Selecting molecules

GSL provides operators to select entire molecules (i.e., groups of bonded atoms) based on specific criteria.

molecule with (or mol with) operator

  • Function: Selects all atoms in the same molecule(s) as the atoms matching the inner query.

  • Syntax:

    molecule with <query>

    Or:

    mol with <query>

  • Examples:

    molecule with serial 15

    Selects all atoms in the molecule containing the atom with serial number 15.

    molecule with resid 4 17 29

    Selects all atoms in molecules containing any atom from residues 4, 17, or 29.

    molecule with name P

    Selects all atoms in molecules that include an atom named P.

Operator precedence with molecule with

  • Example 1:

    molecule with serial 15 or name BB

    Selects atoms in the molecule containing serial 15 + selects atoms named BB.

  • Example 2:

    molecule with (serial 15 or name BB)

    Selects all atoms in molecules that contain either atom 15 or any atom named BB.

Note:

  • Topology requirement: The system must contain topology information to use molecule selections. Without it, no atoms will be selected. Topology information is available, for instance, in TPR files and some PDB files.