0: DR U DL aka 210 90 330 SCAF_LOW = [[1, 12], [8, 19], [5, 15]] SCAF_HIGH = [[2, 13], [9, 20], [6, 16]] STAP_LOW = [[17], [3], [10]] STAP_HIGH = [[18], [4], [11]]

HELICAL_PITCH = 10.5

STEP = 21

SUB_STEP_SIZE = 7.0

TURNS_PER_STEP = 2.0

TWIST_OFFSET = -34.285714285714285

TWIST_PER_BASE = 34.285714285714285

static isEvenParity(row, column)

static isOddParity(row, column)

static latticeCoordToPositionXY(radius, row, column, scale_factor=1.0)

make sure radius is a float

static legacyLatticeCoordToPositionXY(radius, row, column, scale_factor=1.0)

make sure radius is a float

static positionToLatticeCoord(radius, x, y, scale_factor=1.0)

static positionToLatticeCoordRound(radius, x, y, round_up_row, round_up_col, scale_factor=1.0)

class SquareDnaPart

Bases: object

SCAF_LOW = [[4, 26, 15], [18, 28, 7], [10, 20, 31], [2, 12, 23]] SCAF_HIGH = [[5, 27, 16], [19, 29, 8], [11, 21, 0], [3, 13, 24]] STAP_LOW = [[31], [23], [15], [7]] STAP_HIGH = [[0], [24], [16], [8]]

HELICAL_PITCH = 10.666666666666666

STEP = 32

SUB_STEP_SIZE = 8.0

TURNS_PER_STEP = 3.0

TWIST_OFFSET = 196.875

TWIST_PER_BASE = 33.75

static isEvenParity(row, column)

static isOddParity(row, column)

static latticeCoordToPositionXY(radius, row, column, scale_factor=1.0)

static legacyLatticeCoordToPositionXY(radius, row, column, scale_factor=1.0)

static positionToLatticeCoord(radius, x, y, scale_factor=1.0)

static positionToLatticeCoordRound(radius, x, y, scale_factor=1.0)

cadnano.fileio.nnodecode module

cadnano.fileio.nnoencode module

cadnano.fileio.v2decode module

cadnano.fileio.v3decode module

decode(document, obj)

Decode a a deserialized Document dictionary

Parameters:

• document (Document) –
• obj (dict) – deserialized file object

decodePart(document, part_dict)

Decode a a deserialized Part dictionary

Parameters:

• document (Document) –
• part_dict (dict) – deserialized dictionary describing the Part

importToPart(part_instance, copy_dict, use_undostack=True)

Use this to duplicate virtual_helices within a Part. duplicate id_nums will start numbering part.getIdNumMax() rather than the lowest available id_num. TODO should this numbering change?

Parameters:

• part_instance (ObjectInstance) –
• copy_dict (dict) –

cadnano.fileio.v3encode module

encodeDocument(document)

Encode a Document to a dictionary to enable serialization

Parameters:document (Document) – Returns:dict

encodePart(part)

Parameters:part (Part) – Returns:dict

encodePartList(part_instance, vh_group_list)

Used for copying and pasting TODO: unify encodePart and encodePartList

Parameters:

• part (Part) –
• vh_group_list (list) – of int, virtual_helices IDs to encode to be used with copy and paste serialization

Returns:

dict

Module contents

cadnano.math package

Submodules

cadnano.math.box module

class Box(min_point, max_point)

Bases: object

Cube box object

For doing an oct tree type thing

Parameters:

• min_point (Tuple) – length 3 lower left corner
• max_point (Tuple) – length 3 diagonal opposite top corner

center()

Return the center of this Box

Returns:Vector3 – the center point of this box.

clone()

Clone this Box

Returns:Box – a copy of this box.

containsBox(box)

Does this object contain the Box box?

Parameters:Box – Returns:bool – True if box is in self otherwise False

containsPoint(point)

Is the point within this Box?

Parameters:point (Vector3) – to check for inclusion. Returns:bool –

True if the specified point lies within the boundaries

of this box False otherwise

doesBoxSpan(box)

doe this object contain the Box box? :param Box:

Returns:bool – True if box spans self otherwise False

set(min_point, max_point)

Set the Tuples

Setter for setting the bounding points of the Box

Parameters:

• min_point (Tuple) – length 3 lower left corner
• max_point (Tuple) – length 3 diagonal opposite top corner

size()

Find the dimensions of the Box

Returns:Tuple – the width, height, and depth of this box.

cadnano.math.face module

class Face(normal, v1, v2, v3)

Bases: tuple

namedtuple of tuple: 4 x 3 tuple of tuples corresponding

to the normal and the three points comprising a Face

normal

Alias for field number 0

v1

Alias for field number 1

v2

Alias for field number 2

v3

Alias for field number 3

cadnano.math.matrix3 module

class Matrix3(n11, n12, n13, n21, n22, n23, n31, n32, n33)

Bases: tuple

namedtuple: 3 x 3 matrix

n11

Alias for field number 0

n12

Alias for field number 1

n13

Alias for field number 2

n21

Alias for field number 3

n22

Alias for field number 4

n23

Alias for field number 5

n31

Alias for field number 6

n32

Alias for field number 7

n33

Alias for field number 8

getInverse(m4)

Parameters:m4 (Matrix4) – Returns:Matrix3

getNormalMatrix(m)

Normalize the matrix m :param m: :type m: Matrix3

Returns:Matrix3

transpose(m)

Compute the inverse of m

Parameters:m (Matrix3) – Returns:Matrix3 – the inverse

cadnano.math.matrix4 module

class Matrix4(n11, n12, n13, n14, n21, n22, n23, n24, n31, n32, n33, n34, n41, n42, n43, n44)

Bases: tuple

namedtuple: 4 x 4 matrix

n11

Alias for field number 0

n12

Alias for field number 1

n13

Alias for field number 2

n14

Alias for field number 3

n21

Alias for field number 4

n22

Alias for field number 5

n23

Alias for field number 6

n24

Alias for field number 7

n31

Alias for field number 8

n32

Alias for field number 9

n33

Alias for field number 10

n34

Alias for field number 11

n41

Alias for field number 12

n42

Alias for field number 13

n43

Alias for field number 14

n44

Alias for field number 15

makeRotationZ(theta)

Create a rotation matrix of angle theta

Parameters:theta (float) – Angle in radians Returns:Matrix4 – rotation matrix about the Z axis

makeTranslation(x, y, z)

create a translation matrix given a displacement x, y, z

Parameters:

• x (float) –
• y (float) –
• z (float) –

Returns:

Matrix4 – translation matrix

cadnano.math.solid module

class Solid(name)

Bases: object

addFace(v1, v2, v3, normal=None)

List vertices using right hand rule so that unit normal will point out of the surface

vertices are given by index into vertices list

Parameters:

