.. _atom_selection_usage:

Atom selection in the SilcsBio GUI
----------------------------------

The SilcsBio GUI uses the same atom selection syntax as the NGL
molecular structure viewer. This syntax is described at
https://nglviewer.org/ngl/api/manual/selection-language.html and is
reproduced below for convenience.

Keywords
^^^^^^^^
* all, *
* sidechain
* sidechainAttached (not backbone or .CA or (PRO and .N))
* backbone
* protein
* nucleic
* rna
* dna
* hetero
* ligand (( not polymer or hetero ) and not ( water or ion ))
* ion
* saccharide/sugar
* polymer
* water
* hydrogen
* helix
* sheet
* turn (not helix and not sheet)
* small (Gly or Ala or Ser)
* nucleophilic (Ser or Thr or Cys)
* hydrophobic (Ala or Val or Leu or Ile or Met or Pro or Phe or Trp)
* aromatic (Phe or Tyr or Trp or His)
* amid (Asn or Gln)
* acidic (Asp or Glu)
* basic (His or Lys or Arg)
* charged (Asp or Glu or His or Lys or Arg)
* polar (Asp or Cys or Gly or Glu or His or Lys or Arg or Asn or Gln or Ser or Thr or Tyr)
* nonpolar (Ala or Ile or Leu or Met or Phe or Pro or Val or Trp)
* cyclic (His or Phe or Pro or Trp or Tyr)
* aliphatic (Ala or Gly or Ile or Leu or Val)
* bonded (all atoms with at least one bond)
* ring (all atoms within rings)

Expressions
^^^^^^^^^^^
* residue number: 1, 2, 100
* residue number range: 3-40 (Note that around the dash - no spaces are allowed)
* chain name: :A
* atom name: .CA, .C, .N, ...
* model: /0, /1, ...
* residue name: ALA, GLU, SOL, DMPC, ...
* numeric residue name: [032], [1AB], ...
* list of residue names: [ALA,GLU,MET], [ARG,LYS], ...
* element name: _H, _C, _O, ...
* alternate location: %A, %B, ... or % for non-alternate location atoms
* insertion code: ^A, ^B, ... or ^ for residues with no insertion code

Some of these expressions can be combined (in this order) - residue number
(range), insertion code, chain name, atom name, alternate location, model
- like this

   .. code-block:: none

      // select C-alpha atoms of residue 10 with insertion code A
      // from chain F in model 0 at alternate location C
      10^A:F.CA%C/0

which is the same as

   ::

      10 and ^A and :F and .CA and %C and /0

Single expressions may be left out as long as the order (see above) is kept,
for example:

   ::

      :A/0 # select chain A from model 0

Atomindex
^^^^^^^^^
A list of atom indices can be given as a comma seperated list (no spaces in between) prefixed with the @ character.

   ::

      @0,1,4,5,11,23,42

Logical operators (in order of binding strength)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* NOT
* AND
* OR

Additionally, parentheses () can be used for grouping:

   ::

      :A and ( 1 or 10 or 100 ) # select residues 1, 10 and 100 from chain A