| Class | MolEnumerable |
| Parent: | Object |
| Includes: | Enumerable |
The class MolEnumerable provides array-like interfaces (i.e. methods of the module Enumerable) for collective data in Molecule. MolEnumerable does not implement initialize nor new methods. Instead, an instance of MolEnumerable is created by methods of Molecule, i.e. Molecule#atoms, Molecule#bonds, Molecule#angles, Molecule#dihedrals, Molecule#impropers, and Molecule#residues. These methods give MolEnumerable objects that are tied to the Molecule object and have a designated type (atom, bond, etc.)
The index operator MolEnumerable#[] gives an access to the index-th entry of the given type in the associated Molecule. The assignment operator ([]=) is not implemented, because any modification should be performed through methods of Molecule or AtomRef.
Among the six types of MolEnumerable objects, by far the most useful is the "atom" type object, which gives an AtomRef object.
Get the n-th atom, bond, etc. of the associated Molecule. For the atom, the return value is AtomRef. For the residue, the return value is a String. Otherwise, the return value is an Array of Integers. For the atom type, a string description of the atom is also acceptable. See "Atom index" description of Molecule.
% mol.dump 0 MNO.1 Mn1 Mn Mn 10.802 3.764 12.297 0.000 [3,22,4,7,10,13] 1 MNO.1 Mn2 Mn Mn 12.443 2.189 14.627 0.000 [3,33,11,14,16,19] 2 MNO.1 Mn3 Mn Mn 10.196 4.404 15.428 0.000 [3,44,17,20,5,8] 3 MNO.1 O1 ox O 11.148 3.452 14.117 0.000 [0,1,2] ... --> % a = mol.atoms # A MolEnumerable object -->#<MolEnumerable:0x16493688> % ap = a["Mn1"] # Get an AtomRef object -->#<AtomRef:0x1648a54c> % ap.name -->"Mn1" %
Call the block for each atom, bond, etc. The block argument is an AtomRef for atoms, a String for residues, and an Array of Integers for others. For the atoms, a same AtomRef object is passed (with different internal information) for each invocation of block. Otherwise, a new Ruby object will be created and passed for each iteration.