Topology

Work with the bond and residue topology of structures

Animate Dihedrals

nodes.geometry.AnimateDihedrals(
    atoms=None,
    selection=True,
    frames=None,
    smoother_step=False,
    interpolate=True,
    frame=0.0,
)

GUI reference: Animate Dihedrals.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None
selection	InputBoolean	Selection of atoms to apply this node to	True
frames	InputCollection	Collection which holds the frames of the trajectory	None
smoother_step	InputBoolean	Ease in and out of the individual frames if interpolating	False
interpolate	InputBoolean	Whether to interpolate between frames of a trajectory or snap	True
frame	InputFloat	Which frame to select from the collection. The fraction component of the float is how much to interpolate between the current and next frame	0.0

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges
i.selection	BooleanSocket	Selection of atoms to apply this node to
i.frames	CollectionSocket	Collection which holds the frames of the trajectory
i.smoother_step	BooleanSocket	Ease in and out of the individual frames if interpolating
i.interpolate	BooleanSocket	Whether to interpolate between frames of a trajectory or snap
i.frame	FloatSocket	Which frame to select from the collection. The fraction component of the float is how much to interpolate between the current and next frame

Outputs

Name	Type	Description
o.atoms	GeometrySocket	Atomic geometry with new positions based on the trajectory

Atoms to CA Curves

nodes.geometry.AtomsToCACurves(
    atoms=None,
    selection=True,
    bs_smoothing=1.0,
    threshold=4.5,
)

GUI reference: Atoms to CA Curves.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None
selection	InputBoolean	Selection of atoms to apply this node to	True
bs_smoothing	InputFloat	BS Smoothing	1.0
threshold	InputFloat	Distance (Angstroms) over which subsequent CA points are treated as a new chain	4.5

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges
i.selection	BooleanSocket	Selection of atoms to apply this node to
i.bs_smoothing	FloatSocket	BS Smoothing
i.threshold	FloatSocket	Distance (Angstroms) over which subsequent CA points are treated as a new chain

Outputs

Name	Type	Description
o.curves	GeometrySocket	Curves

Atoms to Curves

nodes.geometry.AtomsToCurves(
    atoms=None,
    selection=True,
    sort_points=False,
    cutoff=6.0,
)

GUI reference: Atoms to Curves.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None
selection	InputBoolean	Points to maintain and use for splines, non-selected points are removed	True
sort_points	InputBoolean	Sort points first by atom_id and chain_id before splitting to curves	False
cutoff	InputFloat	Cutoff	6.0

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges
i.selection	BooleanSocket	Points to maintain and use for splines, non-selected points are removed
i.sort_points	BooleanSocket	Sort points first by atom_id and chain_id before splitting to curves
i.cutoff	FloatSocket	Cutoff

Outputs

Name	Type	Description
o.curves	GeometrySocket	Curves

Backbone C

nodes.geometry.BackboneC(method='Compute')

GUI reference: Backbone C.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.c	VectorSocket	C

Backbone CA

nodes.geometry.BackboneCA(method='Compute')

GUI reference: Backbone CA.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.ca	VectorSocket	CA

Backbone N

nodes.geometry.BackboneN(method='Compute')

GUI reference: Backbone N.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.n	VectorSocket	N

Backbone NH

nodes.geometry.BackboneNH(menu='Compute')

GUI reference: Backbone NH.

Parameters

Name	Type	Description	Default
menu	InputMenu | Literal['Read', 'Compute']	Menu	'Compute'

Inputs

Name	Type	Description
i.menu	MenuSocket	Menu

Outputs

Name	Type	Description
o.nh	VectorSocket	NH

Backbone O

nodes.geometry.BackboneO(method='Compute')

GUI reference: Backbone O.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.o	VectorSocket	O

Backbone Positions

nodes.geometry.BackbonePositions(method='Compute')

GUI reference: Backbone Positions.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.o	VectorSocket	The position of the backbone O atom for the residue
o.c	VectorSocket	The position of the backbone C atom for the residue
o.ca	VectorSocket	The position of the backbone CA atom for the residue
o.n	VectorSocket	The position of the backbone N atom for the residue
o.nh	VectorSocket	NH

Backbone Vector List

nodes.geometry.BackboneVectorList(ca_atoms=None, index=0)

GUI reference: Backbone Vector List.

