Attributes

Below are the attributes which are potentially created when a structure is imported. Explanations of type and domain conversions can be found in the Blender documentation here

World Scale

In Molecular Nodes, the world scale determines how real-world measurements are translated into the 3D environment of Blender which uses metres. Currently, 1 nanometre (nm) is equivalent to 1 metre (m). Scaling structural coordinates (which are in Å) by 0.1 correctly converts them and 0.1 is referred to as the world_scale.

This changed with Molecular Nodes v520: previously the world scale was 0.01, so 1 Å equalled 1 cm.

When an attribute is going to be read from the geometry, it is colored red like so: Index, chain_id, while when a specific data type is referenced it will be colored according to the data type like so: Int, Float, Vector, etc.

Data Types

Attribute Types

Attributes are always associated with Geometry. They will be stored on one of the domains of the geometry. The type of the attribute is determined by the type of the data it contains. The following types are supported by Geometry Nodes.

Type	Description
Int	32-bit integers
Float	32-bit floating point numbers
Bool	A simple True or False value
Vector	A vector of (x, y, z) values. Can also be 2D, 3D or 4D although support outside of 3D vectors is limited.
Matrix	4x4 floating point matrices, also references as Transform inside of Geometry Nodes
Color	Linear RGBA colors, stored as (0..1, 0..1, 0..1, 0..1) values
Rotation	A (w, x, y, z) rotation that internally is represented as a quaternion, but can implicitly be converted to an Euler vector.

Other Data Types

Additional data types which are not supported as Attributes but can be used in the node tree are:

Type	Description
String	String support in Geometry Nodes is limited at the moment and you cannot store strings as attributes
Object	Access to objects in the 3D scene and their associated data
Collection	Access a collection of objects from the scene. Objects are returned as instances
Material	Material to be applied to the created geometry
Menu	A menu for selecting a value from a list of options
Image	A reference to an image data-block, for sampling or texturing
Shader	The output of shader nodes, used when building materials rather than geometry
Bundle	New in Blender 5.0: multiple sockets packed together and passed along a single link
Closure	New in Blender 5.0: a piece of node tree logic passed around as a value, to be evaluated elsewhere

Attributes

All of the molecular attributes which are defined as strings such as chain_id, res_name, etc. are stored as integers in the geometry because Geometry Nodes does not support string attributes.

For chain_id, entity_id and other dynamic attributes, the unique values are first sorted alphabetically and then assigned an integer value based on their order.

For other attributes such as res_name, they are looked up from the dictionary and assigned an integer value.

Point Attributes

Attribute	Type	Description
Position	Vector	Coordinates in 3D space of the points, read from the molecular data file. They are scaled by the world scale 0.1 on import so that 1 nm == 1 m.
b_factor	Float	The temperature factor for the atom on import. If importing an AlphaFold structure this corresponds to the pLDDT value.
occupancy	Float	The crystallographic occupancy of the atom, or 0.0 if the file has none.
charge	Float	The charge of the atom: partial charges when the topology provides them (e.g. simulation topologies), formal charges from structure files, or 0.0 if unavailable.
vdw_radii	Float	The radii of the atom, stored in world space (~0.15). Values sourced from Wikipedia.
lipophobicity	Float	Lipophobicity value for the atom, looked up from its residue and atom name.
sec_struct	Int	Defines secondary structure for the residue the atom is part of. 0 for not a protein. 1 for helices, 2 for sheets, 3 for coils / unstructured.
mass	Float	Mass of the element
chain_id	Int	The integer representation of the chain ID, for it’s position in the sorted list of chain IDs in the structure.
segid	Int	The index of the segment the atom belongs to, when the topology defines segments. The segment names are stored as metadata on the object.
entity_id	Int	Multiple chains can be the same entity, if they are copies of the same protein that appear multiple times in the structure. Also sorted and assigned integers on import.
res_name	Int	Residues are mapped to integer values based on the lookup table.
res_id	Int	The residue number, which starts at 1 for the first residue in each chain. If a structure is truncated it might not start at 1.
ures_id	Int	The ures_id starts at 0 and increases by 1 for each residue across the whole structure, compared to the res_id which starts at 1 and restarts at 1 for each chain.
atomic_number	Int	Stores the atomic number of the atom for it’s position on the periodic table, instead of the element’s name.
atom_name	Int	Atom names are mapped to integer values based on the lookup table.
atom_types	Int	The force-field atom types from simulation topologies, sorted uniquely and assigned integers on import. The type names are stored as metadata on the object.
Color	Color	Color of the atom, assigned on import but often changed in node trees.
atom_id	Int	Unique ascending value for each atom in the file, starting at 1
is_alpha_carbon	Bool	Whether the atom is an alpha carbon (atom name CA, or BB for coarse-grained structures).
is_side_chain	Bool	Whether the atom is part of a side chain: a peptide or nucleic atom that is not part of the backbone.
is_backbone	Bool	Whether the atom is part of the peptide or nucleic backbone, based on its atom name.
is_solvent	Bool	Whether the atom is part of a solvent molecule, based on its residue and atom names.
is_nucleic	Bool	Whether the atom is part of a nucleic acid.
is_peptide	Bool	Whether the atom is part of a peptide, including coarse-grained (Martini) beads.
is_lipid	Bool	Whether the atom is part of a lipid, based on its residue name.
is_hetero	Bool	Whether the atom is flagged as a hetero atom in the structure file.
is_carb	Bool	Whether the atom is part of a carbohydrate, based on its residue name.

Edge Attributes

Bonds between atoms are represented as edges in the geometry, and only the bond type is stored on the edge domain.

Attribute	Type	Description
bond_type	Int	The type of bond between the atoms.

Bond types are currently the values used by biotite

Bond Type	Integer Value	Description
ANY	0	Used if the actual type is unknown
SINGLE	1	Single bond
DOUBLE	2	Double bond
TRIPLE	3	Triple bond
QUADRUPLE	4	A quadruple bond
AROMATIC_SINGLE	5	Aromatic bond with a single formal bond
AROMATIC_DOUBLE	6	Aromatic bond with a double formal bond
AROMATIC_TRIPLE	7	Aromatic bond with a triple formal bond

Domains

Domain	Description
Point	Individual points of geometry. These can be the vertices in a mesh, the points in a point cloud, or the control points of a curve.
Edge	The edges of a mesh, defined as the indices between two points.
Face	A face of a mesh, defined as a collection of edges.
Corner	Corners of a face, where two edges meet.
Curve	A curve object, which contains multiple control points, but can itself store attributes.
Instance	Instances are references to other geometry. Instancing is useful for making lots of copies of some geometry for performance.
Layer	Layers are for Grease Pencil, and contain a collection of curves.