Example

This is an example file to showcase the easiest way to run provis in particular how to plot a single protein. For this you should have this file in the root directory of the special directroy structure specified in the setup section of the documentation. Otherwise set the base_path variable of the NameChecker object.

If this is fullfilled path to the “root directory”/data/tmp will automatically be found. This way you can have your pdb files nicely organized in the data/pdb directory (or simply have them in the root directory). Your temporary files will be in the data/tmp directory and the screenshots of the plots in the data/img directory.

Import the necessairy files.

from provis.src.processing.protein import Protein
from provis.src.processing.residue import Residue

First: Define variables needed later:

name = "2fd7"
density = 3.0
plot_solvent = False
msms = True
notebook = False

Second: Create a Protein class instance. Initialize it with your .pdb file name and other parameters.

If you want to plot multiple proteins (or different models of the same trajectory) this is also possible. Simply create a second Protein class instance and pass it to the Plotter

prot = Protein(name, base_path=None, density=density)
prot2 = Protein(name, base_path=None, density=density, model_id=30)

Initialize the Plotter class. This creates all the necessairy classes in the background and you are already good to go!

plot = Plotter(prot, prot2, msms=msms, notebook=notebook, plot_solvent=plot_solvent)

Third: Plot!

Use the Plotter to plot.

plotter.plot_backbone()
plotter.plot_atoms()
plotter.plot_bonds()
plotter.plot_vw()
plotter.plot_stick_point()
plotter.plot_residues()
r = Residue(1)
r.add_residue(3)
r. add_residue(1, 1)
r.remove_residue(1, 1)
plotter.plot_structure(atoms=1, box=1, bonds=1, vw=0, residues=0, res=r, bb=0)

plotter.plot_surface()
plotter.plot_hydrophob()
plotter.plot_shape()
plotter.plot_charge()

And finally clean up everything with the “cleanup” function of the Protein.file_converter (FileConverter class) member variable.

prot.file_converter.cleanup()

The following image shows the hydrophobicity of the 2fd7 protein.