DNA

Nodes for working with oxDNA and other DNA models

DNA From Curve

nodes.geometry.DNAFromCurve(
    curves=None,
    base_resolution=0,
    menu='Static',
    wind=1.0,
    base_instance='Instance',
)

GUI reference: DNA From Curve.

Parameters

Name	Type	Description	Default
curves	InputGeometry	Curves	None
base_resolution	InputInteger	Base Resolution	0
menu	InputMenu | Literal['Static', 'Simulate']	Menu	'Static'
wind	InputFloat	Wind	1.0
base_instance	InputMenu | Literal['Instance', 'Realize']	Base Instance	'Instance'

Inputs

Name	Type	Description
i.curves	GeometrySocket	Curves
i.base_resolution	IntegerSocket	Base Resolution
i.menu	MenuSocket	Menu
i.wind	FloatSocket	Wind
i.base_instance	MenuSocket	Base Instance

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

oxDNA Realize Vectors

nodes.geometry.OxDNARealizeVectors(atoms=None)

GUI reference: oxDNA Realize Vectors.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Geometry to duplicate elements of	None

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Geometry to duplicate elements of

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

oxDNA Recover Vectors

nodes.geometry.OxDNARecoverVectors(geometry=None)

GUI reference: oxDNA Recover Vectors.

Parameters

Name	Type	Description	Default
geometry	InputGeometry	Geometry	None

Inputs

Name	Type	Description
i.geometry	GeometrySocket	Geometry

Outputs

Name	Type	Description
o.atoms	GeometrySocket	Atoms

oxDNA Style Ribbon

nodes.geometry.OxDNAStyleRibbon(
    atoms=None,
    selection=True,
    quality=2,
    backbone_shape='Arrows',
    backbone_radius=0.8,
    ball_radius=2.0,
    arrow_taper=0.3,
    base_shape='Sphere',
    base_geometry=None,
    base_scale=None,
    stem_scale=None,
    base_colors='Uniform',
    bases=None,
    a=None,
    c=None,
    g=None,
    t_u=None,
    strand_color='Color',
    strands=None,
    strand_1=None,
    strand_2=None,
    strand_3=None,
    strand_4=None,
    shade_smooth=True,
    material=None,
)

GUI reference: oxDNA Style Ribbon.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atoms	None
selection	InputBoolean	Selection of atoms to apply this node to	True
quality	InputInteger	Quality	2
backbone_shape	InputMenu | Literal['Arrows', 'Curve']	Backbone Shape	'Arrows'
backbone_radius	InputFloat	Backbone Radius	0.8
ball_radius	InputFloat	Ball Radius	2.0
arrow_taper	InputFloat	Arrow Taper	0.3
base_shape	InputMenu | Literal['Sphere', 'Cylinder', 'None']	Base Shape	'Sphere'
base_geometry	InputGeometry	Base Geometry	None
base_scale	InputVector	Base Scale	None
stem_scale	InputVector	Stem Scale	None
base_colors	InputMenu | Literal['Uniform', 'Base', 'Color']	Base Colors	'Uniform'
bases	InputColor	Bases	None
a	InputColor	A	None
c	InputColor	C	None
g	InputColor	G	None
t_u	InputColor	T / U	None
strand_color	InputMenu | Literal['Uniform', 'Strand', 'Color']	Strand Color	'Color'
strands	InputColor	Becomes the output value if it is chosen by the menu input	None
strand_1	InputColor	Strand 1	None
strand_2	InputColor	Strand 2	None
strand_3	InputColor	Strand 3	None
strand_4	InputColor	Strand 4	None
shade_smooth	InputBoolean	Shade Smooth	True
material	InputMaterial	Material to apply to the resulting geometry	None

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atoms
i.selection	BooleanSocket	Selection of atoms to apply this node to
i.quality	IntegerSocket	Quality
i.backbone_shape	MenuSocket	Backbone Shape
i.backbone_radius	FloatSocket	Backbone Radius
i.ball_radius	FloatSocket	Ball Radius
i.arrow_taper	FloatSocket	Arrow Taper
i.base_shape	MenuSocket	Base Shape
i.base_geometry	GeometrySocket	Base Geometry
i.base_scale	VectorSocket	Base Scale
i.stem_scale	VectorSocket	Stem Scale
i.base_colors	MenuSocket	Base Colors
i.bases	ColorSocket	Bases
i.a	ColorSocket	A
i.c	ColorSocket	C
i.g	ColorSocket	G
i.t_u	ColorSocket	T / U
i.strand_color	MenuSocket	Strand Color
i.strands	ColorSocket	Becomes the output value if it is chosen by the menu input
i.strand_1	ColorSocket	Strand 1
i.strand_2	ColorSocket	Strand 2
i.strand_3	ColorSocket	Strand 3
i.strand_4	ColorSocket	Strand 4
i.shade_smooth	BooleanSocket	Shade Smooth
i.material	MaterialSocket	Material to apply to the resulting geometry

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

oxDNA Vectors

nodes.geometry.OxDNAVectors(index=0)

GUI reference: oxDNA Vectors.

Parameters

Name	Type	Description	Default
index	InputInteger	Index	0

Inputs

Name	Type	Description
i.index	IntegerSocket	Index

Outputs

Name	Type	Description
o.base_vector	VectorSocket	base_vector
o.base_normal	VectorSocket	base_normal
o.backbone_offset	VectorSocket	Backbone Offset
o.base_offset	VectorSocket	Base Offset
o.rotation	RotationSocket	Rotation