Select

Create boolean selections based on the atomic attributes

Is Alpha Carbon

Video

Outputs a selection for all of the points that are alpha carbons (CA) in the structure

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsAlphaCarbon

Is Backbone

Video

Outputs a selection for the backbone atoms of a peptide or nucleic acid polymer. Peptide backbone includes the peptide oxygen and the alpha carbon as part of the backbone

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsBackbone

Is Backbone Edge

If both vertices of an edge are an alpha carbon and the edge is part of the same chain_id.

Outputs

Name	Type	Description
Is Backbone Edge	Bool

API Reference: nodes.geometry.IsBackboneEdge

Is Boundary Edge

Inputs

Name	Type	Description
Mask	Bool

Outputs

Name	Type	Description
Selection	Bool	The calculated selection

API Reference: nodes.geometry.IsBoundaryEdge

Is Helix

Video

Outputs a selection for points that are part of a helix. The sec_struct attribute must exist, either imported from the file or computed with the Topology DSSP node

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsHelix

Is Hydrogen

Outputs a selection for all of the hydrogen atoms in the structure

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	Computed selection that includes Hydrogen atoms
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsHydrogen

Is Lipid

Select the atoms involved in lipid molecules.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsLipid

Is Loop

Video

Outputs a selection for those points in a peptide which are not part of any secondary structure (loop or helix)

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsLoop

Is Nucleic

Video

Outputs a selection for all of the points in a nucleic acid molecule

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsNucleic

Is Peptide

Video

Outputs a selection for all of the points in a peptide

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsPeptide

Is Sheet

Video

Outputs a selection for points that are part of a sheet. The sec_struct attribute must exist, either import from the file or computed with the Topology DSSP node

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsSheet

Is Side Chain

Video

Outputs a selection for the side chain atoms of a peptide or nucleic acid polymer. Peptide side chain can optionally include or exclude the alpha carbon CA of the side chain

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
Include CA	Bool	Include the alpha carbon as part of the side chain

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsSideChain

Is Solvent

Select the atoms that are part of the solvent.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.IsSolvent

Menu Atom Name

Inputs

Name	Type	Description
Atom Name	Menu

Outputs

Name	Type	Description
atom_name	Int
Selection	Bool
atom_name	String

API Reference: nodes.geometry.MenuAtomName

Select Atomic Number

Video

Select points based on their atomic_number attribute, corresponding to the element’s atomic number. Useful for selecting single elements quickly

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
atomic_number	Int	Create a selection based on the inputted atomic number.

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectAtomicNumber

Select Attribute

Select atoms that have true for the given attribute name.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
Name	String

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectAttribute

Select Bonded

Video

Based on an initial selection, finds atoms which are within a certain number of bonds of this selection. Output can include or excluded the original selection.

Inputs

Name	Type	Description
Selection	Bool	Selection of atoms to apply this node to
Depth	Int	Number of bonds to expand the selection by

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Bonded	Bool	Expanded Selection that excludes the original selection

API Reference: nodes.geometry.SelectBonded

Select Cube

Video

Create a selection that is inside the Empty_Cube object. When this node is first created, an empty object called Empty_Cube should be created. You can always create additional empty objects through the add menu, to use a different object. The rotation and scale of the object will be taken into account for the selection.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
Object	Object	The position, rotation and scale from this Object will be used for the distance calculation for the selection. By default an Empty object is used, but any object can be used in principle

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectCube

Select Element

Video

Select points for the first 80 elemnts of the preiodic table, via a boolean input. Elements are grouped into panels of 20 each for orgnaisation and convenience