Parameters

Name	Type	Description	Default
ca_atoms	InputGeometry	CA Atoms	None
index	InputInteger	The Index at which to sample the Position field from	0

Inputs

Name	Type	Description
i.ca_atoms	GeometrySocket	CA Atoms
i.index	IntegerSocket	The Index at which to sample the Position field from

Outputs

Name	Type	Description
o.value	VectorSocket	Output list with evaluated field values
o.ca_atoms	GeometrySocket	CA Atoms

Backbone Vectors

nodes.geometry.BackboneVectors(method='Compute')

The Vectors that are useful for a curve when reading from a peptide backbone

GUI reference: Backbone Vectors.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.normal	VectorSocket	The vector used for the Normal of a curve when reading positions from a peptide backbone
o.tangent	VectorSocket	The vector used as the Tangent for a curve when reading values from a peptide backbone
o.bitangent	VectorSocket	Cross product of the Normal and Tangent

Bond Count

nodes.geometry.BondCount(index=0)

GUI reference: Bond Count.

Parameters

Name	Type	Description	Default
index	InputInteger	Index	0

Inputs

Name	Type	Description
i.index	IntegerSocket	Index

Outputs

Name	Type	Description
o.is_bonded	BooleanSocket	If the point has an edge / bond to another point
o.bonds	IntegerSocket	The number of bonds or edges that a point has

Break Bonds

nodes.geometry.BreakBonds(atoms=None, selection=False, cutoff=2.5)

GUI reference: Break Bonds.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None
selection	InputBoolean	Selection of atoms to apply this node to	False
cutoff	InputFloat	Cutoff distance over which to remove bonds (Angstrom)	2.5

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges
i.selection	BooleanSocket	Selection of atoms to apply this node to
i.cutoff	FloatSocket	Cutoff distance over which to remove bonds (Angstrom)

Outputs

Name	Type	Description
o.atoms	GeometrySocket	Atomic geometry that contains vertices and edges

Chain Parameter

nodes.geometry.ChainParameter()

Information for each residue within the context of the chain

GUI reference: Chain Parameter.

Outputs

Name	Type	Description
o.factor	FloatSocket	A residues relative position along a chain. 0 being the first residue in a chain, 1 being the last
o.residue_count	IntegerSocket	Number of residues in the chain
o.residue_index	IntegerSocket	Res ID along the chain if counting from 1
o.first_res_id	IntegerSocket	The first Res ID in a chain (truncated chains start above 1)
o.last_res_id	IntegerSocket	The Res ID of the last residue in chain (not equal to Length if chain is truncated)
o.index_of_first	IntegerSocket	Index in whole structure of the first atom in the chain
o.index_of_last	IntegerSocket	Index in the whole structure the last atom in the chain

Color Backbone

nodes.geometry.ColorBackbone(backbone=None, side_chain=None)

GUI reference: Color Backbone.

Parameters

Name	Type	Description	Default
backbone	InputColor	Backbone	None
side_chain	InputColor	Side Chain	None

Inputs

Name	Type	Description
i.backbone	ColorSocket	Backbone
i.side_chain	ColorSocket	Side Chain

Outputs

Name	Type	Description
o.color	ColorSocket	Color

Curve Offset Dihedral

nodes.geometry.CurveOffsetDihedral(
    position=None,
    normal=None,
    index=0,
    offset=0,
)

Offset from the current point a number of points, then use their Position and Normal to calculat a dihdral angle between them

GUI reference: Curve Offset Dihedral.

Parameters

Name	Type	Description	Default
position	InputVector	The vector to use as the B & C components for Dihedral Angle calculation	None
normal	InputVector	The normal that will be added the Position to create the A & D components of the dihedral calcaulation	None
index	InputInteger	The index of the current point to calculate from	0
offset	InputInteger	The number of points to offset before calculating the angle	0

Inputs

Name	Type	Description
i.position	VectorSocket	The vector to use as the B & C components for Dihedral Angle calculation
i.normal	VectorSocket	The normal that will be added the Position to create the A & D components of the dihedral calcaulation
i.index	IntegerSocket	The index of the current point to calculate from
i.offset	IntegerSocket	The number of points to offset before calculating the angle

Outputs

Name	Type	Description
o.angle	FloatSocket	The calculated angle in radians

Dihedral Chi Angle

nodes.geometry.DihedralChiAngle()

GUI reference: Dihedral Chi Angle.