• v1 (Vector3) –
• v2 (Vector3) –
• v3 (Vector3) –
• normal (Vector3) – face normal

addVertex(vertex)

Add a vertex to the Solid :param vertex: :type vertex: Vector3

applyMatrix(matrix4)

computeFaceNormals()

cadnano.math.vector module

class Vector2(x, y)

Bases: tuple

x

Alias for field number 0

y

Alias for field number 1

class Vector3(x, y, z)

Bases: tuple

x

Alias for field number 0

y

Alias for field number 1

z

Alias for field number 2

addVectors(v1, v2)

applyMatrix3(m, v)

applyMatrix4(m, v)

crossProduct(a, b)

return normalized cross product

multiplyScalar(v, s)

return v1*s

normalToPlane(v1, v2, v3)

Calculate unit normal to the normal to the plane defined by vertices v1, v2, and v3

normalizeV2(v)

normalizeV3(v)

subVectors(v1, v2)

return v1 - v2

v2AngleBetween(a, b)

v2DistanceAndAngle(a, b)

v2dot(a, b)

v3SetX(v, x)

v3SetY(v, y)

v3SetZ(v, z)

Module contents

cadnano.oligo package

Submodules

cadnano.oligo.applycolorcmd module

class ApplyColorCommand(oligo, color)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.oligo.applysequencecmd module

class ApplySequenceCommand(oligo, sequence)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

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()

cadnano.oligo.removeoligocmd module

class RemoveOligoCommand(oligo)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

Module contents

Oligo is a lightweight convenience module that facilitates certain types of manipulation of connected groups of Strands that correspond to physical pieces of DNA. It maintains properties such as sequence, color, visiblity, and length.

cadnano.part package

Submodules

cadnano.part.changeviewpropertycmd module

cadnano.part.createvhelixcmd module

class CreateVirtualHelixCommand(part, x, y, z, length, id_num=None, properties=None, safe=True)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.part.nucleicacidpart module

cadnano.part.part module

class Part(*args, **kwargs)

Bases: cadnano.cnobject.CNObject

A Part is a group of VirtualHelix items that are on the same lattice. Parts are the model component that most directly corresponds to a DNA origami design.

Parts are always parented to the document. Parts know about their oligos, and the internal geometry of a part Copying a part recursively copies all elements in a part: StrandSets, Strands, etc

PartInstances are parented to either the document or an assembly PartInstances know global position of the part Copying a PartInstance only creates a new PartInstance with the same Part(), with a mutable parent and position field.

changeInstanceProperty(part_instance, view, key, value, use_undostack=True)

destroy()

document()

Get this objects Document

Returns:Document

editable_properties = ['name', 'color', 'is_visible', 'grid_type']

getColor()

getInstanceProperty(part_instance, key)

Get an instance property

Parameters:

• part_instance (ObjectInstance) –
• key (str) –

Returns:

object

getModelProperties()

Get the dictionary of model properties

Returns:dict – group properties

getName()

getOutlineProperties()

Convenience method for getting the properties used in the outlinerview

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

getProperty(key)

Parameters:key (str) –

instanceProperties()

Generator yielding all instance properties

partActiveChangedSignal = <cadnano.cnproxy.DummySignal object>

self, is_active

partDocumentSettingChangedSignal = <cadnano.cnproxy.DummySignal object>

self, key, value

partInstanceAddedSignal = <cadnano.cnproxy.DummySignal object>

self

partInstancePropertySignal = <cadnano.cnproxy.DummySignal object>

self, view, key, val

partParentChangedSignal = <cadnano.cnproxy.DummySignal object>

self

partPropertyChangedSignal = <cadnano.cnproxy.DummySignal object>

self, property_name, new_value

partRemovedSignal = <cadnano.cnproxy.DummySignal object>

self

partSelectedChangedSignal = <cadnano.cnproxy.DummySignal object>

self, is_selected

partZDimensionsChangedSignal = <cadnano.cnproxy.DummySignal object>

self, id_min, id_max, zoom_to_fit

setDocument(document)

set this object’s Document

Parameters:document (Document) –

setInstanceProperty(part_instance, key, value)

Set an instance property

Parameters:

• part_instance (ObjectInstance) –
• key (str) –
• value (object) –

setProperty(key, value, use_undostack=True)

Get the value of the key model properties

Parameters:

• key (str) –
• value (object) –
• use_undostack (bool, optional) – default True

cadnano.part.refresholigoscmd module

class RefreshOligosCommand(part)

Bases: cadnano.undocommand.UndoCommand

RefreshOligosCommand is a post-processing step for AutoStaple.

Normally when an xover is created, all strands in the 3’ direction are assigned the oligo of the 5’ strand. This becomes very expensive during autoStaple, because the Nth xover requires updating up to N-1 strands.

Hence, we disable oligo assignment during the xover creation step, and then do it all in one pass at the end with this command.

This command is meant for non-undoable steps, like file-io.

redo()

undo()

Doesn’t reassign

cadnano.part.refreshsegmentscmd module

class RefreshSegmentsCommand(part, id_nums)

Bases: cadnano.undocommand.UndoCommand

Add an UndoCommand to the undostack calling Part.refreshSegments

redo()

undo()

cadnano.part.removepartcmd module

class RemovePartCommand(part)

Bases: cadnano.undocommand.UndoCommand

RemovePartCommand deletes a part. Emits partRemovedSignal.

redo()

undo()

cadnano.part.removevhelixcmd module

class RemoveVirtualHelixCommand(part, id_num)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.part.renumbercmd module

class RenumberVirtualHelicesCommand(part, coord_list)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.part.resizevirtualhelixcmd module

class ResizeVirtualHelixCommand(part, id_num, is_right, delta)

Bases: cadnano.undocommand.UndoCommand

set the maximum and mininum base index in the helical direction

need to adjust all subelements in the event of a change in the minimum index

redo()

undo()

cadnano.part.translatevhelixcmd module

class TranslateVirtualHelicesCommand(part, virtual_helix_set, dx, dy, dz)

Bases: cadnano.undocommand.UndoCommand

Move Virtual Helices around

doSignals(part, vh_set)

redo()

specialUndo()

does not deselect

undo()

cadnano.part.xovercmds module

class CreateXoverCommand(part, strand5p, strand5p_idx, strand3p, strand3p_idx, update_oligo=True)

Bases: cadnano.undocommand.UndoCommand

Creates a Xover from the 3’ end of strand5p to the 5’ end of strand3p this needs to 1. preserve the old oligo of strand3p 2. install the crossover 3. apply the strand5p oligo to the strand3p

redo()

undo()

class RemoveXoverCommand(part, strand5p, strand3p)

Bases: cadnano.undocommand.UndoCommand

Removes a Xover from the 3’ end of strand5p to the 5’ end of strand3p this needs to 1. preserve the old oligo of strand3p 2. install the crossover 3. update the oligo length 4. apply the new strand3p oligo to the strand3p

redo()

undo()

Module contents

cadnano.removeinstancecmd module

class RemoveInstanceCommand(cnobj, obj_instance)

Bases: cadnano.undocommand.UndoCommand

Undo ready command for removing an instance.

