Selection syntax

MView provides a simple way to collect the id of atoms and bonds in the system using a syntax combining built-in keywords and python list syntax. A syntax-block is composed of a keyword and its input, and multiple syntax-blocks can be concatenated using the operations available.

The inital operations currently available are: + and -

The syntax-block operations currently available are: and, in, not


The keywords currently available are:

Keyword    Subgroup     Syntax   Input type   Example 
      Numeric Strings
  • all
  All atoms in the system    all   X X  all
  • atom
   Atoms
   atom <pylist>   Atom ids Atomic Symbols  atom ["C","O"]
  • attype
  Atom types    attype <pylist>   X  Atom type label  attype ["ca","Hc"]
  • atlabel
  Atom labels    atlabel <pylist>   X Atom labels  atlabel "cc1"
  • fragment
  Fragments    fragment <pylist>   Fragment ids Fragment labels  fragment range(0,3)
  • residue
  Residues    residue <pylist>    Residue ids Residue labels  residue range(4,7)+[11,23]
  • group
  Groups    group <pylist>    Group ids Group labels  group 3
  • chain
  Chain    group <pylist>
   Chain ids Chain labels  chain ["A","B"]
  • within
  Atoms    within dist <syntax-block>
   Single distance value X  within 3 atom "Mg"
  • rep
  Representations    rep <pylist>
   Rep. ids X  rep [0,3]
  • sel
  Selected atoms    sel    X X  sel
  • complete
  Complete subsets   complete <type>   subset type x complete residue
  • bond
  Bonds    bond <pylist>
   Bond ids  Atom types forming the bond "C-H"  bond ["C-O","h-N"]

 

Examples

atom

Collects all atoms matching the information provided.

The lists of intergers are processed as atom ids, and lists of string are processed as atomic symbols.

atom range(0,6)       atom range(0,6) and atom ["O","n"]       atom range(0,6) and atom ["O","n"] and bond
keyword atom 1     keyword atom 2     keyword atom 3

 

within

 Collects the ids of all atoms within a certain radius of the atoms of reference.

within 10 rep 0 and bond        within 20 rep 0 and bond        within 30 rep 0 and bond 
within 1      within 2      within 3 

 

complete

  Collects the ids of atoms in order to complete a subset.

The subsets currently accepted are fragment, residue, and group.

rep 0
      within 10 rep 0 and bond
      within 10 rep 0 and complete residue and bond
within complete 1      within complete 2      within complete 3 

 


 


 

 

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