Outputs

Name	Type	Description
o.angle	FloatSocket	Angle
o.up	VectorSocket	Up
o.axis	VectorSocket	Axis

Dihedral Nucleic Angle

nodes.geometry.DihedralNucleicAngle()

GUI reference: Dihedral Nucleic Angle.

Outputs

Name	Type	Description
o.angle	FloatSocket	The angle between the vectors AB and CD, when made perpendicular to BC.
o.up	VectorSocket	The vector BA when made perpendicular to the axis BC
o.axis	VectorSocket	The axis vector BC

Dihedral Phi

nodes.geometry.DihedralPhi(menu='Compute')

GUI reference: Dihedral Phi.

Parameters

Name	Type	Description	Default
menu	InputMenu | Literal['Read', 'Compute']	Menu	'Compute'

Inputs

Name	Type	Description
i.menu	MenuSocket	Menu

Outputs

Name	Type	Description
o.phi	FloatSocket	The calculated Phi angle for the residue, in the range of (-pi, pi)
o.up	VectorSocket	The perpendicular vector from the line of BC to the point A
o.axis	VectorSocket	The vector BC corresponding to the backbone vector around which the angle is calculated

Dihedral Psi

nodes.geometry.DihedralPsi(method='Compute')

GUI reference: Dihedral Psi.

Parameters

Name	Type	Description	Default
method	InputMenu | Literal['Read', 'Compute']	Method	'Compute'

Inputs

Name	Type	Description
i.method	MenuSocket	Method

Outputs

Name	Type	Description
o.psi	FloatSocket	The calculated Psi angle for the residue, in the range of (-pi, pi)
o.up	VectorSocket	The perpendicular vector from the line of BC to the point A
o.axis	VectorSocket	The vector BC corresponding to the backbone vector around which the angle is calculated

Edge Group ID

nodes.geometry.EdgeGroupID(group_id=0)

GUI reference: Edge Group ID.

Parameters

Name	Type	Description	Default
group_id	InputInteger	Group ID	0

Inputs

Name	Type	Description
i.group_id	IntegerSocket	Group ID

Outputs

Name	Type	Description
o.difference	IntegerSocket	Difference
o.is_equal	BooleanSocket	Is Equal

Edge Info

nodes.geometry.EdgeInfo(vertex_index=0, edge_index=0)

GUI reference: Edge Info.

Parameters

Name	Type	Description	Default
vertex_index	InputInteger	Vertex Index	0
edge_index	InputInteger	Index within the gorup of edges that are connected to this point	0

Inputs

Name	Type	Description
i.vertex_index	IntegerSocket	Vertex Index
i.edge_index	IntegerSocket	Index within the gorup of edges that are connected to this point

Outputs

Name	Type	Description
o.is_valid	BooleanSocket	Whether there is a valid edge corresponding to the given index
o.point_index	IntegerSocket	The index for the other point involved in this edge, -1 if not connected
o.point_position	VectorSocket	The position for the other point involved in this edge, (0, 0, 0) if not connected
o.edge_index	IntegerSocket	The index on the edge domain for the selected edge. -1 if not connected
o.edge_vector	VectorSocket	The vector along the selected edge. (0, 0, 0) if not connected
o.edge_length	FloatSocket	Length of the selected edge, -1 if not connected

Edge Length

nodes.geometry.EdgeLength()

GUI reference: Edge Length.

Outputs

Name	Type	Description
o.length	FloatSocket	Length

Find Bonded Atom

nodes.geometry.FindBondedAtom(
    index=0,
    method='Exact',
    atom_name='N',
    distance=2,
)

GUI reference: Find Bonded Atom.

