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]
NH	Vector		[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]