Parameters:obj_instance (ObjectInstance) – Object instance remove

redo()

undo()

cadnano.strand package

Submodules

cadnano.strand.insertioncmd module

class AddInsertionCommand(strand, idx, length)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

class ChangeInsertionCommand(strand, idx, new_length)

Bases: cadnano.undocommand.UndoCommand

Changes the length of an insertion to a non-zero value the caller of this needs to handle the case where a zero length is required and call RemoveInsertionCommand

redo()

undo()

class RemoveInsertionCommand(strand, idx)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.strand.modscmd module

class AddModsCommand(document, strand, idx, mod_id)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

class RemoveModsCommand(document, strand, idx, mod_id)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.strand.resizecmd module

class ResizeCommand(strand, new_idxs, update_segments=True)

Bases: cadnano.undocommand.UndoCommand

redo()

undo()

cadnano.strand.strand module

class Strand(strandset, base_idx_low, base_idx_high, oligo=None)

Bases: cadnano.cnobject.CNObject

A Strand is a continuous stretch of bases that are all in the same StrandSet (recall: a VirtualHelix is made up of two StrandSets).

Every Strand has two endpoints. The naming convention for keeping track of these endpoints is based on the relative numeric value of those endpoints (low and high). Thus, Strand has a ‘_base_idx_low’, which is its index with the lower numeric value (typically positioned on the left), and a ‘_base_idx_high’ which is the higher-value index (typically positioned on the right)

Strands can be linked to other strands by “connections”. References to connected strands are named “_strand5p” and “_strand3p”, which correspond to the 5’ and 3’ phosphate linkages in the physical DNA strand, respectively. Since Strands can point 5’-to-3’ in either the low-to-high or high-to-low directions, connection accessor methods (connectionLow and connectionHigh) are bound during the init for convenience.

Parameters:

• strandset (StrandSet) –
• base_idx_low (int) – low index
• base_idx_high (int) – high index
• oligo (cadnano.oligo.Oligo) – optional, defaults to None.

abstractSeq()

addInsertion(idx, length, use_undostack=True)

Adds an insertion or skip at idx. length should be:

>0 for an insertion
-1 for a skip

Parameters:

• idx (int) –
• length (int) –
• use_undostack (bool) – optional, default is True

addMods(document, mod_id, idx, use_undostack=True)

Used to add mods during a merge operation.

applyAbstractSequence()

Assigns virtual index from 5’ to 3’ on strand and it’s complement location.

canInstallXoverAt(idx, from_strand, from_idx)

Assumes idx is: self.lowIdx() <= idx <= self.highIdx()

canResizeTo(new_low, new_high)

Checks to see if a resize is allowed. Similar to getResizeBounds but works for two bounds at once.

changeInsertion(idx, length, use_undostack=True)

Parameters:

• idx (int) –
• length (int) –
• use_undostack (bool) – optional, default is True

clearAbstractSequence()

clearDecoratorCommands()

clearInsertionsCommands(insertions, idxL, idxH)

clear out insertions in this range

connection3p()

connection5p()

copyAbstractSequenceToSequence()

destroy()

document()

dump5p()

generator3pStrand()

Iterate from self to the final _strand3p is None 5prime to 3prime Includes originalCount to check for circular linked list

Yields:Strand – 3’ connected Strand

generator5pStrand()

Iterate from self to the final _strand5p is None 3’ to 5’

Includes originalCount to check for circular linked list

Yields:Strand – 5’ connected Strand

getColor()

getComplementStrands()

Return the list of complement strands that overlap with this strand.

getRemoveInsertionCommands(new_idxs)

Removes Insertions, Decorators, and Modifiers that have fallen out of range of new_idxs.

For insertions, it finds the ones that have neither Staple nor Scaffold strands at the insertion idx as a result of the change of this strand to new_idxs

getResizeBounds(idx)

Determines (inclusive) low and high drag boundaries resizing from an endpoint located at idx.

When resizing from _base_idx_low:

low bound is determined by checking for lower neighbor strands.
high bound is the index of this strand's high cap, minus 1.

When resizing from _base_idx_high:

low bound is the index of this strand's low cap, plus 1.
high bound is determined by checking for higher neighbor strands.

When a neighbor is not present, just use the Part boundary.

getSequenceList()

return the list of sequences strings comprising the sequence and the inserts as a tuple with the index of the insertion [(idx, (strandItemString, insertionItemString), …]

This takes advantage of the fact the python iterates a dictionary by keys in order so if keys are indices, the insertions will iterate out from low index to high index

hasInsertionAt(idx)

hasXoverAt(idx)

An xover is necessarily at an enpoint of a strand

highIdx()

idNum()

idx3Prime()

Returns the absolute base_idx of the 3’ end of the strand. overloaded in __init__

idx5Prime()

Returns the absolute base_idx of the 5’ end of the strand. overloaded in __init__

idxs()

insertionLengthBetweenIdxs(idxL, idxH)

includes the length of insertions in addition to the bases

insertionsOnStrand(idxL=None, idxH=None)

if passed indices it will use those as a bounds

isForward()

length()

lowIdx()

merge(idx)

Check for neighbor, then merge if possible.

Parameters:idx (int) – Raises:IndexError

modifersOnStrand()

oligo()

part()

reapplySequence()

removeInsertion(idx, use_undostack=True)

Parameters:

• idx (int) –
• use_undostack (bool) – optional, default is True

removeMods(document, mod_id, idx, use_undostack=True)

Used to add mods during a merge operation.

resize(new_idxs, use_undostack=True, update_segments=True)

sequence(for_export=False)

setComplementSequence(sequence_string, strand)

This version takes anothers strand and only sets the indices that align with the given complimentary strand.

As it depends which direction this is going, and strings are stored in memory left to right, we need to test for is_forward to map the reverse compliment appropriately, as we traverse overlapping strands.

