View source for LiteMol:SelectionAlgebra

LiteMol has an atom selection language available, similarly to the other structure visualization tools such as VMD or PyMOL. The '''LiteMol selection algebra''' is inspired by our other service - [[PatternQuery:UserManual | PatternQuery]], although in the present version the amount of integrated queries is somewhat limited. Additionally, as a feature LiteMol will contain a parser of syntax enabling the use of [[LiteMol:SelectionAlgebra#PyMOL | PyMOL ]] and possibly [[LiteMol:SelectionAlgebra#VMD| VMD]] selection algebra.


=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 named selection using 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 the PDB entries, whereas Gly, or gly does not exist. 

{| class="wikitable"
! colspan="3" | List of selection queries
|-
!
Query
!
Examples
!
Selection description
|-
| <code>  atomsByElement() </code >
| <code>  atomsByElement('C'), atomsByElement('C','O') </code>
| Atoms based on their element symbol (field ''_atom_site.type_symbol'').
|-
| <code>  atomsByName() </code>
| <code>  atomsByName('C'), atomsByName('N','CA','C','O') </code>
| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
|-
| <code>  atomsById() </code>
| <code>  atomsById(1), atomsById(1,2,3) </code>
| Atoms based on their integer identifier (field ''_atom_site.id '').
|-
| <code>  atomsByName() </code>
| <code>  atomsByName('C'), atomsByName('N', 'CA', 'C', 'O') </code>
| Atoms based on their atom name (field ''_atom_site.label_atom_id'').
|-
| <code>  residuesByName() </code>
| <code>  residuesByName('GLY'), residuesByName('ALA', 'HEM', 'PO4') </code>
| Residues based on their residue name (field ''_atom_site.label_comp_id'').
|-
| <code>  residuesById() </code>
| <code>  residuesById(100), residuesById(42,157,238) </code>
| Residues based on integer identified (field ''_atom_site.auth_seq_id'').
|-
| <code>  chains() </code>
| <code>  chains('A'), chains('A','B','C') </code>
| Polymer chains based on their id (field ''_atom_site.auth_asym_id'').
|}

{{huge | TODO inside query and logical combinations}}

==PyMOL==
In preparation...

==VMD==
In preparation...