Topology
Topology DSSP
Calculate the secondary structure attributes for the protein chains, based on the 1983 Kabsch algorithm
Calculate the secondary structure of a structure, storing it on the sec_struct attribute.
Outputs
The input Atoms with updated sec_struct attributes based on the DSSP algorithm |
Atoms |
Dihedral Phi
Outputs
The calculated Phi angle for the residue, in the range of (-pi, pi) |
Phi |
| The perpendicular vector from the line of BC to the point A |
Up |
| The vector BC corresponding to the backbone vector around which the angle is calculated |
Axis |
Dihedral Psi
Outputs
The calculated Psi angle for the residue, in the range of (-pi, pi) |
Psi |
| The perpendicular vector from the line of BC to the point A |
Up |
| The vector BC corresponding to the backbone vector around which the angle is calculated |
Axis |
Dihedral Nucleic Angle
Outputs
| The angle between the vectors AB and CD, when made perpendicular to BC. |
Angle |
| The vector BA when made perpendicular to the axis BC |
Up |
| The axis vector BC |
Axis |
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.
Outputs
| Group contains only one occurrance of the selected atom. None or more than one returns False |
Is Valid |
| Index for the group’s atom with specified name, returns -1 if not valid |
Index |
| Position of the picked point in the group, returns (0, 0, 0) if not valid |
Position |
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.
Outputs
| The position of the backbone O atom for the residue |
O |
| The position of the backbone C atom for the residue |
C |
| The position of the backbone CA atom for the residue |
CA |
| The position of the backbone N atom for the residue |
N |
|
NH |
Peptide Dihedral
Rotate the atoms cumulatively for each residue, adjusting the phi and psi angles for the selected residues
Outputs
| Transformed vector |
Position |
Peptide Chi
Rotate the Chi angles for amino acid side chains
Nucleic Dihedral
Rotate the dihedral angles for nucleic acid backbone
Outputs
| Transformed vector |
Position |
Nucleic Chi
Rotate the Chi angles for nucleic acid side chains
Outputs
| Transformed vector |
Position |
Backbone Vectors
The Vectors that are useful for a curve when reading from a peptide backbone
Calculate Normal, Tangent and Bitangent values from protein backbone atom positions
Outputs
The vector used for the Normal of a curve when reading positions from a peptide backbone |
Normal |
The vector used as the Tangent for a curve when reading values from a peptide backbone |
Tangent |
| Cross product of the Normal and Tangent |
Bitangent |
Edge Group ID
Check if both vertices of an edge are in the same Group ID.
Is Backbone Edge
If both vertices of an edge are an alpha carbon and the edge is part of the same chain_id.
Sample Atomic Attributes
Sample relevant atomic attributes from a set of sample atoms, onto a new set of atoms / points. Attributes are selected based on the Index input.
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
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
Outputs
| Atomic geometry that contains vertices and edges |
Atoms |
Bond Count
The number of bonds for an atom
Outputs
| If the point has an edge / bond to another point |
Is Bonded |
| The number of bonds or edges that a point has |
Bonds |
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.
Outputs
| Whether there is a valid edge corresponding to the given index |
Is Valid |
| The index for the other point involved in this edge, -1 if not connected |
Point Index |
| The position for the other point involved in this edge, (0, 0, 0) if not connected |
Point Position |
| The index on the edge domain for the selected edge. -1 if not connected |
Edge Index |
| The vector along the selected edge. (0, 0, 0) if not connected |
Edge Vector |
| Length of the selected edge, -1 if not connected |
Edge Length |
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.
Outputs
| Both of the selected edges are valid |
Is Valid |
| Angle between the two selected edges in radians. Returns 0 if not valid |
Angle |
| Index for “Edge A” in the Edge domain of the geometry. Returns -1 if not valid |
Edge Index A |
| Index for “Edge B” in the Edge domain of the geometry. Returns -1 if not valid |
Edge Index B |
| Vector from the current point to the other point in Edge A. Returns (0, 0, 0) if not valid. |
Edge Vector A |
| Vector from the current point to the other point in Edge B. Returns (0, 0, 0) if not valid. |
Edge Vector B |
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.
Outputs
| Index for the 0th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self |
0 |
| Index for the 1th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self |
1 |
| Index for the 2th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self |
2 |
| Index for the 3th point, connected to the point at the end of the selected edge. Returns -1 if not connected or self |
3 |
| Number of edges conncted to the connected point, including this edge |
Total |