We reverse the sequence ahead of time if we are applying it 5’ to 3’, otherwise we reverse the sequence post parsing if it’s 3’ to 5’

Again, sequences are stored as strings in memory 5’ to 3’ so we need to jump through these hoops to iterate 5’ to 3’ through them correctly

Perhaps it’s wiser to merely store them left to right and reverse them at draw time, or export time

Parameters:

• sequence_string (str) –
• strand (Strand) –

Returns:

str – the used portion of the sequence_string

setConnection3p(strand)

setConnection5p(strand)

setIdxs(idxs)

setOligo(new_oligo, emit_signal=True)

setSequence(sequence_string)

Applies sequence string from 5’ to 3’ return the tuple (used, unused) portion of the sequence_string

Parameters:sequence_string (str) – Returns:tuple –

of str of form:

(used, unused)

shallowCopy()

split(idx, update_sequence=True)

Called by view items to split this strand at idx.

strandFilter()

strandHasNewOligoSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject) – strand

strandInsertionAddedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, object) – (strand, insertion object)

strandInsertionChangedSignal = <cadnano.cnproxy.DummySignal object>

#pyqtSignal(QObject, object) – (strand, insertion object)

strandInsertionRemovedSignal = <cadnano.cnproxy.DummySignal object>

#pyqtSignal(QObject, int) – # Parameters: (strand, insertion index)

strandModsAddedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, object, str, int) – (strand, document, mod_id, idx)

strandModsChangedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, object, str, int) – (strand, document, mod_id, idx)

strandModsRemovedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, object, str, int) – (strand, document, mod_id, idx)

strandRemovedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject) – strand

strandResizedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, tuple)

strandSelectedChangedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, tuple) – (strand, value)

strandSet()

strandType()

strandUpdateSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject) – strand

strandXover5pRemovedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, QObject) – (strand3p, strand5p)

totalLength()

includes the length of insertions in addition to the bases

sixb(x)

tostring(x)

Module contents

cadnano.strandset package

Submodules

cadnano.strandset.createstrandcmd module

class CreateStrandCommand(strandset, base_idx_low, base_idx_high, color, update_segments=True)

Bases: cadnano.undocommand.UndoCommand

Create a new Strand based with bounds (base_idx_low, base_idx_high), and insert it into the strandset at position strandset_idx. Also, create a new Oligo, add it to the Part, and point the new Strand at the oligo.

redo()

undo()

cadnano.strandset.mergecmd module

class MergeCommand(strand_low, strand_high, priority_strand)

Bases: cadnano.undocommand.UndoCommand

This class takes two Strands and merges them. This Class should be private to StrandSet as knowledge of a strandsetIndex outside of this of the StrandSet class implies knowledge of the StrandSet implementation

Must pass this two different strands, and nominally one of the strands again which is the priority_strand. The resulting “merged” strand has the properties of the priority_strand’s oligo. Decorators are preserved

the strand_low and strand_high must be presorted such that strand_low has a lower range than strand_high

low_strandset_idx should be known ahead of time as a result of selection

redo()

undo()

cadnano.strandset.removestrandcmd module

class RemoveStrandCommand(strandset, strand, solo=True)

Bases: cadnano.undocommand.UndoCommand

RemoveStrandCommand deletes a strand. It should only be called on strands with no connections to other strands.

Parameters:

• strandset (StrandSet) –
• strand (Strand) –
• solo (bool, optional) – set to True if only one strand is being removed to minimize signaling

redo()

undo()

cadnano.strandset.splitcmd module

class SplitCommand(strand, base_idx, update_sequence=True)

Bases: cadnano.undocommand.UndoCommand

The SplitCommand takes as input a strand and “splits” the strand in two, such that one new strand 3’ end is at base_idx, and the other new strand 5’ end is at base_idx +/- 1 (depending on the direction of the strands).

Under the hood: On redo, this command actually is creates two new copies of the original strand, resizes each and modifies their connections. On undo, the new copies are removed and the original is restored.

redo()

undo()

cadnano.strandset.strandset module

class StrandSet(is_fwd, id_num, part, initial_size)

Bases: cadnano.cnobject.CNObject

StrandSet is a container class for Strands, and provides the several publicly accessible methods for editing strands, including operations for creation, destruction, resizing, splitting, and merging strands.

Views may also query StrandSet for information that is useful in determining if edits can be made, such as the bounds of empty space in which a strand can be created or resized.

Internally StrandSet uses redundant heap and a list data structures to track Strands objects, with the list of length of a virtual helix looking like:

strand_array = [strandA, strandA, strandA, ..., None, strandB, strandB, ...]

Where every index strandA spans has a reference to strandA and strand_heap:

strand_heap = [strandA, strandB, strandC, ...]

is merely a sorted list from low index to high index of strand objects

Parameters:

• is_fwd (bool) – is this a forward or reverse StrandSet?
• id_num (int) – ID number of the virtual helix this is on
• part (Part) – Part object this is a child of
• initial_size (int) – initial_size to allocate

complementStrandSet()

Returns the complementary strandset. Used for insertions and sequence application.

Returns:StrandSet – the complementary StrandSet

createDeserializedStrand(base_idx_low, base_idx_high, color, use_undostack=False)

Passes a strand to AddStrandCommand that was read in from file input. Omits the step of checking _couldStrandInsertAtLastIndex, since we assume that deserialized strands will not cause collisions.

createStrand(base_idx_low, base_idx_high, color=None, use_undostack=True)

Assumes a strand is being created at a valid set of indices.

Parameters:

• base_idx_low (int) – low index of strand
• base_idx_high (int) – high index of strand
• color (str, optional) – default=True
• use_undostack (bool, optional) – default=True

Returns:

int – 0 if successful, -1 otherwise

destroy()

Destroy this object

document()

Get model Document

Returns:Document – the Document

dump(xover_list)

Serialize a StrandSet, and append to a xover_list of xovers adding a xover if the 3 prime end of it is founds TODO update this to support strand properties

Parameters:xover_list (list) – A list to append xovers to Returns:list of tuple – indices low and high of each strand in the StrandSet

getBoundsOfEmptyRegionContaining(base_idx)

Return the bounds of the empty region containing base index <base_idx>.

Parameters:base_idx (int) – the index of interest Returns:tuple –

of int of form:

(low_idx, high_idx)

getNeighbors(strand)

Given a Strand in this StrandSet find it’s internal neighbors

Parameters:strand (Strand) – Returns:tuple – (low neighbor, high neighbor) of types Strand or None

getOverlappingStrands(idx_low, idx_high)

Gets Strand list that overlap the given range.

Parameters:

• idx_low (int) – low index of overlap region
• idx_high (int) – high index of overlap region

Returns:

list of Strand – all Strand objects in range

getStrand(base_idx)

Returns the Strand that overlaps with base_idx

Parameters:base_idx (int) – Returns:Strand – Strand at base_idx if it exists

getStrandIndex(strand)

Get the index of strand if it exists

Returns:tuple – (bool, int) Raises:ValueError

hasStrandAt(idx_low, idx_high)

Check if set has a strand on the interval given

Parameters:

• idx_low (int) – low index
• idx_high (int) – high index

Returns:

bool – True if strandset has a strand in the region between idx_low and idx_high (both included). False otherwise

idNum()

Get the associated virtual helix ID number

Returns:int – virtual helix ID number

indexOfRightmostNonemptyBase()

Returns the high base_idx of the last strand, or 0.

isForward()

Is the set 5’ to 3’ (forward) or is it 3’ to 5’ (reverse)

Returns:bool – True if is forward, False otherwise

isReverse()

isStrandInSet(strand)

length()

length of the StrandSet and therefore also the associated virtual helix in bases

Returns:int – length of the set

mergeStrands(priority_strand, other_strand, use_undostack=True)

Merge the priority_strand and other_strand into a single new strand. The oligo of priority should be propagated to the other and all of its connections.