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
H	Bool	Select the element H
He	Bool	Select the element He
Li	Bool	Select the element Li
Be	Bool	Select the element Be
B	Bool	Select the element B
C	Bool	Select the element C
N	Bool	Select the element N
O	Bool	Select the element O
F	Bool	Select the element F
Ne	Bool	Select the element Ne
Na	Bool	Select the element Na
Mg	Bool	Select the element Mg
Al	Bool	Select the element Al
Si	Bool	Select the element Si
P	Bool	Select the element P
S	Bool	Select the element S
Cl	Bool	Select the element Cl
Ar	Bool	Select the element Ar
K	Bool	Select the element K
Ca	Bool	Select the element Ca
Sc	Bool	Select the element Sc
Ti	Bool	Select the element Ti
V	Bool	Select the element V
Cr	Bool	Select the element Cr
Mn	Bool	Select the element Mn
Fe	Bool	Select the element Fe
Co	Bool	Select the element Co
Ni	Bool	Select the element Ni
Cu	Bool	Select the element Cu
Zn	Bool	Select the element Zn
Ga	Bool	Select the element Ga
Ge	Bool	Select the element Ge
As	Bool	Select the element As
Se	Bool	Select the element Se
Br	Bool	Select the element Br
Kr	Bool	Select the element Kr
Rb	Bool	Select the element Rb
Sr	Bool	Select the element Sr
Y	Bool	Select the element Y
Zr	Bool	Select the element Zr
Nb	Bool	Select the element Nb
Mo	Bool	Select the element Mo
Tc	Bool	Select the element Tc
Ru	Bool	Select the element Ru
Rh	Bool	Select the element Rh
Pd	Bool	Select the element Pd
Ag	Bool	Select the element Ag
Cd	Bool	Select the element Cd
In	Bool	Select the element In
Sn	Bool	Select the element Sn
Sb	Bool	Select the element Sb
Te	Bool	Select the element Te
I	Bool	Select the element I
Xe	Bool	Select the element Xe
Cs	Bool	Select the element Cs
Ba	Bool	Select the element Ba
La	Bool	Select the element La
Ce	Bool	Select the element Ce
Pr	Bool	Select the element Pr
Nd	Bool	Select the element Nd
Pm	Bool	Select the element Pm
Sm	Bool	Select the element Sm
Eu	Bool	Select the element Eu
Gd	Bool	Select the element Gd
Tb	Bool	Select the element Tb
Dy	Bool	Select the element Dy
Ho	Bool	Select the element Ho
Er	Bool	Select the element Er
Tm	Bool	Select the element Tm
Yb	Bool	Select the element Yb
Lu	Bool	Select the element Lu
Hf	Bool	Select the element Hf
Ta	Bool	Select the element Ta
W	Bool	Select the element W
Re	Bool	Select the element Re
Os	Bool	Select the element Os
Ir	Bool	Select the element Ir
Pt	Bool	Select the element Pt
Au	Bool	Select the element Au
Hg	Bool	Select the element Hg

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectElement

Select Nucleic Type

Select either purines or pyrimidines

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection

Outputs

Name	Type	Description
is_purine	Bool
is_pyrimidine	Bool

API Reference: nodes.geometry.SelectNucleicType

Select Proximity

Video

Create a selection based on the proximity to the Target Atoms of the input. A sub-selection of the Target atoms can be used if the Subset input is used. You can expand the selection to include an entire residue if a single atom in that residue is selected, by setting Expand to True. In the example below, the Style Spheres is being applied to a selection, which is being calculated from the proximity of atoms to specific chains. As the cutoff for the selection is changed, it includes or excludes more atoms. The Whole Residue option also ensures that entire residues are shown.

Inputs

Name	Type	Description
Target Atoms	Geometry	The atoms to measure the distance from.
Subset	Bool	Subset of input atoms to use for proximity calculation
Expand	Bool	Include an entire residue if even a single atom is within the threshold
Distance (A)	Float	Cutoff distance for the selection in Angstroms

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectProximity

Select Res ID

Video

Select a atoms based on their res_id number.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
Res ID	Int	A single res_id selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectResID

Select Res ID Range

Video

Select multiple residues by specifying a Min and a Max, defining a range that includes or excludes based on the res_id number.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
Min	Int	Minimum of a res_id range selection
Max	Int	Maximum of a res_id range selection

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectResIDRange

Select Res ID String

Inputs

Name	Type	Description
String	String

Outputs

Name	Type	Description
Selection	Bool

API Reference: nodes.geometry.SelectResIDString

Select Res Name

Video

Select points based on their res_id attribute for different peptide or nucleic acid residue names. Inputs are arranged alphabetically and in panels of Protein, RNA and DNA for layout

