Tutorial

This section provides a tutorial on how to use the AtomPacker package to pack nanoparticle atoms inside a target supramolecular cage. For detailed reference documentation of the functions and classes contained in the package, see the API reference.

For this tutorial, we will use the ZOCXOH cage structure from the ZOCXOH.pdb file.

First of all, import AtomPacker package on Python and create a AtomPacker.Cage object.

>>> import AtomPacker
>>> cage = AtomPacker.Cage()

The Cage object will be used to load the cage structure from the PDB file (eg., ZOCXOH.pdb).

>>> cage.load('ZOCXOH.pdb')

If you want to preview the cage structure, you can use the Cage.preview method.

>>> cage.preview()

The next step is to detect the cavity inside the cage structure. The Cage.detect_cavity method will detect the cavity using the pyKVFinder detection parameters (step, probe_in, probe_out, removal_distance, volume_cutoff, surface). We adjust the parameters to detect the cavity inside the cage structure.

The detected cavity will be stored in the cavity attribute of the Cage object.

>>> cage.detect_cavity(step=0.6, probe_in=1.4, probe_out=10.0, removal_distance=1.0, volume_cutoff=5.0)

If you want to preview the cavity structure for quality control in your cavity detection, you can use the Cavity.preview method.

>>> cage.cavity.preview()

You can access the cavity coordinates using the coordinates attribute of the Cavity object.

>>> print(cage.cavity.coordinates)
[[-11.998       28.644       13.149     ]
 [-11.998       28.644       13.749     ]
 [-11.998       28.644       14.349     ]
 ...
 [ -1.1980003   30.443998    14.349     ]
 [ -1.1980003   30.443998    14.948999  ]
 [ -0.59800035  29.844       13.749     ]]

You can access the cavity grid using the grid attribute of the Cavity object.

>>> print(cage.cavity.grid)
[[[-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  ...
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]]

 [[-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  ...
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]]

 [[-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  ...
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]]

 ...

 [[-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  ...
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]]

 [[-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  ...
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]]

 [[-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  ...
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]
  [-1 -1 -1 ... -1 -1 -1]]]

You can access the cavity volume using the volume attribute of the Cavity object.

>>> print(cage.cavity.volume)
531.58

You can also save the cavity structure using the Cavity.save method.

>>> cage.cavity.save("cavity.pdb")

The next step is to pack the nanoparticle atoms inside the cavity. The Cage.pack method will pack the atoms inside the cavity using the specified parameters (atom_type, lattice_type, a, b, c). We pack a gold (Au) nanoparticle inside the cavity using the face-centered cubic (fcc) lattice.

The packed cluster will be stored in the cluster attribute of the Cage object.

>>> cage.pack(atom_type="Au", lattice_type="fcc", a=None, b=None, c=None)

If you want to preview the cluster structure for quality control, you can use the Cluster.preview method.

>>> cage.cluster.preview()

Also, you can preview the cage, cavity and cluster structure using the Cage.preview method.

>>> cage.preview(show_cavity=True, show_cluster=True)

You can access the cluster coordinates using the coordinates attribute of the Cluster object.

>>> print(cage.cluster.coordinates)
[[ -8.56353   25.718132  13.873403]
 [ -8.56353   27.758131  11.833403]
 [-10.60353   27.758131  13.873403]
 [-10.60353   29.798132  15.913403]
 [ -8.56353   27.758131  15.913403]
 [ -8.56353   29.798132  13.873403]
 [ -8.56353   29.798132  17.953403]
 [ -8.56353   31.838133  11.833403]
 [ -8.56353   31.838133  15.913403]
 [ -8.56353   33.87813   13.873403]
 [ -6.52353   25.718132  15.913403]
 [ -4.48353   25.718132  13.873403]
 [ -6.52353   29.798132  11.833403]
 [ -4.48353   27.758131  11.833403]
 [ -4.48353   29.798132   9.793403]
 [ -6.52353   27.758131  13.873403]
 [ -6.52353   29.798132  15.913403]
 [ -4.48353   27.758131  15.913403]
 [ -4.48353   29.798132  13.873403]
 [ -4.48353   29.798132  17.953403]
 [ -6.52353   31.838133   9.793403]
 [ -6.52353   33.87813   11.833403]
 [ -4.48353   31.838133  11.833403]
 [ -6.52353   31.838133  13.873403]
 [ -6.52353   33.87813   15.913403]
 [ -4.48353   31.838133  15.913403]
 [ -4.48353   33.87813   13.873403]
 [ -6.52353   31.838133  17.953403]
 [ -2.44353   29.798132  11.833403]
 [ -2.44353   27.758131  13.873403]
 [ -2.44353   29.798132  15.913403]
 [ -2.44353   31.838133  13.873403]]

You can also save the cavity structure using the Cluster.save method.

>>> cage.cluster.save("cluster.pdb")

Finally, you can access the summary of the cluster using the summary attribute of the Cluster object.

>>> print(cage.cluster.summary)
                             Au32
Atom Type                      Au
Atom Radius              1.442498
Cavity Volume (Å³)         531.58
Diameter (maximum)       9.123157
Diameter (shape)             8.16
Diameter (volume)        10.12412
Lattice Constants            4.08
Lattice Type                  fcc
Maximum Number of Atoms        43
Number of Atoms                32