Molecular Nodes

Separate Atoms

Select only the desired input atoms. The output is bits of geometry, which include the selection and include the inverse of the selected atoms. You can expand the selection to include an entire residue if a single atom in that residue is selected, by setting Whole Residue to True.

Inputs

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

Outputs

Name	Type	Description	Default
`Atoms`	Geometry	The selected atoms	required
`Inverted`	Geometry	The non-selected atoms	required
`Index`	Int	Index of the atoms before they were separated	`0`

Separate Polymers

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

Inputs

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

Outputs

Name	Type	Default
`Peptide`	Geometry	required
`Nucleic`	Geometry	required
`Other`	Geometry	required

Chain

Select single or multiple of the different chains. Creates a selection based on the chain_id attribute.

Inputs

Name	Type	Description	Default
`Chain A`	Bool	Select the atoms in Chain A	`True`
`Chain B`	Bool	Select the atoms in Chain B	`True`
`Chain ...`	Bool	Select the atoms in Chain …	`True`

Outputs

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

Entity

Select single or multiple of the different entities. Creates a selection based on the entity_id attribute.

Inputs

Name	Type	Description	Default
`Entity A`	Bool	Select the atoms in Entity A	`True`
`Entity B`	Bool	Select the atoms in Entity B	`True`
`Entity ...`	Bool	Select the atoms in Entity …	`True`

Outputs

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

Ligand

Select single or multiple of the different ligands.

Inputs

Name	Type	Description	Default
`Ligand A`	Bool	Select the atoms in Ligand A	`True`
`Ligand B`	Bool	Select the atoms in Ligand B	`True`
`Ligand ...`	Bool	Select the atoms in Ligand …	`True`

Outputs

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

Segment

Inputs

Name	Type	Description	Default
`Segment A`	Bool	Select the atoms in Ligand A	`True`
`Segment B`	Bool	Select the atoms in Ligand B	`True`
`Segment ...`	Bool	Select the atoms in Ligand …	`True`

Outputs

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

Atomic Number

Select single elements, by matching to the atomic_number field. Useful for selecting single elements, or combining to select elements higher than 20 on the periodic table.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`
`atomic_number`	Int	Create a selection based on the inputted atomic number.	`6`

Outputs

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

Element

Select individual elements, for the first 20 elements on the periodic table. For selections of higher elements, use MN_select_atomic_number. Creating a node which includes more elements becomes too large to be practical.

Inputs

Name	Type	Default
`And`	Bool	`True`
`Or`	Bool	`False`
`H`	Bool	`False`
`He`	Bool	`False`
`Li`	Bool	`False`
`Be`	Bool	`False`
`B`	Bool	`False`
`C`	Bool	`False`
`N`	Bool	`False`
`O`	Bool	`False`
`F`	Bool	`False`
`Ne`	Bool	`False`
`Na`	Bool	`False`
`Mg`	Bool	`False`
`Al`	Bool	`False`
`Si`	Bool	`False`
`P`	Bool	`False`
`S`	Bool	`False`
`Cl`	Bool	`False`
`Ar`	Bool	`False`
`K`	Bool	`False`
`Ca`	Bool	`False`
`Sc`	Bool	`False`
`Ti`	Bool	`False`
`V`	Bool	`False`
`Cr`	Bool	`False`
`Mn`	Bool	`False`
`Fe`	Bool	`False`
`Co`	Bool	`False`
`Ni`	Bool	`False`
`Cu`	Bool	`False`
`Zn`	Bool	`False`
`Ga`	Bool	`False`
`Ge`	Bool	`False`
`As`	Bool	`False`
`Se`	Bool	`False`
`Br`	Bool	`False`
`Kr`	Bool	`False`
`Rb`	Bool	`False`
`Sr`	Bool	`False`
`Y`	Bool	`False`
`Zr`	Bool	`False`
`Nb`	Bool	`False`
`Mo`	Bool	`False`
`Tc`	Bool	`False`
`Ru`	Bool	`False`
`Rh`	Bool	`False`
`Pd`	Bool	`False`
`Ag`	Bool	`False`
`Cd`	Bool	`False`
`In`	Bool	`False`
`Sn`	Bool	`False`
`Sb`	Bool	`False`
`Te`	Bool	`False`
`I`	Bool	`False`
`Xe`	Bool	`False`
`Cs`	Bool	`False`
`Ba`	Bool	`False`
`La`	Bool	`False`
`Ce`	Bool	`False`
`Pr`	Bool	`False`
`Nd`	Bool	`False`
`Pm`	Bool	`False`
`Sm`	Bool	`False`
`Eu`	Bool	`False`
`Gd`	Bool	`False`
`Tb`	Bool	`False`
`Dy`	Bool	`False`
`Ho`	Bool	`False`
`Er`	Bool	`False`
`Tm`	Bool	`False`
`Yb`	Bool	`False`
`Lu`	Bool	`False`
`Hf`	Bool	`False`
`Ta`	Bool	`False`
`W`	Bool	`False`
`Re`	Bool	`False`
`Os`	Bool	`False`
`Ir`	Bool	`False`
`Pt`	Bool	`False`
`Au`	Bool	`False`
`Hg`	Bool	`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool		`False`
`Inverted`	Bool		`False`

Res Name

Select protein or nucleic acids based on their residue name.

