Topology

Topology DSSP

Calculate the secondary structure of a structure, storing it on the sec_struct attribute.

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

Inputs

Name	Type	Description	Default
Atoms	Geometry	Atomic geometry that contains vertices and edges	None
Selection	Bool	The selection of points at which to override any existing sec_struct attribute. Unselected points will still be used for the calculation	True

Outputs

Name	Type	Description	Default
Atoms	Geometry	The input Atoms with updated sec_struct attributes based on the DSSP algorithm	None

Residue Mask

Returns the index for the atom for each unique group (from res_id) for each point in that group. Allows for example, all atoms in a group to be rotated around the position of the selected atom.

In the video example, the atom_name is used to select an atom within the groups. Each atom’s position is then offset to that position, showing the group-wise selection.

Inputs

Name	Type	Description	Default
atom_name	Int	Atom to pick from the group	None
Use Fallback	Bool	Uses a calculated Unique Group ID as a fallback. Disabling can increase performance if pre-computing a Group ID for multiple nodes	True
Group ID	Int		None

Outputs

Name	Type	Description	Default
Is Valid	Bool	Group contains only one occurrance of the selected atom. None or more than one returns False	False
Index	Int	Index for the group’s atom with specified name, returns -1 if not valid	None
Position	Vector	Position of the picked point in the group, returns (0, 0, 0) if not valid	[0.0, 0.0, 0.0]
Group ID	Int		None

Backbone Positions

If the atoms have been through the “Compute Backbone” node, then the backbone atom positions will be available as attributes through this node.

In the video example, the Alpha Carbons output is styled as spheres, where the position is mixed with some of the backbone posiitons. The backbone positions can also be selected from the AA residue higher or lower with the specified offset.

Inputs

Name	Type	Description	Default
Index	Int	The index at which to read the values from	Index
Offset	Int	Offset the sampling of the	None

Outputs

Name	Type	Description	Default
O	Vector	The position of the backbone O atom for the residue	[0.0, 0.0, 0.0]
C	Vector	The position of the backbone C atom for the residue	[0.0, 0.0, 0.0]
CA	Vector	The position of the backbone CA atom for the residue	[0.0, 0.0, 0.0]
N	Vector	The position of the backbone N atom for the residue	[0.0, 0.0, 0.0]

Dihedral Phi

Outputs

Name	Type	Description	Default
Phi	Float	The calculated Phi angle for the residue, in the range of (-pi, pi)	0.0
BA⟂(BC)	Vector	The perpendicular vector from the line of BC to the point A	[0.0, 0.0, 0.0]
CD⟂(BC)	Vector	The perpendicular vector from the line of BC to the point D	[0.0, 0.0, 0.0]
BC	Vector	The vector BC corresponding to the backbone vector around which the angle is calculated	[0.0, 0.0, 0.0]

Dihedral Psi

Outputs

Name	Type	Description	Default
Psi	Float	The calculated Psi angle for the residue, in the range of (-pi, pi)	0.0
BA⟂(BC)	Vector	The perpendicular vector from the line of BC to the point A	[0.0, 0.0, 0.0]
CD⟂(BC)	Vector	The perpendicular vector from the line of BC to the point D	[0.0, 0.0, 0.0]
BC	Vector	The vector BC corresponding to the backbone vector around which the angle is calculated	[0.0, 0.0, 0.0]

Backbone Position

Return the backbone position for the peptide residue, and recalculate if the attribute doesn’t exist

Inputs

Name	Type	Description	Default
Menu	Menu	the particular backbone residue to read the value from	backbone_N
Index	Int	The index for the point to read the value from	Index
Offset	Int	The offset to apply to the Index before reading the residue	None

Outputs

Name	Type	Description	Default
Position	Vector		[0.0, 0.0, 0.0]

Backbone Vectors

Calculate Normal, Tangent and Bitangent values from protein backbone atom positions

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

Outputs

Name	Type	Description	Default
Normal	Vector	The vector used for the Normal of a curve when reading positions from a peptide backbone	[0.0, 0.0, 0.0]
Tangent	Vector	The vector used as the Tangent for a curve when reading values from a peptide backbone	[0.0, 0.0, 0.0]
Bitangent	Vector	Cross product of the Normal and Tangent	[0.0, 0.0, 0.0]

Atom ID

The atom_id attribute which is read from the file. Will be increasing linearly for each subsequent atom

Outputs

Name	Type	Description	Default
atom_id	Int	The atom_id attribute, read from geometry. Corresponds to the order of the atoms when they were read from the file	None

Chain ID

The ‘chain_id’ attribute, an integer representation of the Chain IDs from the structure. Chains are sorted alphabetically then assigned an ID startin at 0 and increasing.