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
ALA	Bool	Select the residue ALA
ARG	Bool	Select the residue ARG
ASN	Bool	Select the residue ASN
ASP	Bool	Select the residue ASP
CYS	Bool	Select the residue CYS
GLU	Bool	Select the residue GLU
GLN	Bool	Select the residue GLN
GLY	Bool	Select the residue GLY
HIS	Bool	Select the residue HIS
ILE	Bool	Select the residue ILE
LEU	Bool	Select the residue LEU
LYS	Bool	Select the residue LYS
MET	Bool	Select the residue MET
PHE	Bool	Select the residue PHE
PRO	Bool	Select the residue PRO
SER	Bool	Select the residue SER
THR	Bool	Select the residue THR
TRP	Bool	Select the residue TRP
TYR	Bool	Select the residue TYR
VAL	Bool	Select the residue VAL
A	Bool	Select the residue A
C	Bool	Select the residue C
G	Bool	Select the residue G
T	Bool	Select the residue T
rA	Bool	Select the residue rA
rC	Bool	Select the residue rC
rG	Bool	Select the residue rG
rU	Bool	Select the residue rU

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectResName

Select Res Whole

Video

Expand the given selection to include a whole residue, if a single atom in that residue is selected. Useful for when a distance or proximity selection includes some of the residue and you wish to include all of the residue.

Inputs

Name	Type	Description
Selection	Bool	Selection of atoms to apply this node to
Expand	Bool	Whether to expand the selection to the whole residue if at least one atom is selected

Outputs

Name	Type	Description
Selection	Bool	The calculated selection

API Reference: nodes.geometry.SelectResWhole

Select Sphere

Video

Create a selection that is within a spherical radius of an object, based on that object’s scale. By default an empty object called Empty_Sphere is created. You can use other objects or create a new empty to use. The origin point for the object will be used, which should be taken in to account when using molecules. Use Select Proximity node for selections which are within a certain distance of a selection of atoms instead of a single origin point.

Inputs

Name	Type	Description
And	Bool	The resulting selection must overlap with this input selection
Or	Bool	The resulting selection can be calculated from this node or be from this input selection
Object	Object	The position from this Object will be used for the distance calculation for the selection. By default an Empty object is used, but any object can be used in principle

Outputs

Name	Type	Description
Selection	Bool	The calculated selection
Inverted	Bool	The inverse of the calculated selection

API Reference: nodes.geometry.SelectSphere

Selected Instances

Check if instances are selected based on the field (usually based on Position attribute)

Inputs

Name	Type	Description
Instances	Geometry	Geometry containing instances to check if they are selected or not
Selection	Bool	The selection to apply to the bounding boxes of the Instances

Outputs

Name	Type	Description
Entirely Selected	Bool	All points of the instances bounding box are selected
Partially Selected	Bool	Some points of the Instance’s bounding box are selected
Not Selected	Bool	No points of the Instance’s bounding box are selected

API Reference: nodes.geometry.SelectedInstances

Separate Atoms

Video

Separate the input atoms into the Atoms and Inverted based on the input Selection. For simply styling this can the same as inputting the Selection directly into the Style node. The one additional output for this node is the Index field, which is the index of the atom in the original structure before the selection happened and potentially changed it’s index

Inputs

Name	Type	Description
Atoms	Geometry	Atomic geometry that contains vertices and edges
Selection	Bool	Selection field for which atoms to separate

Outputs

Name	Type	Description
Atoms	Geometry	The selected atoms
Inverted	Geometry	The parts of the geometry not in the selection
Index	Int	Index of the point before being separated.

API Reference: nodes.geometry.SeparateAtoms

Separate Polymers

Video

Separate the input atomic geometry into it’s different polymers or Protein, Nucleic Acid and other.

Inputs

Name	Type	Description
Atoms	Geometry	Atomic geometry that contains vertices and edges

Outputs

Name	Type	Description
Peptide	Geometry
Nucleic	Geometry
Other	Geometry

API Reference: nodes.geometry.SeparatePolymers