Parameters:

• priority_strand (Strand) – priority strand
• other_strand (Strand) – other strand
• use_undostack (bool, optional) – default=True

oligoStrandRemover(strand, cmds, solo=True)

Used for removing all Strand`s from an :class:`Oligo

Parameters:

• strand (Strand) – a strand to remove
• cmds (list) – a list of UndoCommand objects to append to
• solo (bool, optional) – to pass on to RemoveStrandCommand,
• default=True –

part()

Get model Part

Returns:Part – the Part

removeAllStrands(use_undostack=True)

Remove all Strand objects in the set

Parameters:use_undostack (bool, optional) – default=True

removeStrand(strand, use_undostack=True, solo=True)

Remove a Strand from the set

Parameters:

• strand (Strand) – the Strand to remove
• use_undostack (bool, optional) – default=True
• solo (bool, optional) – solo is an argument to enable
• signals emiting from the command in the case the command (limiting) –
• instantiated part of a larger command, default=True (is) –

resize(delta_low, delta_high)

Resize this StrandSet. Pad each end when growing otherwise don’t do anything

Parameters:

• delta_low (int) – amount to resize the low index end
• delta_high (int) – amount to resize the high index end

simpleCopy(part)

Create an empty copy (no strands) of this strandset with the only a new virtual_helix_group parent

TODO: consider renaming this method

Parameters:part (Part) – part to copy this into

splitStrand(strand, base_idx, update_sequence=True, use_undostack=True)

Break strand into two strands. Reapply sequence by default.

Parameters:

• strand (Strand) – the Strand
• base_idx (int) – the index
• update_sequence (bool, optional) – whether to emit signal, default=True
• use_undostack (bool, optional) – default=True

Returns:

bool – True if successful, False otherwise

strandCanBeSplit(strand, base_idx)

Make sure the base index is within the strand Don’t split right next to a 3Prime end Don’t split on endpoint (AKA a crossover)

Parameters:

• strand (Strand) – the Strand
• base_idx (int) – the index to split at

Returns:

bool – True if can be split, False otherwise

strandCount()

Getter for the number of Strands in the set

Returns:int – the number of Strands in the set

strandFilter()

Get the filter type for this set

Returns:str – ‘forward’ if is_fwd else ‘reverse’

strandType()

Store the enum of strand type

Returns:int – StrandType.FWD if is forward, otherwise StrandType.REV

strands()

Get raw reference to the strand_heap of this StrandSet

Returns:list – the list of strands

strandsCanBeMerged(strandA, strandB)

Only checks that the strands are of the same StrandSet and that the end points differ by 1. DOES NOT check if the Strands overlap, that should be handled by addStrand

Returns:tuple – empty tuple if the strands can’t be merged if the strands can be merged it returns the strand with the lower index in the form:

(strand_low, strand_high)

strandsetStrandAddedSignal = <cadnano.cnproxy.DummySignal object>

pyqtSignal(QObject, QObject) – strandset, strand

Module contents

Modules

cadnano

cadnano package

Subpackages

cadnano.data package

Subpackages

cadnano.data.fasta package

Module contents

This convenience module is to hard-code some example FASTA files for testing and development.

cadnano.data.genbank package

Module contents

This convenience module is to hard-code some example GenBank files for testing and development.

Submodules

cadnano.data.dnasequences module

cadnano.data.sequencemods module

Module contents

__init__.py

Created by Shawn Douglas on 2011-01-23.

cadnano.gui package

Subpackages

cadnano.gui.controllers package

Subpackages

cadnano.gui.controllers.itemcontrollers package

Subpackages

cadnano.gui.controllers.itemcontrollers.strand package

Submodules

cadnano.gui.controllers.itemcontrollers.strand.abstractstranditemcontroller module

class AbstractStrandItemController(strand_item, model_strand)

Bases: object

connectOligoSignals()

connectSignals()

Connects modelStrant signals to strandItem slots.

disconnectOligoSignals()

disconnectSignals()

reconnectOligoSignals()

cadnano.gui.controllers.itemcontrollers.strand.endpointitemcontroller module

class EndpointItemController(strandItem, modelOligo, modelStrand)

Bases: cadnano.gui.controllers.itemcontrollers.strand.abstractstranditemcontroller.AbstractStrandItemController

cadnano.gui.controllers.itemcontrollers.strand.stranditemcontroller module

class StrandItemController(strand_item, model_strand)

Bases: cadnano.gui.controllers.itemcontrollers.strand.abstractstranditemcontroller.AbstractStrandItemController

connectOligoSignals()

connectSignals()

Connects modelStrant signals to strandItem slots.

disconnectOligoSignals()

disconnectSignals()

reconnectOligoSignals()

use this for whenever a strands oligo changes

Module contents

Submodules

cadnano.gui.controllers.itemcontrollers.nucleicacidpartitemcontroller module

class NucleicAcidPartItemController(nucleicacid_part_item, model_na_part)

Bases: cadnano.gui.controllers.itemcontrollers.partitemcontroller.PartItemController

connections = [('partZDimensionsChangedSignal', 'partZDimensionsChangedSlot'), ('partParentChangedSignal', 'partParentChangedSlot'), ('partRemovedSignal', 'partRemovedSlot'), ('partPropertyChangedSignal', 'partPropertyChangedSlot'), ('partSelectedChangedSignal', 'partSelectedChangedSlot'), ('partDocumentSettingChangedSignal', 'partDocumentSettingChangedSlot'), ('partActiveVirtualHelixChangedSignal', 'partActiveVirtualHelixChangedSlot'), ('partActiveBaseInfoSignal', 'partActiveBaseInfoSlot'), ('partActiveChangedSignal', 'partActiveChangedSlot'), ('partInstancePropertySignal', 'partInstancePropertySlot'), ('partVirtualHelixAddedSignal', 'partVirtualHelixAddedSlot'), ('partVirtualHelixRemovingSignal', 'partVirtualHelixRemovingSlot'), ('partVirtualHelixRemovedSignal', 'partVirtualHelixRemovedSlot'), ('partVirtualHelixResizedSignal', 'partVirtualHelixResizedSlot'), ('partVirtualHelicesTranslatedSignal', 'partVirtualHelicesTranslatedSlot'), ('partVirtualHelicesSelectedSignal', 'partVirtualHelicesSelectedSlot'), ('partVirtualHelixPropertyChangedSignal', 'partVirtualHelixPropertyChangedSlot'), ('partOligoAddedSignal', 'partOligoAddedSlot')]

cadnano.gui.controllers.itemcontrollers.oligoitemcontroller module

class OligoItemController(oligo_item, model_oligo)