Integer representation of the Chain IDs that were present in the structure

Outputs

Name	Type	Description	Default
chain_id	Int	The chain_id attribute read from the points, corresponding to the different chains that were read from the structure	None

Entity ID

The entity_id attribute of the point

The entity_id attribute read from the points, corresponding to the unique entities in the structure (that may appear several times as different chains)

Outputs

Name	Type	Description	Default
entity_id	Int	The entity_id attribute read from the points, corresponding to the unique entities in the structure (that may appear several times as different chains)	None

Residue ID

The residue_id attribute of the point, which is the assigned number of the residue inside the chain of the structure

Outputs

Name	Type	Description	Default
res_id	Int		None

Atomic Number

The atomic_number attribute, ascending from 1 for each element on the periodic table

Outputs

Name	Type	Description	Default
atomic_number	Int		None

Atom Name

The atom_name attribute, an integer representation of the atom names such as C for carbon, CA for alpha carbon

Geometry Nodes doesn’t currently support text attributes, so strings like atom names have to be first converted to integers and mapping to atom names back and forth. Definitions for the atom names are available on the GitHub page

Outputs

Name	Type	Description	Default
atom_name	Int	The atom_name attribute read from the points, an integer representation of the atom names. Corresponds to CA and O in the file etc.	None

Residue Name

The res_name attribute, an integer representation of the residue names. Amino acids are sorted alphabetically and assigned a value starting at 0. DNA starts at 40 and DNA starts at 30

Outputs

Name	Type	Description	Default
res_name	Int		None

Secondary Structure

The sec_struct attribute of the point. 0 is non-peptide, 1 is helix, 2 is sheet and 3 is loop

Outputs

Name	Type	Description	Default
sec_struct	Int		None

VDW Radii

The vdw_radii attribute of the point, corresponding the radius of the element as defined in the data dictionary. Used for scaling sphers for Style Spheres and Style Ball and Stick

Outputs

Name	Type	Description	Default
vdw_radii	Float		0.0

Mass

The mass attribute of the point, used for centre of mass calculations

Outputs

Name	Type	Description	Default
mass	Float		0.0

B Factor

The b_factor attribute of the point, representing the ‘temperature’ of the point

Outputs

Name	Type	Description	Default
b_factor	Float		0.0

Color

The Color attribute of the point, used for coloring the final generated geometry inside of the materials

Outputs

Name	Type	Description	Default
Color	Color		[0.0, 0.0, 0.0, 1.0]

Res Info

Read information about the atoms with the context of each residue the atom is in

Outputs

Name	Type	Description	Default
Factor	Float	An atom’s relative position in a residue, with the first atom being 0 and the last atom being 1	0.0
Length	Int	Number of atoms in a residue	None
Counted Index	Int	Index of an atom in a residue when counting from 0	None
First atom_name	Int	the atom_name for the first atom in a residue	None
Last atom_name	Int	The atom_name for the last atom in a residue	None
First Index	Int	Index (in the whole structure) for the first atom in a residue	None
Last Index	Int	Index (in the whole structure) for the last atom in a residue	None

Chain Info

Read information about the residues within the context of each chain

Inputs

Name	Type	Description	Default
Per Chain	Bool		True

Outputs

Name	Type	Description	Default
Factor	Float	A residues relative position along a chain. 0 being the first residue in a chain, 1 being the last	0.0
Length	Int	Number of residues in the chain	None
Counted Index	Int	Res ID along the chain if counting from 1	None
First Res ID	Int	The first Res ID in a chain (truncated chains start above 1)	None
Last Res ID	Int	The Res ID of the last residue in chain (not equal to Length if chain is truncated)	None
Index First	Int	Index in whole structure of the first atom in the chain	None
Index Last	Int	Index in the whole structure the last atom in the chain	None

Res Group ID

A unique Group ID that is calculated for every residue in the structure

Outputs

Name	Type	Description	Default
Unique Group ID	Int	A unique Group ID for eash residue	None

Topology Find Bonds

Finds bonds between atoms based on distance. Based on the vdw_radii for each point, finds other points within a certain radius to create a bond to. Does not preserve the index for the points, detect bond type, or transfer all attributes

Inputs

Name	Type	Description	Default
Atoms	Geometry	Atomic geometry that contains vertices and edges	None
Selection	Bool	Selection of atoms to apply this node to	True
Scale	Float	Scale the VDW radii of the atoms when searching for bonds	1.0

