# Viewing Molecules¶

## Using the MolecularViewer¶

MolecularViewer is a library-agnostic tool to display molecules in chemview. In this section we will see how to use it, and what representations are currently available.

To create a MolecularViewer instance we need the **positions** of the atoms,
as an array of x, y, z coordinates, and a description of
the features and connectivity of the system (also called **topology**).

The *topology* is a nested dictionary with the following fields:

- atom_types
(required field) A list of strings, each representing an atom symbol.

Example:

`["H", "C", "N", "O", ..]`

- bonds
A list of tuples indicating the index of the bond extrema.

Example:

`[(0, 1), (1, 2), ...]`

- atom_names
A list of atom names, like the ones used in pdb files

Example:

`["HA", "CA", "N", ...]`

- residue_indices
A nested list of indices (as tuples) for each residue present in the molecule.

Example:

`[(0, 1, 2, 3, 4, 5), (6, 7, 8, 9, 10), ... ]`

- residue_types
A list of strings corresponding to residue types.

Example:

`["ALA", "GLY", ...]`

- secondary_structure
A list of strings representing the secondary structure of each residue,

`H`

for helix,`E`

for sheet,`C`

for coil.Example:

`["H", "H", "H", "C", "C", "E", "E" ...]`

Note

As the description of the topology is quite involved, you can combine chemview with another library that provides the topology directly from the chemical data files (such as chemlab and mdtraj).

Once you create your molecular viewer, you can display the molecule in a variety of ways:

points: the atomic positions will be represented as points, color-coded by atom.

Example:

mv.points()

lines: the bonds will be represented as lines

Example:

mv.lines()

ball_and_sticks: the classical ball and stick representation. Atom are spheres, bonds are cylinders. At the moment this representation is not suitable for very large molecules and animations.

Example:

mv.ball_and_sticks()

line_ribbon: the protein backbone is represented by a smooth line.

Example:

mv.line_ribbon()

cylinder_and_strand: the protein backbone is represented by a smooth, solid tube, and the helices are represented as cylinders.

Example:

mv.line_ribbon()

See also

The `MolecularViewer`

documentation at api/index

You can also add isosurfaces with the command `MolecularViewer.add_isosurface()`

that takes a function and an isovalue. Given a function \(f(x, y, z)\), an isosurface is the set of points for which the function assumes a certain value. For example if you want to plot the surface of sphere with radius 1, we can select a function of the type:

and set the isovalue would be 1, so that we obtain the surface whose set of points that satisfy the equation of a sphere:

See also

## Viewing Molecules with Chemlab¶

The development version of chemlab provides a preliminary integration with chemview, check out the example notebook.

## Viewing Molecules with MDTraj¶

In the near future, mdtraj will provide integration.

While you wait, take a look at the docs and learn about mdtraj.

## Making custom representations¶

chemview provides an easy-to-use API to create new ways to display your data and build novel tools. The class RepresentationViewer contains methods to display common 3D shapes.

To create a RepresentationViewer instance, type:

```
rv = RepresentationViewer()
rv
```

This will display an empty viewer. To add objects, we can use the method
`RepresentationViewer.add_representation()`

. The method takes two
parameters: the **name** of the representation to display, and a dictionary of
**options**, that are specific for each representation.

For example, to add three points on the screen we will use the following parameters:

```
rv.add_representation('points', {'coordinates', np.array([[0.0, 0.0, 0.0],
1.0, 0.0, 0.0],
2.0, 0.0, 0.0])})
```

Warning

The RepresentationViewer communicates directly with the Javascript layer and, being outside of the realm of Python doesn’t provide nice exception tracebacks. Be rigorous with parameter types.

For more examples (with pictures) you can check the test notebook.

Below reference of the available representations, along with their options:

- points
display a set of coordinates as points with different colors and sizes.

Options:

- coordinates
numpy array of 3D coordinates (float32)

- sizes
python list of floats representing the size of each point

- colors
python list of 32 bit integers representing the color of each point.

Example using HEX representation:

`[0xffffff, 0x00ffff, 0xff0000, ...]`

- lines
display a set of lines with different colors.

Options:

- startCoords
- numpy array of 3D coordinates representing the starting point of each line

- endCoords
- numpy array of 3D coordinates representing the ending point of each line

- startColors
- list of 32 bit integers corresponding to the color of the starting point

- endColors
- list of 32 bit integers corresponding to the color of the ending point

- cylinders
display a set of cylinders. This is a slow primitive, avoid using it for animations; use lines instead.

Options:

- startCoords
- numpy array of 3D coordinates representing the starting point of each cylinder

- endCoords
- numpy array of 3D coordinates representing the ending point of each cylinder

- colors
- list of 32 bit integers corresponding to the color of each cylinder

- radii
- list of float corresponding to the radius of each cylinder

- smoothline
display a smooth line that passes through a set of points.

Options:

- coordinates
- numpy array of 3D coordinates representing the control points of the smooth line.

- color
- 32 bit integer (hex) color of the line

- resolution
- int, number of subdivision along the path between control points. Controls the smoothness

- smoothtube
display a smooth tube that passes through a set of points. This is a slow primitive, not suitable for animating very large objects; use smoothline instead.

Options:

- coordinates
- numpy array of 3D coordinates representing the control points of the smooth tube.

- color
- 32 bit integer (hex) color of the tube

- radius
- float representing the radius of the tube

- resolution
- int, number of subdivision along the path between control points. Controls the smoothness

- spheres
display a set of spheres. This primitive is slow, avoid using it for animations; use points instead.

Options:

- coordinates
- numpy array of 3D coordinates representing the position of the spheres.

- colors
- list of 32 bit integers representing the color of each sphere

- radii
- list of float, radius of each sphere

- resolution
- int, number of vertical and horizontal subdivisions to make the sphere: high resolution means slow performance.