molPX Di-Ala example

Guillermo Pérez-Hernández  guille.perez@fu-berlin.de

In this notebook we will be using a trajectory of Di-Ala-peptide to easily identify conformations in the Ramachandran plot.

import molpx
%matplotlib ipympl

Start from files on disk

top = molpx._molpxdir(join='notebooks/data/ala2.pdb')
MD_trajfiles = [molpx._molpxdir(join='notebooks/data/ala2.mini.xtc')] #short trajectory
rama_files = [molpx._molpxdir(join='notebooks/data/ala2.mini.phi.psi.dat')]

Visualize a FES and the molecular structures behind it

Execute the following cell and click either on the FES or on the slidebar. Once you get familiar with it, try uncommenting these options and see what happens:

• proj_idxs=[1]
• n_overlays=5
• sticky=True
• color_list='random'

With sticky option is True, you can see the effect of a right-click on the dots of the FES

mpx_wdg_box = molpx.visualize.FES(MD_trajfiles,
                                  top,
                                  rama_files,
                                  nbins=50,
                                  proj_labels=['$\phi$',
                                               '$\psi$'],
                                  atom_selection="symbol != H",
                                  #proj_idxs=[1],
                                  #n_overlays=5,
                                  #sticky=True,
                                  #color_list='random'
                                 )
mpx_wdg_box

Visualize trajectories and molecular structures (and the FES, optionally)

from molpx import visualize, _linkutils
from imp import reload
reload(visualize)
reload(_linkutils)
from matplotlib import pyplot as plt
plt.close('all')
mpx_wdg_box = molpx.visualize.traj(MD_trajfiles,
                                   top,
                                   rama_files,
                                   plot_FES = True,
                                   proj_labels=['$\phi$', '$\psi$']
                          )

mpx_wdg_box

Repeat from memory

You can load the trajectory data using mdtraj and numpy and use that directly as an input:

import numpy as np
import mdtraj as md
MD_trajs = [md.load(fname, top=top) for fname in MD_trajfiles]
phi_psi = [np.loadtxt(fname) for fname in rama_files]

mpx_wdg_box = molpx.visualize.FES(MD_trajs,
                                  top,
                                  phi_psi,
                                  nbins=50,
                                  proj_labels=['$\phi$',
                                               '$\psi$'],
                                  atom_selection="symbol != H",
                                  #proj_idxs=[1],
                                  #n_overlays=5,
                                  #sticky=True,
                                  #color_list='random'
                                 )
mpx_wdg_box

The mpx_wdg_box

It is a class derived from the ipython widgets HBox and VBox, with molPX’s extra information as attributes starting with “linked_*”

for attr in dir(mpx_wdg_box):
    if attr.startswith('linked_'):
        print(attr)

linked_ax_wdgs
linked_axes
linked_data_arrays
linked_figs
linked_mdgeoms
linked_ngl_wdgs