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]

Rotate Backbone

Rotate the atoms cumulatively for each residue, adjusting the phi and psi angles for the selected residues

Rotate around the _ph_i and psi angles of a protein backbone.Rotations accumulate up the peptide backbone

Inputs

Name Type Description Default
Selection Bool Selected alpha carbons will have the dihedral rotations applied True
Phi Float Rotation to apply to the phi backbone angle 0.0
Psi Float Rotation to apply to the Psi backbone angle 0.0

Outputs

Name Type Description Default
Position Vector The Position after rotating the backbone dihedral angles [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 Read the res_id attribute from the geometry 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 Read the atomic_number attribute from the geometry corresponding to elements 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 Read the res_name attribute from the geometry 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 Read the vdw_radii attribute from the geometry 0.0

Mass

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

Outputs

Name Type Description Default
mass Float Read the mass attribute from the geometry 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 Read the Color attribute from the geometry [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

Information for each residue within the context of the chain

Inputs

Name Type Description Default
Per Chain Bool Whether to calculate these parameters indivudually for each chain, defined by chain_id 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 If the point has an edge / bond to another point 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