Bases: object

connectSignals()

connections = [('oligoSequenceAddedSignal', 'oligoSequenceAddedSlot'), ('oligoSequenceClearedSignal', 'oligoSequenceClearedSlot'), ('oligoPropertyChangedSignal', 'oligoPropertyChangedSlot')]

disconnectSignals()

cadnano.gui.controllers.itemcontrollers.partitemcontroller module

class PartItemController(part_item, model_part)

Bases: object

connectSignals()

connections = [('partZDimensionsChangedSignal', 'partZDimensionsChangedSlot'), ('partParentChangedSignal', 'partParentChangedSlot'), ('partRemovedSignal', 'partRemovedSlot'), ('partPropertyChangedSignal', 'partPropertyChangedSlot'), ('partSelectedChangedSignal', 'partSelectedChangedSlot'), ('partDocumentSettingChangedSignal', 'partDocumentSettingChangedSlot')]

disconnectSignals()

cadnano.gui.controllers.itemcontrollers.virtualhelixitemcontroller module

class VirtualHelixItemController(virtualhelix_item, model_part, do_wire_part, do_wire_strands)

Bases: object

Since there is no model VirtualHelix Object, we need a specialized controller for the property view

connectSignals()

disconnectSignals()

part_connections = [('partVirtualHelixPropertyChangedSignal', 'partVirtualHelixPropertyChangedSlot'), ('partVirtualHelixRemovedSignal', 'partVirtualHelixRemovedSlot'), ('partVirtualHelixResizedSignal', 'partVirtualHelixResizedSlot')]

strand_connections = [('strandsetStrandAddedSignal', 'strandAddedSlot')]

Module contents

Submodules

cadnano.gui.controllers.documentcontroller module

cadnano.gui.controllers.viewrootcontroller module

class ViewRootController(view_root, model_document)

Bases: object

connectSignals()

disconnectSignals()

Module contents

cadnano.gui.plugins package

Submodules

cadnano.gui.plugins.dummyplugin module

Module contents

cadnano.gui.ui package

Subpackages

cadnano.gui.ui.dialogs package

Submodules

cadnano.gui.ui.dialogs.dialogicons_rc module

cadnano.gui.ui.dialogs.ui_about module

cadnano.gui.ui.dialogs.ui_addseq module

cadnano.gui.ui.dialogs.ui_latticetype module

cadnano.gui.ui.dialogs.ui_mods module

cadnano.gui.ui.dialogs.ui_preferences module

cadnano.gui.ui.dialogs.ui_warning module

Module contents

cadnano.gui.ui.mainwindow package

Submodules

cadnano.gui.ui.mainwindow.icons_rc module

cadnano.gui.ui.mainwindow.svgbutton module

cadnano.gui.ui.mainwindow.ui_mainwindow module

Module contents

Module contents

cadnano.gui.views package

Subpackages

cadnano.gui.views.abstractitems package

Submodules

cadnano.gui.views.abstractitems.abstractoligoitem module

class AbstractOligoItem

Bases: object

AbstractOligoItem is a base class for oligoitems in all views. It includes slots that get connected in OligoController which can be overridden.

Slots that must be overridden should raise an exception.

oligoPropertyChangedSlot(property_key, new_value)

oligoSequenceAddedSlot(oligo)

oligoSequenceClearedSlot(oligo)

cadnano.gui.views.abstractitems.abstractpartitem module

cadnano.gui.views.abstractitems.abstracttoolmanager module

cadnano.gui.views.abstractitems.abstractvirtualhelixitem module

class AbstractVirtualHelixItem(model_virtual_helix=None, parent=None)

Bases: object

AbstractVirtualHelixItem is a base class for virtualhelixitem in all views. It includes slots that get connected in VirtualHelixItemController which can be overridden.

Slots that must be overridden should raise an exception.

cnModel()

fwdStrand(idx)

getAllPropertiesForIdNum(id_num)

getAngularProperties()

Returns:Tuple –

‘bases_per_repeat, ‘bases_per_turn’,

’twist_per_base’, ‘minor_groove_angle’

getAxisPoint(idx)

getColor()

getModelProperties()

getName()

getProperty(keys)

getSize()

getTwistPerBase()

Returns:Tuple – twist per base in degrees, eulerZ

idNum()

isActive()

part()

partItem()

revStrand(idx)

setActive(is_fwd, idx)

Makes active the virtual helix associated with this item.

setProperty(keys, values, id_nums=None)

setSize(new_size, id_nums=None)

setZ(new_z, id_nums=None)

strandAddedSlot(sender, strand)

virtualHelixPropertyChangedSlot(virtual_helix, transform)

virtualHelixRemovedSlot()

