Editing LiteMol:SelectionAlgebra (section)

=LiteMol selection algebra=

Molecular selections can be created in two different active contexts - [[LiteMol:Hierarchy#Molecule_Model_.28MM.29 | model of molecule]] or [[LiteMol:Hierarchy#Molecule_Visual_.28VM.29 | molecule visual]]. If either of the contexts is active in the entity tree, the right panel is populated with the '''Selection''' action. Next, you can create a named selection using the dedicated query language and further modify the visual part of your selection. 


 {{large| '''Notice:'''}} Arguments of LiteMol selection queries are '''case sensitive'''!

Meaning: '''GLY''' is a common non-polar residue found in PDB entries, whereas '''Gly''', '''gly''', or '''G''' do not exist. 

==Basic queries==
{| class="wikitable"
! colspan="3" | List of selection queries
|-
!Query definition
!Example
!Selection description
|-
| <code>  atomsByElement(elements: string[]) </code >
| <code>  atomsByElement('C'), atomsByElement('C','O') </code>
| Atoms based on their element symbol (field ''_atom_site.type_symbol'').
|-
| <code>  atomsByName(elements: string[]) </code>
| <code>  atomsByName('C'), atomsByName('N','CA','C','O') </code>
| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
|-
| <code>  atomsById(numbers: number[]) </code>
| <code>  atomsById(1), atomsById(1,2,3) </code>
| Atoms based on their integer identifier (field ''_atom_site.id '').
|-
| <code>  residuesByName(elements: string[]) </code>
| <code>  residuesByName('GLY'), residuesByName('ALA', 'PO4') </code>
| Residues based on their residue name (field ''_atom_site.label_comp_id'').
|-
| <code>  residuesById(numbers: number[]) </code>
| <code>  residuesById(100), residuesById(42,157,238) </code>
| Residues based on integer identified (field ''_atom_site.auth_seq_id'').
|-
| <code>  chainsById(elements: string[]) </code>
| <code>  chainsById('A'), chainsById('A', 'B') </code>
| Polymer chains based on their id (field ''_atom_site.auth_asym_id'').
|-
| <code> backbone() </code>
| <code> backbone() </code>
| Extracts structure backbone defined by certain atom names. '''Protein:''' ''N'', ''CA'', ''C'', ''O''. '''Nucleotide:''' ''P'', ''OP1'', ''OP2'', ''O3' '', ''O5' '', ''C3' '', ''C5' ''.
|-
| <code> sidechain() </code>
| <code> sidechain() </code>
| Complement to the previous query, i.e. all ''polymer'' atoms without such name are reported.
|-
| <code> hetGroups() </code>
| <code> hetGroups() </code>
| ''HETATM'' atoms defined by the field ''_atom_site.group_PDB''.
|-
| <code> nonHetPolymer() </code>
| <code> nonHetPolymer() </code>
| ''ATOM'' atoms defined by the field ''_atom_site.group_PDB''.
|-
|<code> cartoon() </code>
|<code> cartoon() </code>
| Extracts atoms vital for ''polymer'' cartoon visualization based on their names: ''CA'', ''O'', ''O5' '', ''C3' '', ''N3''.
|-
| <code> everything() </code>
| <code> everything() </code>
| All atoms in the active context.
|-
|}

==Advanced queries==
{| class="wikitable"
! colspan="3" | List of selection queries
|-
!
Query
!
Examples
!
Selection description
|-
| <code>  inside(where: Selection, sel: Selection) </code>
| <code>  residuesByName('GLY').inside(chainsById('A')) </code>
| Finds selection within another selection.
|-
| <code>  ambientResidues(where: Selection, nmb: number ) </code>
| <code>  residuesByName('HEM').ambientResidues(5) </code>
| Surrounds the inner selection by residues that have at least one atom within the given radius
|-
| <code>  wholeResidues(where: Selection) </code>
| <code>  atomsByElement('Pt').wholeResidues() </code>
| Surrounds the inner selection by all atoms of residue's origin.
|-
|}

==Logical queries==
{| class="wikitable"
! colspan="3" | List of selection queries
|-
!Query
!Examples
!Selection description
|-
| <code>  or(selections: Selection[]) </code>
| <code>  or(residuesByName('HEM').ambientResidues(5), chainsById('A')) </code>
| Merges several selections.
|-
| <code>  intersectWith(where: Selection, sel: Selection) </code>
| <code>  residuesByName('HEM').ambientResidues(5).intersectWith(chainsById('A')) </code>
| Finds intersection between two selections.
|-
| <code>  complement(where: Selection) </code>
| <code>  chainsById('A').complement() </code>
| Finds the complement of the inner selection to the active context.
|-
|}