Parameters

Name	Type	Description	Default
index	InputInteger	Index	0
method	InputMenu | Literal['Any', 'Exact']	Method	'Exact'
atom_name	InputMenu | Literal['N', 'CA', 'C', 'O', 'CB', 'CG', 'CG1', 'CG2', 'OG', 'OG1', 'SG', 'CD', 'CD1', 'CD2', 'ND1', 'ND2', 'OD1', 'OD2', 'SD', 'CE', 'CE1', 'CE2', 'CE3', 'NE', 'NE1', 'NE2', 'OE1', 'OE2', 'CH2', 'NH1', 'NH2', 'OH', 'CZ', 'CZ2', 'CZ3', 'NZ', 'OXT', 'P', 'O1P', 'OP1', 'OP2', 'O2P', 'O5', 'C5', 'C4', 'O4', 'C3', 'O3', 'C2', 'O2', 'C1', 'N1', 'N9', 'N3', 'C8', 'N7', 'C5', 'C6', 'N6', 'C2', 'C4', 'O6', 'N2', 'N4', 'O2', 'O4', 'C7']	Atom Name	'N'
distance	InputInteger	Distance	2

Inputs

Name	Type	Description
i.index	IntegerSocket	Index
i.method	MenuSocket	Method
i.atom_name	MenuSocket	Atom Name
i.distance	IntegerSocket	Distance

Outputs

Name	Type	Description
o.is_valid	BooleanSocket	Is Valid
o.index	IntegerSocket	Index
o.position	VectorSocket	Position

Find Bonds

nodes.geometry.FindBonds(atoms=None, selection=True, scale=1.0)

GUI reference: Find Bonds.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None
selection	InputBoolean	Selection of atoms to apply this node to	True
scale	InputFloat	Scale the VDW radii of the atoms when searching for bonds	1.0

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges
i.selection	BooleanSocket	Selection of atoms to apply this node to
i.scale	FloatSocket	Scale the VDW radii of the atoms when searching for bonds

Outputs

Name	Type	Description
o.atoms	GeometrySocket	Atoms

Menu Residue Mask

nodes.geometry.MenuResidueMask(atom_name='N')

GUI reference: Menu Residue Mask.

Parameters

Name	Type	Description	Default
atom_name	InputMenu | Literal['N', 'CA', 'C', 'O', 'CB', 'CG', 'CG1', 'CG2', 'OG', 'OG1', 'SG', 'CD', 'CD1', 'CD2', 'ND1', 'ND2', 'OD1', 'OD2', 'SD', 'CE', 'CE1', 'CE2', 'CE3', 'NE', 'NE1', 'NE2', 'OE1', 'OE2', 'CH2', 'NH1', 'NH2', 'OH', 'CZ', 'CZ2', 'CZ3', 'NZ', 'OXT', 'P', 'O1P', 'OP1', 'OP2', 'O2P', 'O5', 'C5', 'C4', 'O4', 'C3', 'O3', 'C2', 'O2', 'C1', 'N1', 'N9', 'N3', 'C8', 'N7', 'C5', 'C6', 'N6', 'C2', 'C4', 'O6', 'N2', 'N4', 'O2', 'O4', 'C7']	Atom Name	'N'

Inputs

Name	Type	Description
i.atom_name	MenuSocket	Atom Name

Outputs

Name	Type	Description
o.is_valid	BooleanSocket	Group contains only one occurrance of the selected atom. None or more than one returns False
o.index	IntegerSocket	Index for the group’s atom with specified name, returns -1 if not valid
o.position	VectorSocket	Position of the picked point in the group, returns (0, 0, 0) if not valid

Menu Residue Name

nodes.geometry.MenuResidueName(residue_name='ALA')

GUI reference: Menu Residue Name.

Parameters

Name	Type	Description	Default
residue_name	InputMenu | Literal['UNK', 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'SNC', 'MSE', 'ASH', 'CYM', 'CYX', 'GLH', 'HID', 'HIE', 'HIP', 'HYP', 'LYN', 'DA', 'DC', 'DG', 'DT', 'PST', 'rA', 'rC', 'rG', 'rU']	Residue Name	'ALA'

Inputs

Name	Type	Description
i.residue_name	MenuSocket	Residue Name

Outputs

Name	Type	Description
o.res_name	IntegerSocket	res_name
o.selection	BooleanSocket	Selection

Nucleic Chi

nodes.geometry.NucleicChi(position=None, selection=True, x1=0.0)

GUI reference: Nucleic Chi.

