Attributes
Read attributes from structures
Atom ID
The atom_id attribute which is read from the file. Will be increasing linearly for each subsequent atom
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| atom_id | Int |
The atom_id attribute, read from geometry. Corresponds to the order of the atoms when they were read from the file |
API Reference: nodes.geometry.AtomID
Atom Name
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
The atom_name attribute, an integer representation of the atom names such as C for carbon, CA for alpha carbon
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| 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. |
API Reference: nodes.geometry.AtomName
Atomic Number
The atomic_number attribute, ascending from 1 for each element on the periodic table
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| atomic_number | Int |
Read the atomic_number attribute from the geometry corresponding to elements |
API Reference: nodes.geometry.AtomicNumber
B Factor
The b_factor attribute of the point, how well resolved the individual atoms are
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| b_factor | Float |
API Reference: nodes.geometry.BFactor
Chain ID
Integer representation of the Chain IDs that were present in the structure
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 |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| chain_id | Int |
The chain_id attribute read from the points, corresponding to the different chains that were read from the structure |
API Reference: nodes.geometry.ChainID
Color
The Color attribute of the point, used for coloring the final generated geometry inside of the materials
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| Color | Color |
Read the Color attribute from the geometry |
API Reference: nodes.geometry.Color
Entity ID
The entity_id attribute read from the points, corresponding to the unique entities in the structure (that may appear several times as different chains)
The entity_id attribute of the point
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| 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) |
API Reference: nodes.geometry.EntityID
Frame ID
Read the frame_id attribute, created when multiple frames from a trajectory are merged into a single structure
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| frame_id | Int |
Read the frame_id attribute from the geometry |
API Reference: nodes.geometry.FrameID
Mass
The mass attribute of the point, used for centre of mass calculations
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| mass | Float |
Read the mass attribute from the geometry |
API Reference: nodes.geometry.Mass
Residue ID
The residue_id attribute of the point, which is the assigned number of the residue inside the chain of the structure
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| res_id | Int |
Read the res_id attribute from the geometry |
API Reference: nodes.geometry.ResidueID
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 30 and RNA starts at 40. Check the attributes for a full listing.
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| res_name | Int |
Read the res_name attribute from the geometry |
API Reference: nodes.geometry.ResidueName
Secondary Structure
The sec_struct attribute of the point. 0 is non-peptide, 1 is helix, 2 is sheet and 3 is loop
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| sec_struct | Int |
API Reference: nodes.geometry.SecondaryStructure
URes ID
The ures_id attribute of the point, a unique identifier for each residue across the whole structure that is computed when the structure is loaded.
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| ures_id | Int |
|
| Size | Int |
The total of all of the values in the corresponding group |
API Reference: nodes.geometry.UResID
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 nodes, and for calculating the surface of the molecule in Style Surface
Inputs
| Name | Type | Description |
|---|---|---|
| Index | Int |
Outputs
| Name | Type | Description |
|---|---|---|
| vdw_radii | Float |
Read the vdw_radii attribute from the geometry |
API Reference: nodes.geometry.VDWRadii