Topology

DSSP

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

Inputs

Name	Type	Description	Default
Atoms	Geometry		required
Selection	Bool		True

Outputs

Name	Type	Description	Default
Atoms	Geometry		required

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	1
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		0

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	0
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		0

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
Offset	Int		0

Outputs

Name	Type	Description	Default
O	Vector		[0.0, 0.0, 0.0]
C	Vector		[0.0, 0.0, 0.0]
CA	Vector		[0.0, 0.0, 0.0]
N	Vector		[0.0, 0.0, 0.0]

Dihedral Phi

Outputs

Name	Type	Description	Default
Phi	Float		0.0
BA⟂(BC)	Vector		[0.0, 0.0, 0.0]
CD⟂(BC)	Vector		[0.0, 0.0, 0.0]
BC	Vector		[0.0, 0.0, 0.0]

Dihedral Psi

Outputs

Name	Type	Description	Default
Psi	Float		0.0
BA⟂(BC)	Vector		[0.0, 0.0, 0.0]
CD⟂(BC)	Vector		[0.0, 0.0, 0.0]
BC	Vector		[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
Index	Int		0
Menu	Menu		backbone_N
Offset	Int		0

Outputs

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

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	0
Counted Index	Int	Index of an atom in a residue when counting from 0	0
First atom_name	Int	the atom_name for the first atom in a residue	0
Last atom_name	Int	The atom_name for the last atom in a residue	0
First Index	Int	Index (in the whole structure) for the first atom in a residue	0
Last Index	Int	Index (in the whole structure) for the last atom in a residue	0

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	0
Counted Index	Int	Res ID along the chain if counting from 1	0
First Res ID	Int	The first Res ID in a chain (truncated chains start above 1)	0
Last Res ID	Int	The Res ID of the last residue in chain (not equal to Length if chain is truncated)	0
Index First	Int	Index in whole structure of the first atom in the chain	0
Index Last	Int	Index in the whole structure the last atom in the chain	0

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	0

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	required
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		required

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	required
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	required

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	0

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
Edge Index	Int	Index within the gorup of edges that are connected to this point	0

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	-1
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	-1
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

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
Edge A	Int	Index within the gorup of edges that are connected to this point	0
Edge B	Int	Index within the gorup of edges that are connected to this point	1

Outputs

Name	Type	Description	Default
Is Valid	Bool	Whether both edges are valid corresponding to the given indices and are not the same	False
Angle	Float	Angle between the two selected edges in radians. Returns -1 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	-1
Edge Index B	Int	Index for “Edge B” in the Edge domain of the geometry. Returns -1 if not valid	-1
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	0

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	-1
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	-1
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	-1
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	-1
Total	Int	Number of edges conncted to the connected point, including this edge	0