Molecular Nodes

Select

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	The selection to separate the atoms.	`True`

Outputs

Name	Type	Description	Default
`Atoms`	Geometry	The selected atoms.	required
`Inverted`	Geometry	The inverse of the calculated selection	required
`Index`	Int	Index of the Atoms before selection.	`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`

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
`Object`	Object	Empty object (ideally Cube) to use as the selection tool.	required
`From Min (A)`	Float	Minimum distance for falloff, in Angstroms.	`0.0`
`From Max (A)`	Float	Maximum distance for falloff, in Angstroms.	`10.0`

Outputs

Name	Type	Description	Default
`Selection`	Bool	The calculated selection	`False`
`Inverted`	Bool	The inverse of the calculated selection	`False`
`0..1`	Float	Falloff value from 0 to 1, based on the From Min and From Max.	`0.0`

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
`Object`	Object	required
`From Min (A)`	Float	`0.0`
`From Max (A)`	Float	`10.0`

Outputs

Name	Type	Description	Default
`Selection`	Bool	The calculated selection	`False`
`Inverted`	Bool	The inverse of the calculated selection	`False`
`0..1`	Float		`0.0`

Secondary Structure

Select based on the assigned secondary structure information. Only returns a selection if the sec_struct attribute exists on the atoms. Will be imported from files where it is present

Outputs

Name	Type	Default
`is_alpha_helix`	Bool	`False`
`is_beta_sheet`	Bool	`False`
`is_not_loop`	Bool	`False`
`is_loop`	Bool	`False`

Backbone

Selection fields for the backbone and side chains of the protein and nucleic acids.

Outputs

Name	Type	Default
`is_alpha_carbon`	Bool	`False`
`is_backbone`	Bool	`False`
`is_side_chain`	Bool	`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
`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	Description	Default
`H`	Bool	Select the element H	`False`
`He`	Bool	Select the element He	`False`
`Li`	Bool	Select the element Li	`False`
`Be`	Bool	Select the element Be	`False`
`B`	Bool	Select the element B	`False`
`C`	Bool	Select the element C	`False`
`N`	Bool	Select the element N	`False`
`O`	Bool	Select the element O	`False`
`F`	Bool	Select the element F	`False`
`Ne`	Bool	Select the element Ne	`False`
`Na`	Bool	Select the element Na	`False`
`Mg`	Bool	Select the element Mg	`False`
`Al`	Bool	Select the element Al	`False`
`Si`	Bool	Select the element Si	`False`
`P`	Bool	Select the element P	`False`
`S`	Bool	Select the element S	`False`
`Cl`	Bool	Select the element Cl	`False`
`Ar`	Bool	Select the element Ar	`False`
`K`	Bool	Select the element K	`False`
`Ca`	Bool	Select the element Ca	`False`

Outputs

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

Attribute

Selections based on the different attributes that are available on the atomic geometry.

Outputs

Name	Type	Default
`is_alpha_carbon`	Bool	`False`
`is_backbone`	Bool	`False`
`is_peptide`	Bool	`False`
`is_nucleic`	Bool	`False`
`is_lipid`	Bool	`False`
`is_carb`	Bool	`False`
`is_solvent`	Bool	`False`

Bonded Atoms

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	Initial selection to find which atoms are bonded to	`False`
`Bond Depth`	Int	Number of bonds to expand the selection by	`2`

Outputs

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

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 MN_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
`Selection`	Bool	Additional selection to apply to the target atoms	`True`
`Whole Residue`	Bool	Expand selection to entire residue if single atom is selected	`False`
`Distance (A)`	Float	Cutoff distance for the selection in Angrstoms	`5.0`

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 single residue based on the res_id number.

Inputs

Name	Type	Description	Default
`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 minimum and a maximum which will create the selection based on the res_id number.

Inputs

Name	Type	Description	Default
`res_id: Min`	Int	Minimum of a `res_id` range selection	`10`
`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`

Res Name Peptide

Select single or multiple protein residues by name. Includes the 20 naturally occurring amino acids.

Inputs

Name	Type	Description	Default
`ALA`	Bool	Select the AA residue ALA	`False`
`ARG`	Bool	Select the AA residue ARG	`False`
`ASN`	Bool	Select the AA residue ASN	`False`
`ASP`	Bool	Select the AA residue ASP	`False`
`CYS`	Bool	Select the AA residue CYS	`False`
`GLU`	Bool	Select the AA residue GLU	`False`
`GLN`	Bool	Select the AA residue GLN	`False`
`GLY`	Bool	Select the AA residue GLY	`False`
`HIS`	Bool	Select the AA residue HIS	`False`
`ILE`	Bool	Select the AA residue ILE	`False`
`LEU`	Bool	Select the AA residue LEU	`False`
`LYS`	Bool	Select the AA residue LYS	`False`
`MET`	Bool	Select the AA residue MET	`False`
`PHE`	Bool	Select the AA residue PHE	`False`
`PRO`	Bool	Select the AA residue PRO	`False`
`SER`	Bool	Select the AA residue SER	`False`
`THR`	Bool	Select the AA residue THR	`False`
`TRP`	Bool	Select the AA residue TRP	`False`
`TYR`	Bool	Select the AA residue TYR	`False`
`VAL`	Bool	Select the AA residue VAL	`False`

Outputs

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

Res Name Nucleic

Select single or multiple nucleic residues by name.

Inputs

Name	Type	Description	Default
`A`	Bool	Select the nucleic residue A	`True`
`C`	Bool	Select the nucleic residue C	`True`
`G`	Bool	Select the nucleic residue G	`True`
`T`	Bool	Select the nucleic residue T	`True`
`rA`	Bool	Select the nucleic residue rA	`True`
`rG`	Bool	Select the nucleic residue rG	`True`
`rC`	Bool	Select the nucleic residue rC	`True`
`rU`	Bool	Select the nucleic residue rU	`True`

Outputs

Name	Type	Description	Default
`Selection`	Bool	The calculated selection	`False`
`Inverted`	Bool	The inverse of the calculated 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	Expands given selection to include the entire residue.	`False`

Outputs

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