Inputs

Name	Type	Default
`And`	Bool	`True`
`Or`	Bool	`False`
`ALA`	Bool	`False`
`ARG`	Bool	`False`
`ASN`	Bool	`False`
`ASP`	Bool	`False`
`CYS`	Bool	`False`
`GLU`	Bool	`False`
`GLN`	Bool	`False`
`GLY`	Bool	`False`
`HIS`	Bool	`False`
`ILE`	Bool	`False`
`LEU`	Bool	`False`
`LYS`	Bool	`False`
`MET`	Bool	`False`
`PHE`	Bool	`False`
`PRO`	Bool	`False`
`SER`	Bool	`False`
`THR`	Bool	`False`
`TRP`	Bool	`False`
`TYR`	Bool	`False`
`VAL`	Bool	`False`
`A`	Bool	`False`
`C`	Bool	`False`
`G`	Bool	`False`
`T`	Bool	`False`
`rA`	Bool	`False`
`rC`	Bool	`False`
`rG`	Bool	`False`
`rU`	Bool	`False`

Outputs

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

Res ID Single

Select a atoms based on their res_id number.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`
`Res ID`	Int	A single `res_id` selection	`10`

Outputs

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

Res ID Range

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	Default
`And`	Bool		`True`
`Or`	Bool		`False`
`Min`	Int	Minimum of a `res_id` range selection	`10`
`Max`	Int	Maximum of a `res_id` range selection	`100`

Outputs

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

Res ID

Create a more complex selection for the res_id field, by specifying multiple ranges and potential single res_id numbers. This node is built uniquely each time, to the inputs will look different for each user. In the example below, residues 10 & 15 are selected, as well as residues between and including 20-100. The node was created by inputting 10, 15, 20-100 into the node creation field.

Inputs

Name	Type	Description	Default
`res_id`	Int	A single `res_id` selection	`15`
`res_id: Min`	Int	Minimum of a `res_id` range selection	`20`
`res_id: Max`	Int	Maximum of a `res_id` range selection	`100`

Outputs

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

Attribute

Select atoms that have true for the given attribute name.

Inputs

Name	Type	Default
`And`	Bool	`True`
`Or`	Bool	`False`
`Name`	String	`is_peptide`

Outputs

Name	Type	Description	Default
`Selection`	Bool	The calculated selection	`False`
`Inverted`	Bool		`False`

Is Peptide

Select the atoms involved in a peptide chain.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if atoms are part of a peptide	`False`
`Inverted`	Bool		`False`

Is Nucleic

Select the atoms involved in nucleic acid polymer.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if atoms are part of a nucleic acid	`False`
`Inverted`	Bool		`False`

Is Lipid

Select the atoms involved in lipid molecules.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if atom is part of a lipid	`False`
`Inverted`	Bool		`False`

Is Solvent

Select the atoms that are part of the solvent.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if atoms is part of the solvent	`False`
`Inverted`	Bool		`False`

Is Alpha Carbon

Select the alpha carbons of a peptide.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if atom is an alpha carbon of an amino acid	`False`
`Inverted`	Bool		`False`

Is Backbone

Select the backbone atoms of a peptide or nucleic acid polymer.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if the atom is part of the backbone for either an amino acid or a peptide chain	`False`
`Inverted`	Bool		`False`

Is Side Chain

Select the side chain atoms of a peptide or nucleic acid polymer.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	True if atom is part of the side chain for either an amino acid or a nucleic acid	`False`
`Inverted`	Bool		`False`

Is Helix

Select the atoms in a alpha-helix or similar.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	Selected atoms form part of an helix	`False`
`Inverted`	Bool		`False`

Is Sheet

Select the atoms in a beta-sheet or similar.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	Selected atoms form part of a sheet	`False`
`Inverted`	Bool		`False`

Is Loop

Select the atoms not in a sheet or helix.

Inputs

Name	Type	Description	Default
`And`	Bool		`True`
`Or`	Bool		`False`

Outputs

Name	Type	Description	Default
`Selection`	Bool	Selected atoms form part of a loop, and not part of any secondary structure	`False`
`Inverted`	Bool		`False`

Bonded

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	Default
`Selection`	Bool	Selection of atoms to apply this node to	`False`
`Depth`	Int	Number of bonds to expand the selection by	`1`

Outputs

Name	Type	Description	Default
`Selection`	Bool	Expanded selection that includes the original selection	`False`
`Bonded`	Bool	Expanded Selection that excludes the original selection	`False`

Res Whole

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	Default
`Selection`	Bool	Selection of atoms to apply this node to	`False`
`Expand`	Bool	Whether to expand the selection to the whole residue if at least one atom is selected	`True`

Outputs

Name	Type	Description	Default
`Selection`	Bool	The calculated selection	`False`

Cube

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	Default
`And`	Bool		`True`
`Or`	Bool		`False`
`Object`	Object	Empty object (ideally Cube) to use as the selection tool.	required

Outputs

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

Sphere

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 MN_select_proximity for selections which are within a certain distance of a selection of atoms instead of a single origin point.

Inputs

Name	Type	Default
`And`	Bool	`True`
`Or`	Bool	`False`
`Object`	Object	required

Outputs

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

Proximity

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 Selection input is used. You can expand the selection to include an entire residue if a single atom in that residue is selected, by setting Whole Residue to True. In the example below, the Style Atoms 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	Default
`Target Atoms`	Geometry	The atoms to measure the distance from.	required
`Subset`	Bool	Subset of input atoms to use for proximity calculation	`True`
`Expand`	Bool	Whether to expand selection to entire residue if single atom is selected	`False`
`Distance (A)`	Float	Cutoff distance for the selection in Angstroms	`5.0`

Outputs

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