Parameters

Name	Type	Description	Default
position	InputVector	Position	None
selection	InputBoolean	The resulting selection must overlap with this input selection	True
x1	InputFloat	Amount to rotate around the axis	0.0

Inputs

Name	Type	Description
i.position	VectorSocket	Position
i.selection	BooleanSocket	The resulting selection must overlap with this input selection
i.x1	FloatSocket	Amount to rotate around the axis

Outputs

Name	Type	Description
o.position	VectorSocket	Transformed vector

Nucleic Dihedral

nodes.geometry.NucleicDihedral(
    position=None,
    selection=True,
    alpha=0.0,
    beta=0.0,
    gamma=0.0,
    epsilon=0.0,
    zeta=0.0,
)

GUI reference: Nucleic Dihedral.

Parameters

Name	Type	Description	Default
position	InputVector	Position	None
selection	InputBoolean	The resulting selection must overlap with this input selection	True
alpha	InputFloat	Alpha	0.0
beta	InputFloat	Beta	0.0
gamma	InputFloat	Gamma	0.0
epsilon	InputFloat	Epsilon	0.0
zeta	InputFloat	Amount to rotate around the axis	0.0

Inputs

Name	Type	Description
i.position	VectorSocket	Position
i.selection	BooleanSocket	The resulting selection must overlap with this input selection
i.alpha	FloatSocket	Alpha
i.beta	FloatSocket	Beta
i.gamma	FloatSocket	Gamma
i.epsilon	FloatSocket	Epsilon
i.zeta	FloatSocket	Amount to rotate around the axis

Outputs

Name	Type	Description
o.position	VectorSocket	Transformed vector

Peptide Chi

nodes.geometry.PeptideChi(
    position=None,
    selection=True,
    x1=0.0,
    x2=0.0,
    x3=0.0,
    x4=0.0,
    x5=0.0,
)

GUI reference: Peptide Chi.

Parameters

Name	Type	Description	Default
position	InputVector	Position	None
selection	InputBoolean	Selection	True
x1	InputFloat	X1	0.0
x2	InputFloat	X2	0.0
x3	InputFloat	X3	0.0
x4	InputFloat	X4	0.0
x5	InputFloat	X5	0.0

Inputs

Name	Type	Description
i.position	VectorSocket	Position
i.selection	BooleanSocket	Selection
i.x1	FloatSocket	X1
i.x2	FloatSocket	X2
i.x3	FloatSocket	X3
i.x4	FloatSocket	X4
i.x5	FloatSocket	X5

Outputs

Name	Type	Description
o.position	VectorSocket	Position

Peptide Dihedral

nodes.geometry.PeptideDihedral(position=None, selection=True, phi=0.0, psi=0.0)

GUI reference: Peptide Dihedral.

Parameters

Name	Type	Description	Default
position	InputVector	Position	None
selection	InputBoolean	The resulting selection must overlap with this input selection	True
phi	InputFloat	Phi	0.0
psi	InputFloat	Psi	0.0

Inputs

Name	Type	Description
i.position	VectorSocket	Position
i.selection	BooleanSocket	The resulting selection must overlap with this input selection
i.phi	FloatSocket	Phi
i.psi	FloatSocket	Psi

Outputs

Name	Type	Description
o.position	VectorSocket	Transformed vector

Point Edge Angle

nodes.geometry.PointEdgeAngle(vertex_index=0, edge_a=0, edge_b=1)

GUI reference: Point Edge Angle.

Parameters

Name	Type	Description	Default
vertex_index	InputInteger	The index of the point at which to evaluate this node	0
edge_a	InputInteger	The index of the edges of this point to select	0
edge_b	InputInteger	The index of the edges of this point to select	1

Inputs

Name	Type	Description
i.vertex_index	IntegerSocket	The index of the point at which to evaluate this node
i.edge_a	IntegerSocket	The index of the edges of this point to select
i.edge_b	IntegerSocket	The index of the edges of this point to select

Outputs

Name	Type	Description
o.is_valid	BooleanSocket	Both of the selected edges are valid
o.angle	FloatSocket	Angle between the two selected edges in radians. Returns 0 if not valid
o.edge_index_a	IntegerSocket	Index for “Edge A” in the Edge domain of the geometry. Returns -1 if not valid
o.edge_index_b	IntegerSocket	Index for “Edge B” in the Edge domain of the geometry. Returns -1 if not valid
o.edge_vector_a	VectorSocket	Vector from the current point to the other point in Edge A. Returns (0, 0, 0) if not valid.
o.edge_vector_b	VectorSocket	Vector from the current point to the other point in Edge B. Returns (0, 0, 0) if not valid.