Module contents

cadnano.gui.views.outlinerview package

Submodules

cadnano.gui.views.outlinerview.cnoutlineritem module

cadnano.gui.views.outlinerview.nucleicacidpartitem module

cadnano.gui.views.outlinerview.oligoitem module

cadnano.gui.views.outlinerview.outlinerstyles module

cadnano.gui.views.outlinerview.outlinertreewidget module

cadnano.gui.views.outlinerview.virtualhelixitem module

Module contents

cadnano.gui.views.pathview package

Subpackages

cadnano.gui.views.pathview.strand package

Subpackages

cadnano.gui.views.pathview.strand.decorators package

Submodules

cadnano.gui.views.pathview.strand.decorators.abstractdecoratoritem module

cadnano.gui.views.pathview.strand.decorators.fluorophoreitem module

cadnano.gui.views.pathview.strand.decorators.insertionitem module

cadnano.gui.views.pathview.strand.decorators.skipitem module

cadnano.gui.views.pathview.strand.decorators.stapleextensionitem module

Module contents

Submodules

cadnano.gui.views.pathview.strand.abstractstranditem module

cadnano.gui.views.pathview.strand.endpointitem module

cadnano.gui.views.pathview.strand.stranditem module

cadnano.gui.views.pathview.strand.xoveritem module

Module contents

cadnano.gui.views.pathview.tools package

Submodules

cadnano.gui.views.pathview.tools.abstractpathtool module

cadnano.gui.views.pathview.tools.addseqtool module

cadnano.gui.views.pathview.tools.breaktool module

cadnano.gui.views.pathview.tools.erasetool module

cadnano.gui.views.pathview.tools.insertiontool module

cadnano.gui.views.pathview.tools.modstool module

cadnano.gui.views.pathview.tools.painttool module

cadnano.gui.views.pathview.tools.pathselection module

cadnano.gui.views.pathview.tools.pathtoolmanager module

cadnano.gui.views.pathview.tools.penciltool module

cadnano.gui.views.pathview.tools.selecttool module

cadnano.gui.views.pathview.tools.skiptool module

Module contents

Submodules

cadnano.gui.views.pathview.colorpanel module

cadnano.gui.views.pathview.nucleicacidpartitem module

cadnano.gui.views.pathview.pathextras module

cadnano.gui.views.pathview.pathrootitem module

cadnano.gui.views.pathview.pathstyles module

cadnano.gui.views.pathview.prexovermanager module

cadnano.gui.views.pathview.virtualhelixhandleitem module

cadnano.gui.views.pathview.virtualhelixitem module

Module contents

cadnano.gui.views.propertyview package

Submodules

cadnano.gui.views.propertyview.abstractproppartitem module

cadnano.gui.views.propertyview.cnpropertyitem module

cadnano.gui.views.propertyview.nucleicacidpartitem module

cadnano.gui.views.propertyview.oligoitem module

cadnano.gui.views.propertyview.propertyeditorwidget module

cadnano.gui.views.propertyview.virtualhelixitem module

Module contents

cadnano.gui.views.sliceview package

Subpackages

cadnano.gui.views.sliceview.tools package

Submodules

cadnano.gui.views.sliceview.tools.abstractslicetool module

cadnano.gui.views.sliceview.tools.createslicetool module

cadnano.gui.views.sliceview.tools.moveslicetool module

cadnano.gui.views.sliceview.tools.selectslicetool module

cadnano.gui.views.sliceview.tools.slicetoolmanager module

Module contents

Submodules

cadnano.gui.views.sliceview.griditem module

cadnano.gui.views.sliceview.nucleicacidpartitem module

cadnano.gui.views.sliceview.prexovermanager module

cadnano.gui.views.sliceview.sliceextras module

cadnano.gui.views.sliceview.slicerootitem module

cadnano.gui.views.sliceview.slicestyles module

cadnano.gui.views.sliceview.virtualhelixitem module

Module contents

Submodules

cadnano.gui.views.customqgraphicsview module

cadnano.gui.views.documentwindow module

cadnano.gui.views.grabcorneritem module

cadnano.gui.views.preferences module

cadnano.gui.views.styles module

Module contents

Submodules

cadnano.gui.palette module

Module contents

Submodules

cadnano.addinstancecmd module

class AddInstanceCommand(document, cnobj)

Bases: cadnano.undocommand.UndoCommand

Undo ready command for adding an instance.

Parameters:

• document (Document) – m
• obj_instance (ObjectInstance) – Object instance to add to Document

redo()

undo()

cadnano.assembly module

class Assembly(document)

Bases: cadnano.cnobject.CNObject

An Assembly is a collection of components, comprised recursively of various levels of individual parts and sub-assembly modules.

The purpose of an Assembly object in radnano is to arrange Parts into larger groups (which may be connected or constrained in specific ways) to facilitate the modeling of more complex designs than a single part.

addInstance(assembly_instance)

assemblyDestroyedSignal = <cadnano.cnproxy.DummySignal object>

assemblyInstanceAddedSignal = <cadnano.cnproxy.DummySignal object>

deepCopy()

Deep copy the assembly by cloning the

This leaves alone assemblyInstances, and only

To finish the job this deepCopy Assembly should be incorporated into a new ObjectInstance and therefore an assemblyInstance

destroy()

document()

instances()

objects()

undoStack()

cadnano.cadnanoqt module

cadnano.cnobject module

class CNObject(parent)

Bases: cadnano.cnproxy.ProxyObject

undoStack()

cadnano.cnproxy module

BaseObject

alias of cadnano.cnproxy.ProxyObject

class DummySignal(*args, **kwargs)

Bases: object

connect(target)

disconnect(target)

emit(*args)

class ProxyObject(parent)

Bases: object

connect(sender, bsignal, method)

deleteLater()

disconnect(sender, bsignal, method)

parent()

setParent(parent)

signals()

ProxySignal

alias of cadnano.cnproxy.DummySignal

class TempApp

Bases: object

documentWasCreatedSignal = <cadnano.cnproxy.DummySignal object>

is_temp_app = True

cadnano.color module

This allows the model to have a Color object class without the need for PyQt5.QtGui.QColor

When running the Qt Application, QColor will be used, otherwise an API compatible class is used and exported as a Color object

Currently Color objects are unused in the model and colors are stored as QColor compatible hex string in format ‘#rrggbbaa’, and therefore is not exposed in the API documentation

class Color(*args)

Bases: object

Overloaded constructor using *args to be compatible with QColor

usage:

Color(r, g, b)

or:

Color('#rrggbb') for hex

hex()

The hex string name.

Returns:str – QColor compatible hex string in format ‘#rrggbbaa’

name()

The hex string name. For QColor compatibility

Returns:str – QColor compatible hex string in format ‘#rrggbbaa’

setAlpha(a)

Set the alpha 8 bit value

Parameters:a (int) – 0 - 255

setRgb(r, g, b, a=255)

Set the r, g, b and alpha 8 bit values

Parameters:

• r (int) – 0 - 255
• g (int) – 0 - 255
• b (int) – 0 - 255
• a (int) – 0 - 255

intToColorHex(color_number)

Convert an integer to a hexadecimal string compatible with QColor

Parameters:color_number (int) – integer value of a RGB color Returns:str – QColor compatible hex string in format ‘#rrggbb’

cadnano.document module

cadnano.enum module

cadnano.objectinstance module

class ObjectInstance(reference_object, parent=None)

Bases: cadnano.cnobject.CNObject

deepCopy(reference_object, parent)

destroy()

getProperty(key)

instanceDestroyedSignal = <cadnano.cnproxy.DummySignal object>

instanceParentChangedSignal = <cadnano.cnproxy.DummySignal object>

instancePropertyChangedSignal = <cadnano.cnproxy.DummySignal object>

parent()

properties()

reference()

setProperty(key, val)

shallowCopy()

cadnano.pointquadtree module

derived from MIT licensed https://github.com/mdrasmus/compbio/blob/master/rasmus/quadtree.py adds in joins and ability to remove nodes

class Quadtree(x, y, size, min_size=4)

Bases: cadnano.pointquadtree.QuadtreeBase

getSize()

insertNode(node)

queryNode(node, distance, scale_factor=1.0)

queryPoint(query_point, distance)

removeNode(node)

class QuadtreeBase(x, y, size, min_size, parent=None, depth=0)

Bases: object

QuadTreeBase that has a configurable lower size limit of a box set class min_size before using with:

Quadtree.min_size = my_min_size

QuadTrees can have both nodes and children Quadtrees if a node’s rect spans a given Quadtree’s center

MAX_DEPTH = 20

SPLIT_THRESHOLD = 10

findNodeByNode(query_node)

look for the exact node assumes same node doesn’t exist more than once in Quadtree return the Node and the nodes parent

findNodeByRect(rect)

look for the exact node assumes same node doesn’t exist more than once in Quadtree return the Node and the nodes parent

getDepth()

getSize()

insertIntoChildren(node)

insertNode(node)

join()

query(point, rect, distance, node_results)

queryRect(rect, node_results)

rect(scale_factor=1.0)

removeNode(node)

resize()

split()

allClose(a, b)

v2Distance(a, b)

cadnano.preferences module

cadnano.proxyconfigure module

proxyConfigure(signal_type=None)

call once per application at the start of the import chain

cadnano.undocommand module

class UndoCommand(name=None)

Bases: object

addCommand(cmd)

redo()

undo()

cadnano.undostack module

class UndoStack(limit=10)

Bases: object

appendUndoStack(undocommand)

beginMacro(message)

canRedo()

canUndo()

endMacro()

push(undocommand)

redo()

setUndoLimit(lim)

undo()

cadnano.util module

util.py

beginSuperMacro(model_object, desc=None)

SuperMacros can be used to nest multiple command lists.

