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`		None
Selection	`Bool`		`True`

Outputs

Name	Type	Description	Default
Atoms	`Geometry`		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
Offset	`Int`		None

Outputs

Name	Type	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

Inputs

Name	Type	Description	Default

Outputs

Name	Type	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

Inputs

Name	Type	Description	Default

Outputs

Name	Type	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	Default
Index	`Int`	`Index`
Menu	`Menu`	`backbone_N`
Offset	`Int`	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

Inputs

Name	Type	Description	Default

Outputs

Name	Type	Default
Normal	`Vector`	`[0.0, 0.0, 0.0]`
Tangent	`Vector`	`[0.0, 0.0, 0.0]`
Bitangent	`Vector`	`[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

Inputs

Name	Type	Description	Default

Outputs

Name	Type	Description	Default
atom_id	`Int`		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.

Inputs

Name	Type	Description	Default

Outputs

Name	Type	Description	Default
chain_id	`Int`		None

Atom Name

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

Inputs

Name	Type	Description	Default

Outputs

Name	Type	Description	Default
atom_name	`Int`		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

Inputs

Name	Type	Description	Default

Outputs

Name	Type	Description	Default
res_name	`Int`		None

Res Info

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

Inputs

Name	Type	Description	Default

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

Inputs

Name	Type	Description	Default

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

Inputs

Name	Type	Description	Default

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
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
Edge A	`Int`	Index within the gorup of edges that are connected to this point	None
Edge B	`Int`	Index within the gorup of edges that are connected to this point	None

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	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