Points of Edge

nodes.geometry.PointsOfEdge(vertex_index=0, edge_index=0)

GUI reference: Points of Edge.

Parameters

Name	Type	Description	Default
vertex_index	InputInteger	Vertex Index	0
edge_index	InputInteger	Index within the gorup of edges that are connected to this point	0

Inputs

Name	Type	Description
i.vertex_index	IntegerSocket	Vertex Index
i.edge_index	IntegerSocket	Index within the gorup of edges that are connected to this point

Outputs

Name	Type	Description
o._0	IntegerSocket	Index for the 0th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self
o._1	IntegerSocket	Index for the 1th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self
o._2	IntegerSocket	Index for the 2th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self
o._3	IntegerSocket	Index for the 3th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self
o.total	IntegerSocket	Number of edges conncted to the connected point, including this edge

Residue Dihedral Angle

nodes.geometry.ResidueDihedralAngle(a=6, c=2, d=3)

GUI reference: Residue Dihedral Angle.

Parameters

Name	Type	Description	Default
a	InputInteger	Atom to pick from the group	6
c	InputInteger	Atom to pick from the group	2
d	InputInteger	Atom to pick from the group	3

Inputs

Name	Type	Description
i.a	IntegerSocket	Atom to pick from the group
i.c	IntegerSocket	Atom to pick from the group
i.d	IntegerSocket	Atom to pick from the group

Outputs

Name	Type	Description
o.value	FloatSocket	Value
o.ba_bc	VectorSocket	The vector BA when made perpendicular to the axis BC
o.cd_bc	VectorSocket	The Vector CD when makde perpendicular to the axis BC
o.bc	VectorSocket	The axis vector BC

Residue Mask

nodes.geometry.ResidueMask(atom_name=1)

GUI reference: Residue Mask.

Parameters

Name	Type	Description	Default
atom_name	InputInteger	Atom to pick from the group	1

Inputs

Name	Type	Description
i.atom_name	IntegerSocket	Atom to pick from the group

Outputs

Name	Type	Description
o.is_valid	BooleanSocket	Group contains only one occurrance of the selected atom. None or more than one returns False
o.index	IntegerSocket	Index for the group’s atom with specified name, returns -1 if not valid
o.position	VectorSocket	Position of the picked point in the group, returns (0, 0, 0) if not valid

Residue Parameter

nodes.geometry.ResidueParameter()

GUI reference: Residue Parameter.

Outputs

Name	Type	Description
o.factor	FloatSocket	An atom’s relative position in a residue, with the first atom being 0 and the last atom being 1
o.atom_count	IntegerSocket	Number of atoms in a residue
o.atom_index	IntegerSocket	Index of an atom in a residue when counting from 0
o.first_atom_name	IntegerSocket	the atom_name for the first atom in a residue
o.last_atom_name	IntegerSocket	The atom_name for the last atom in a residue
o.index_of_first	IntegerSocket	Index (in the whole structure) for the first atom in a residue
o.index_of_last	IntegerSocket	Index (in the whole structure) for the last atom in a residue

Sample Nearest Atoms

nodes.geometry.SampleNearestAtoms(atoms=None)

GUI reference: Sample Nearest Atoms.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges

Outputs

Name	Type	Description
o.color	ColorSocket	Color
o.b_factor	FloatSocket	b_factor
o.atomic_number	IntegerSocket	atomic_number
o.chain_id	IntegerSocket	chain_id
o.res_id	IntegerSocket	res_id
o.res_name	IntegerSocket	res_name

Set Chi Angle

nodes.geometry.SetChiAngle(
    geometry=None,
    selection=True,
    x1=0.0,
    x2=0.0,
    x3=0.0,
    x4=0.0,
    x5=0.0,
)

GUI reference: Set Chi Angle.