Normally execCommandList macros all the commands in a list. In some cases, multiple command lists need to be executed separately because of dependency issues. (e.g. in part.autoStaple, strands must be completely 1. created and 2. split before 3. xover installation.)

clamp(x, min_x, max_x)

comp(seqStr)

Returns the complement of the sequence in seqStr.

doCmd(model_object, command, use_undostack)

Helper for pushing onto the undostack

endSuperMacro(model_object)

Ends a SuperMacro. Should be called after beginSuperMacro.

execCommandList(model_object, commands, desc=None, use_undostack=True)

This is a wrapper for performing QUndoCommands, meant to ensure uniform handling of the undoStack and macro descriptions.

When using the undoStack, commands are pushed onto self.undoStack() as part of a macro with description desc. Otherwise, command redo methods are called directly.

finalizeCommands(model_object, commands, desc=None)

Used to enable interaction with the model but not push commands to the undostack. In practice:

1. Call a bunch of commands and don’t push them to the undostack AKA:

   cmd.redo()

2. call finalizeCommands() to push the cummulative change to the stack

This assumes that the UndoCommands provided this function respresent a transition from the initial state to the final state

Note

UndoCommands need to implement specialUndo (e.g. just call normal undo.)

findChild(self)

When called when self is a QGraphicsItem, iterates through self’s childItems(), placing a red rectangle (a sibling of self) around each item in sequence (press return to move between items). Since the index of each child item is displayed as it is highlighted, one can use findChild() to quickly get a reference to one of self’s children. At each step, one can type a command letter before hitting return. The command will apply to the current child. Command Letter: Action: <return> Advance to next child s<return> Show current child S<return> Show current child, hide siblings h<return> Hide current child r<return> return current child

init_logging(args=None, logdir=None)

Set up standard logging system based on parameters in args, e.g. loglevel and testing.

isLinux()

Returns True if platform is detected as Linux, otherwise False

isMac()

Returns True if platform is detected as Darwin, otherwise False

isWindows()

Returns True if platform is detected as Windows, otherwise False

loadAllPlugins()

loadPlugin(f)

markwhite(seqStr)

methodName()

Returns string containing name of the calling method.

nearest(a, l)

nowhite(seqStr)

Gets rid of non-letters in a string.

overlap(x, y, a, b)

Finds the overlap of (x, y) and (a, b). Assumes an overlap exists, i.e. y >= a and b >= x.

parse_args(argv=None, gui=None)

Uses argparse to process commandline arguments.

Returns:NameSpace object. This can easily be converted to a regular dict through – argns.__dict__

This also presents a nice command line help to the user, exposed with –help flag:

python main.py –help

If gui is set to “qt”, then the parser will use parse_known_args. Unlike parse_args(), parse_known_args() will not cause abort by show the help message and exit, if it finds any unrecognized command-line arguments.

Alternatively, you can initialize your app via:

app = QApplication(sys.argv) parse_args(app.arguments())

QApplication.arguments() returns a list of arguments with all Qt arguments stripped away. Qt command line args include:

-style=<style> -stylesheet=<stylesheet> -widgetcount -reverse -qmljsdebugger -session=<session>

rcomp(seqStr)

Returns the reverse complement of the sequence in seqStr.

read_fasta(fp)

this_path()

trace(n)

Returns a stack trace n frames deep

unloadedPlugins()

Returns a list of plugin paths that have yet to be loaded but are in the top level of one of the search directories specified in pluginDirs

Module contents

app()

getBatch()

getReopen()

initAppWithGui(app_args=None, do_exec=True)

setBatch(is_batch)

setReopen(is_reopen)

GUI

Packages

Modules

Changelog

Unreleased

• GUI: 3D view
• I/O: Export to PDB (experimental)

v2.5

Major changes and new features since cadnano 2:

• Installer: Distribution as a Python package
• Design/GUI: Helices no longer constrained to lattices
• Design/GUI: Added support for “abstract” sequences
• Design/GUI: Added support for parallel crossovers
• Code: Updated from Python 2 → 3
• Code: Updated from PyQt4 → PyQt5
• Code: Rewrote underlying data model
• Code: Better stability
• GUI: Improved hinting across views
• GUI/Installer: Removed Maya plugin code
• I/O: New file format
• I/O: Easier scripting via command-line mode
• I/O: Export to STL (experimental)

Authors

Development Leads

• Nick Conway <nick.conway@wyss.harvard.edu>
• Shawn Douglas <shawn.douglas@ucsf.edu>

Patches and Suggestions

• Rasmus Schøler Sørensen <rasmusscholer@gmail.com>

License

Copyright (c) 2016, Wyss Institute at Harvard University

Files NOT in the paths cadnano/gui and pyqttools/ are licensed as follows:

The BSD 3-Clause License

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Files in the paths cadnano/gui and pyqttools/ are licensed as follows:

GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc.

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

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Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.

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If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.

13. Use with the GNU Affero General Public License.

Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.

14. Revised Versions of this License.

The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.

Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License or any later version applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.

If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version for the Program.

Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.

15. Disclaimer of Warranty.

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM AS IS WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

16. Limitation of Liability.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

17. Interpretation of Sections 15 and 16.

If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

END OF TERMS AND CONDITIONS

How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the copyright line and a pointer to where the full notice is found.

<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year>  <name of author>

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:

<program>  Copyright (C) <year>  <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.

The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an about box.

You should also get your employer (if you work as a programmer) or school, if any, to sign a copyright disclaimer for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see http://www.gnu.org/licenses/.

The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read http://www.gnu.org/philosophy/why-not-lgpl.html.

---

nno2stl/stlwriter.py is derived from visvis/vvio/stl.py in Visvis source.

Visvis License

Visvis is subject to the (new) BSD license:

Copyright (c) 2015, Visvis development team

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
• Neither the name of Science Applied or the University of Twente, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL ALMAR KLEIN BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Visvis contributers:

• Almar Klein (Science Applied)
• Robert Schroll
• Keith Smith
• Rob Reilink (Science Applied)

How to Cite

If you use cadnano in your work, please cite its associated paper. Cadnano is free software, and we rely on grant funding to support its continued development.

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