Outputs

Name	Type	Description	Default
Atoms	Geometry		None

Topology Break Bonds

Will delete a bond between atoms that already exists based on a distance cutoff, or is selected in the Selection input. Leaves the atoms unaffected

Inputs

Name	Type	Description	Default
Atoms	Geometry	Atomic geometry that contains vertices and edges	None
Selection	Bool	Selection of atoms to apply this node to	False
Cutoff	Float	Cutoff distance over which to remove bonds (Angstrom)	2.5

Outputs

Name	Type	Description	Default
Atoms	Geometry	Atomic geometry that contains vertices and edges	None

Bond Count

The number of bonds for an atom

Outputs

Name	Type	Description	Default
Is Bonded	Bool		False
Bonds	Int	The number of bonds or edges that a point has	None

Edge Info

Get information for the selected edge, evaluated on the point domain. The “Edge Index” selects the edge from all possible connected edges. Edges are unfortunately stored somewhat randomly. The resulting information is between the evaluating point and the point that the edge is between. Point Index returns -1 if not connected.

In the video example, cones are instanced on each point where the Edge Index returns a valid connection. The Edge Vector can be used to align the instanced cone along that edge. The length of the edge can be used to scale the cone to the other point. As the “Edge Index” is changed, the selected edge changes. When “Edge Index” == 3, only the atoms with 4 connections are selected, which in this model (1BNA) are just the phosphates.

Inputs

Name	Type	Description	Default
Vertex Index	Int		Index
Edge Index	Int	Index within the gorup of edges that are connected to this point	None

Outputs

Name	Type	Description	Default
Is Valid	Bool	Whether there is a valid edge corresponding to the given index	False
Point Index	Int	The index for the other point involved in this edge, -1 if not connected	None
Point Position	Vector	The position for the other point involved in this edge, (0, 0, 0) if not connected	[0.0, 0.0, 0.0]
Edge Index	Int	The index on the edge domain for the selected edge. -1 if not connected	None
Edge Vector	Vector	The vector along the selected edge. (0, 0, 0) if not connected	[0.0, 0.0, 0.0]
Edge Length	Float	Length of the selected edge, -1 if not connected	-1.0

Point Edge Angle

Calculate the angle between two edges, selected with the edge indices. For molecule bonds, combinations of [(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)] will select all possible bond angles.

In the video example, two edges are selected with their “Edge Index” values. Those atoms which aren’t valid return false and do not get instanced. The two edge vectors are used to calculate the perpendicular vector through cross product, around which the rotation for the cone is rotated. This demonstrates the ability to calculate the edge angle between the two selected edges.

Inputs

Name	Type	Description	Default
Vertex Index	Int	The index of the point at which to evaluate this node	Index
Edge A	Int	The index of the edges of this point to select	None
Edge B	Int	The index of the edges of this point to select	None

Outputs

Name	Type	Description	Default
Is Valid	Bool	Both of the selected edges are valid	False
Angle	Float	Angle between the two selected edges in radians. Returns 0 if not valid	-1.0
Edge Index A	Int	Index for “Edge A” in the Edge domain of the geometry. Returns -1 if not valid	None
Edge Index B	Int	Index for “Edge B” in the Edge domain of the geometry. Returns -1 if not valid	None
Edge Vector A	Vector	Vector from the current point to the other point in Edge A. Returns (0, 0, 0) if not valid.	[0.0, 0.0, 0.0]
Edge Vector B	Vector	Vector from the current point to the other point in Edge B. Returns (0, 0, 0) if not valid.	[0.0, 0.0, 0.0]

Points of Edge

Finds the conntected point for the selected “Edge Index”, and returns each point index for all of the points connected to that point. If the connection doesn’t exist, or the connection is back to the original point, -1 is returned.

In the video example, a new point is selected based on the “Edge Index”. At that point, all of the connecting points are exposed as indices 0, 1, 2, 3. If that index is not a valid point or connection, or the point is the same as the original point that is being evaluated, then -1 is returned.

This is one of the more complicated topology nodes, but allows indexing of the atoms that are bonded to a bonded atom. This helps with doing calculations for planar molecules.

Inputs

Name	Type	Description	Default
Edge Index	Int	Index within the gorup of edges that are connected to this point	None

Outputs

Name	Type	Description	Default
0	Int	Index for the 0th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self	None
1	Int	Index for the 1th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self	None
2	Int	Index for the 2th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self	None
3	Int	Index for the 3th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self	None
Total	Int	Number of edges conncted to the connected point, including this edge	None