Parameters

Name	Type	Description	Default
geometry	InputGeometry	Geometry	None
selection	InputBoolean	Selection	True
x1	InputFloat	X1	0.0
x2	InputFloat	X2	0.0
x3	InputFloat	X3	0.0
x4	InputFloat	X4	0.0
x5	InputFloat	X5	0.0

Inputs

Name	Type	Description
i.geometry	GeometrySocket	Geometry
i.selection	BooleanSocket	Selection
i.x1	FloatSocket	X1
i.x2	FloatSocket	X2
i.x3	FloatSocket	X3
i.x4	FloatSocket	X4
i.x5	FloatSocket	X5

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

Set Nucleic Dihedral

nodes.geometry.SetNucleicDihedral(
    geometry=None,
    selection=True,
    alpha=0.0,
    beta=0.0,
    gamma=0.0,
    epsilon=0.0,
    zeta=0.0,
)

GUI reference: Set Nucleic Dihedral.

Parameters

Name	Type	Description	Default
geometry	InputGeometry	Geometry	None
selection	InputBoolean	The resulting selection must overlap with this input selection	True
alpha	InputFloat	Alpha	0.0
beta	InputFloat	Beta	0.0
gamma	InputFloat	Gamma	0.0
epsilon	InputFloat	Epsilon	0.0
zeta	InputFloat	Amount to rotate around the axis	0.0

Inputs

Name	Type	Description
i.geometry	GeometrySocket	Geometry
i.selection	BooleanSocket	The resulting selection must overlap with this input selection
i.alpha	FloatSocket	Alpha
i.beta	FloatSocket	Beta
i.gamma	FloatSocket	Gamma
i.epsilon	FloatSocket	Epsilon
i.zeta	FloatSocket	Amount to rotate around the axis

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

Set Phi Psi Angle

nodes.geometry.SetPhiPsiAngle(geometry=None, selection=True, phi=0.0, psi=0.0)

GUI reference: Set Phi Psi Angle.

Parameters

Name	Type	Description	Default
geometry	InputGeometry	Geometry	None
selection	InputBoolean	Selection	True
phi	InputFloat	Phi	0.0
psi	InputFloat	Psi	0.0

Inputs

Name	Type	Description
i.geometry	GeometrySocket	Geometry
i.selection	BooleanSocket	Selection
i.phi	FloatSocket	Phi
i.psi	FloatSocket	Psi

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

Set URes ID

nodes.geometry.SetUResID(geometry=None)

GUI reference: Set URes ID.

Parameters

Name	Type	Description	Default
geometry	InputGeometry	Geometry	None

Inputs

Name	Type	Description
i.geometry	GeometrySocket	Geometry

Outputs

Name	Type	Description
o.geometry	GeometrySocket	Geometry

Structure Parameter

nodes.geometry.StructureParameter()

GUI reference: Structure Parameter.

Outputs

Name	Type	Description
o.atom_factor	FloatSocket	Factor of the atom within the structure, which is the relative position of the Index within the overall structure between 0 and 1
o.index	IntegerSocket	Index of the point within the structure. Equal to the Index input node
o.atom_count	IntegerSocket	Number of atoms in the structure, equal to the size of the Point Domain
o.index_of_first	IntegerSocket	Index of first atom in the entire structure, which will always be 0
o.index_of_last	IntegerSocket	Index of last atom in the entire structure. Equal to Atom Count - 1
o.residue_factor	FloatSocket	Residue Factor
o.residue_index	IntegerSocket	A unique Group ID that increases whenever Sub Group ID or Group ID change
o.residue_count	IntegerSocket	Residue Count

Switch Residue Name

nodes.geometry.SwitchResidueName(
    ala=6,
    arg=6,
    asn=6,
    asp=6,
    cys=6,
    glu=6,
    gln=6,
    gly=6,
    his=6,
    ile=6,
    leu=6,
    lys=6,
    met=6,
    phe=6,
    pro=6,
    ser=6,
    thr=6,
    trp=6,
    tyr=6,
    val=6,
)

GUI reference: Switch Residue Name.

