A plot of interactions over time is shown only in black and gray

[AbdulrahamnEid]

I'm trying to show the schematics of protein-ligand interactions in 200 ns from gromacs simulation, but the Figs are only shown in black and gray. What is the solution to that problem?

#!/usr/bin/env python

coding: utf-8

In[1]:

import prolif as plf
import MDAnalysis as mda
from MDAnalysis.topology.guessers import guess_types
import seaborn as sns
import pandas as pd

In[6]:

dir_= r'E:\SCI\MDS\prolif\MVC\223232\'
u = mda.Universe(dir_+'MD.gro',
dir_+'MD_center_test.xtc', guess_bonds=True
)
guessed_elements = guess_types(u.atoms.names)

u.add_TopologyAttr('elements', guessed_elements)

# create selections for the ligand and protein

lig = u.atoms.select_atoms("resname LIG")
prot = u.atoms.select_atoms("protein")

In[7]:

from rdkit import Chem
from rdkit.Chem import Draw
import math as m

create a molecule from the MDAnalysis selection

lmol = plf.Molecule.from_mda(lig)

cleanup before drawing

mol = Chem.RemoveHs(lmol)
mol.RemoveAllConformers()
Draw.MolToImage(mol, size=(400,200))

In[10]:

pmol = plf.Molecule.from_mda(prot)
frags = []

to show all residues, simply use for res in pmol:

for i in range(300):
res = pmol[i]
mol = Chem.RemoveHs(res)
mol.RemoveAllConformers()
frags.append(mol)
Draw.MolsToGridImage(
frags,
legends=[str(res.resid) for res in pmol],
subImgSize=(200, 140),
molsPerRow=4,
maxMols=prot.n_residues,
)

In[11]:

use default interactions

fp = plf.Fingerprint()

run on a slice of frames from begining to end with a step of 1

fp.run(u.trajectory, lig, prot, residues=None, progress=True, n_jobs=None) # detect amino acids close to the ligand (6 A)

In[26]:

df = fp.to_dataframe()

show only the 10 first frames

df.head(5)
df = df[::10]
df

In[36]:

to show the occurence of interaction types for each amino acid

prob=0.5

calculate the occurence of each interaction on the trajectory

occ = df.mean()

restrict to the frequent ones

inter = occ.loc[occ >= prob]
print(inter)
print(inter.reset_index()['interaction'].unique())

In[37]:

drop the ligand residue column since there's only a single ligand residue

df = df.droplevel("ligand", axis=1)
df.head(5)

In[43]:

def plot(sub_data, part, dpi):
sns.set_theme(font_scale=.8, style="white", context="talk")
g = sns.catplot(
data=sub_data, x="interaction", y="Time (ns)", hue="interaction", col="residue",
hue_order=sub_data.interaction.unique(),#['Hydrophobic', 'HBAcceptor', 'PiCation', 'HBDonor', 'PiStacking'], #plf.Fingerprint.list_available(show_hidden=False),#["Hydrophobic", "HBDonor", "HBAcceptor", "PiStacking", "CationPi", "Cationic"],
height=3, aspect=0.2, jitter=0, sharex=False, marker="", s=8, linewidth=.3#, pointsize=2
)
g.set_titles("{col_name}")
g.set(xticks=[], ylim=(-.5, data['Time (ns)'].max()))#(data.Frame.max()+1)/10))
g.set_xticklabels([])
g.set_xlabels("")
g.fig.subplots_adjust(wspace=0)
g.add_legend()
g.despine(bottom=True)
for ax in g.axes.flat:
#ax.invert_yaxis()
ax.set_title(ax.get_title(), pad=15, rotation=60, ha="center", va="baseline")
g.savefig(dir+f"/interactions_occurence_larger_{prob}part{part}.tiff",
dpi=dpi)

reorganize data

data = df.reset_index()
data = pd.melt(data, id_vars=["Frame"], var_name=["residue","interaction"])
data = data[data["value"] != False]
data["Time (ns)"] = data["Frame"]*.01
data.reset_index(inplace=True, drop=True)

plot

number_figs = 3
aa_numb = int(m.ceil(len(data.residue.unique())/number_figs))
unique = data.residue.unique()
for i in range(number_figs):
if (i+1) * aa_numb > len(data.residue.unique()):
aa_names = unique[iaa_numb : ]
else:
aa_names = unique[iaa_numb : (i+1)*aa_numb]
sub_data = data[data.residue.isin(aa_names)]
plot(sub_data, i+1, dpi=500)

[cbouy]

Hi @AbdulrahamnEid,

try downgrading your version of seaborn: pip install seaborn<=0.11.2

[MatiasMarambio]

Hi @cbouy I have the same problem and I try to use the version 0.11.2 of seaborn but the problem is not fixed
can you help me?

thanks

[cbouy]

@MatiasMarambio the newest version of ProLIF (v2) has a plot_barcode method which addresses this issue. You can check the documentation tutorials to use it.

[MatiasMarambio]

Hi! now it is works, but now I'm trying to obtain the barcode of the new version and when I use the command line, I obtain the next error:

[cbouy]

That error message comes from the older version of ProLIF, you didn't install v2 (or didn't restart your kernel in the notebook)