Attributes
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.
Outputs
The chain_id attribute read from the points, corresponding to the different chains that were read from the structure |
chain_id |
Atom ID
The atom_id attribute which is read from the file. Will be increasing linearly for each subsequent atom
Outputs
The atom_id attribute, read from geometry. Corresponds to the order of the atoms when they were read from the file |
atom_id |
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
Outputs
The entity_id attribute read from the points, corresponding to the unique entities in the structure (that may appear several times as different chains) |
entity_id |
Residue ID
The residue_id attribute of the point, which is the assigned number of the residue inside the chain of the structure
Outputs
Read the res_id attribute from the geometry |
res_id |
Atomic Number
The atomic_number attribute, ascending from 1 for each element on the periodic table
Outputs
Read the atomic_number attribute from the geometry corresponding to elements |
atomic_number |
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
Outputs
The atom_name attribute read from the points, an integer representation of the atom names. Corresponds to CA and O in the file etc. |
atom_name |
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
Outputs
Read the res_name attribute from the geometry |
res_name |
Secondary Structure
The sec_struct attribute of the point. 0 is non-peptide, 1 is helix, 2 is sheet and 3 is loop
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
Outputs
Read the vdw_radii attribute from the geometry |
vdw_radii |
Mass
The mass attribute of the point, used for centre of mass calculations
Outputs
Read the mass attribute from the geometry |
mass |
B Factor
The b_factor attribute of the point, representing the ‘temperature’ of the point
Color
The Color attribute of the point, used for coloring the final generated geometry inside of the materials
Outputs
Read the Color attribute from the geometry |
Color |
URes ID
The ures_id attribute of the point, a unique identifier for each residue across the whole structure.
Residue Parameter
Read information about the atoms with the context of each residue the atom is in
Outputs
| An atom’s relative position in a residue, with the first atom being 0 and the last atom being 1 |
Factor |
| Number of atoms in a residue |
Atom Count |
| Index of an atom in a residue when counting from 0 |
Atom Index |
| the atom_name for the first atom in a residue |
First atom_name |
| The atom_name for the last atom in a residue |
Last atom_name |
| Index (in the whole structure) for the first atom in a residue |
Index of First |
| Index (in the whole structure) for the last atom in a residue |
Index of Last |
Chain Parameter
Information for each residue within the context of the chain
Read information about the residues within the context of each chain
Outputs
| A residues relative position along a chain. 0 being the first residue in a chain, 1 being the last |
Factor |
| Number of residues in the chain |
Residue Count |
| Res ID along the chain if counting from 1 |
Residue Index |
| The first Res ID in a chain (truncated chains start above 1) |
First res_id |
| The Res ID of the last residue in chain (not equal to Length if chain is truncated) |
Last res_id |
| Index in whole structure of the first atom in the chain |
Index of First |
| Index in the whole structure the last atom in the chain |
Index of Last |
Structure Parameter
Read information about the atoms with the context of the whole structure
Outputs
Factor of the atom within the structure, which is the relative position of the Index within the overall structure between 0 and 1 |
Atom Factor |
Index of the point within the structure. Equal to the Index input node |
Index |
| Number of atoms in the structure, equal to the size of the Point Domain |
Atom Count |
Index of first atom in the entire structure, which will always be 0 |
Index of First |
Index of last atom in the entire structure. Equal to Atom Count - 1 |
Index of Last |
|
Residue Factor |
A unique Group ID that increases whenever Sub Group ID or Group ID change |
Residue Index |
|
Residue Count |
Unique Residue ID
A unique Group ID that is calculated for every residue in the structure
Outputs
| A unique Group ID for eash residue |
Group ID |
Unique Chain ID
Compute a unique Group ID based on the chain_id attribute, but also incrememnting if subsequent points are over a cutoff distance from each other
Assumes only CA points in the geometry. Unique Group ID for each chain, incrementing if distance between CA points are greater than threshold
Outputs
Calculated Group ID attribute |
Group ID |