Parameters

Name	Type	Description	Default
ala	InputInteger	ALA	6
arg	InputInteger	ARG	6
asn	InputInteger	ASN	6
asp	InputInteger	ASP	6
cys	InputInteger	CYS	6
glu	InputInteger	GLU	6
gln	InputInteger	GLN	6
gly	InputInteger	GLY	6
his	InputInteger	HIS	6
ile	InputInteger	ILE	6
leu	InputInteger	LEU	6
lys	InputInteger	LYS	6
met	InputInteger	MET	6
phe	InputInteger	PHE	6
pro	InputInteger	PRO	6
ser	InputInteger	SER	6
thr	InputInteger	THR	6
trp	InputInteger	TRP	6
tyr	InputInteger	TYR	6
val	InputInteger	VAL	6

Inputs

Name	Type	Description
i.ala	IntegerSocket	ALA
i.arg	IntegerSocket	ARG
i.asn	IntegerSocket	ASN
i.asp	IntegerSocket	ASP
i.cys	IntegerSocket	CYS
i.glu	IntegerSocket	GLU
i.gln	IntegerSocket	GLN
i.gly	IntegerSocket	GLY
i.his	IntegerSocket	HIS
i.ile	IntegerSocket	ILE
i.leu	IntegerSocket	LEU
i.lys	IntegerSocket	LYS
i.met	IntegerSocket	MET
i.phe	IntegerSocket	PHE
i.pro	IntegerSocket	PRO
i.ser	IntegerSocket	SER
i.thr	IntegerSocket	THR
i.trp	IntegerSocket	TRP
i.tyr	IntegerSocket	TYR
i.val	IntegerSocket	VAL

Outputs

Name	Type	Description
o.output	IntegerSocket	Output

Topology DSSP

nodes.geometry.TopologyDSSP(atoms=None)

Calculate the secondary structure attributes for the protein chains, based on the 1983 Kabsch algorithm

GUI reference: Topology DSSP.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atomic geometry that contains vertices and edges	None

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atomic geometry that contains vertices and edges

Outputs

Name	Type	Description
o.atoms	GeometrySocket	The input Atoms with updated sec_struct attributes based on the DSSP algorithm

Unique Chain ID

nodes.geometry.UniqueChainID(cutoff=4.5)

Compute a unique Group ID based on the chain_id attribute, but also incrememnting if subsequent points are over a cutoff distance from each other

GUI reference: Unique Chain ID.

Parameters

Name	Type	Description	Default
cutoff	InputFloat	Threshold distance over which the next points are considered to be part of a new chain	4.5

Inputs

Name	Type	Description
i.cutoff	FloatSocket	Threshold distance over which the next points are considered to be part of a new chain

Outputs

Name	Type	Description
o.group_id	IntegerSocket	Calculated Group ID attribute

Unique Residue ID

nodes.geometry.UniqueResidueID()

GUI reference: Unique Residue ID.

Outputs

Name	Type	Description
o.group_id	IntegerSocket	A unique Group ID for eash residue

Visualize Chi Angle

nodes.geometry.VisualizeChiAngle(
    geometry=None,
    selection=True,
    factor=0.5,
    value=0.61,
    radius=0.2,
)

GUI reference: Visualize Chi Angle.

Parameters

Name	Type	Description	Default
geometry	InputGeometry	Geometry	None
selection	InputBoolean	Selection	True
factor	InputFloat	Factor	0.5
value	InputFloat	A value which will be scaled appropriately for the world	0.61
radius	InputFloat	Radius	0.2

Inputs

Name	Type	Description
i.geometry	GeometrySocket	Geometry
i.selection	BooleanSocket	Selection
i.factor	FloatSocket	Factor
i.value	FloatSocket	A value which will be scaled appropriately for the world
i.radius	FloatSocket	Radius

Outputs

Name	Type	Description
o.mesh	GeometrySocket	Mesh
o.curve	GeometrySocket	Curve

Visualize Relative Atoms

nodes.geometry.VisualizeRelativeAtoms(
    atoms=None,
    selection=True,
    scale=1.0,
    position=None,
    target_index=100,
    target_position=None,
)

GUI reference: Visualize Relative Atoms.

Parameters

Name	Type	Description	Default
atoms	InputGeometry	Atoms	None
selection	InputBoolean	Selection	True
scale	InputFloat	Scale	1.0
position	InputVector	Position	None
target_index	InputInteger	Index for the selected point to measure to	100
target_position	InputVector	Target Position	None

Inputs

Name	Type	Description
i.atoms	GeometrySocket	Atoms
i.selection	BooleanSocket	Selection
i.scale	FloatSocket	Scale
i.position	VectorSocket	Position
i.target_index	IntegerSocket	Index for the selected point to measure to
i.target_position	VectorSocket	Target Position

Outputs

Name	Type	Description
o.instances	GeometrySocket	Instances