Simple indexing#
There are many ways to view the atoms in the molecule. One is to use the index, e.g.
>>> atom = mol[0]
>>> print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
or
>>> atom = mol.atom(0)
>>> print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
would access the first atom in the molecule. The num_atoms()
function returns the total number of atoms.
>>> print(mol.num_atoms())
74
You can loop over all of the atoms via the atoms() function e.g.
>>> for atom in mol.atoms():
... print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
Atom( C:2 [ 0.00, -0.00, 0.00] )
Atom( C:3 [ 0.66, -0.52, 1.29] )
Atom( C:4 [ 1.42, 2.06, -0.00] )
Atom( C:5 [ 2.16, 1.44, 1.17] )
Atom( C:6 [ 2.81, 2.24, 1.98] )
etc.
You can also loop over a slice of atoms, e.g.
>>> for atom in mol[0:5]:
... print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
Atom( C:2 [ 0.00, -0.00, 0.00] )
Atom( C:3 [ 0.66, -0.52, 1.29] )
Atom( C:4 [ 1.42, 2.06, -0.00] )
Atom( C:5 [ 2.16, 1.44, 1.17] )
or
>>> for atom in mol.atoms(range(0, 5)):
... print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
Atom( C:2 [ 0.00, -0.00, 0.00] )
Atom( C:3 [ 0.66, -0.52, 1.29] )
Atom( C:4 [ 1.42, 2.06, -0.00] )
Atom( C:5 [ 2.16, 1.44, 1.17] )
or
>>> for atom in mol.atoms([0, 2, 5, 8]):
... print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
Atom( C:3 [ 0.66, -0.52, 1.29] )
Atom( C:6 [ 2.81, 2.24, 1.98] )
Atom( C:9 [ 4.65, -0.26, 4.19] )
Molecules can be divided into residues, chains and segments. A residue is a collection of atoms, a chain is a collection of residues, and a segment is an arbitrary, but often-larger collection of atoms within a molecule.
You can access residues, chains and segments in similar ways to accessing atoms, e.g.
>>> res = mol.residue(0)
>>> print(res)
Residue( MOL:1 num_atoms=74 )
>>> for res in mol.residues():
... print(res)
Residue( MOL:1 num_atoms=74 )
You access atoms in a residue, chain or segment in a similar way, e.g.
>>> res = mol.residue(0)
>>> atom = res.atom(0)
>>> print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
>>> for atom in res.atoms([0, 2, 4]):
... print(atom)
Atom( C:1 [ -0.02, 1.53, 0.01] )
Atom( C:3 [ 0.66, -0.52, 1.29] )
Atom( C:5 [ 2.16, 1.44, 1.17] )