def ramachandran_plot(atomgroup,
selection,
outputfile1,
outputfile2,
image_format='png'):
# plot standard mdanalysis and seaborn 2D with kde
R = Ramachandran(atomgroup).run()
fig, ax = plt.subplots(figsize=plt.figaspect(1))
R.plot(ax=ax, color='k', marker='.', ref=True)
a = R.angles.reshape(np.prod(R.angles.shape[:2]), 2)
# open hdf file
with h5py.File(args.o_data1, 'a') as f:
setname = "%s" % (selection)
f["/" + setname + "/ramachandran/phi"] = a[:, 0]
f["/" + setname + "/ramachandran/psi"] = a[:, 1]
plt.tight_layout()
# svg is better but sticking with png for now
plt.savefig(outputfile1, format=image_format)
sns.reset_defaults()
importlib.reload(plt)
importlib.reload(sns)
with sns.axes_style("white"):
h = sns.jointplot(x=a[:, 0], y=a[:, 1], kind="kde", space=0)
h.set_axis_labels(r'$\phi$ (deg)', r'$\psi$ (deg)')
h.ax_joint.set_xlim(-180, 180)
h.ax_joint.set_ylim(-180, 180)
h.ax_joint.xaxis.set_major_locator(ticker.MultipleLocator(60))
h.ax_joint.yaxis.set_major_locator(ticker.MultipleLocator(60))
plt.savefig(outputfile2, format=image_format, bbox_inches='tight')
def test_ramachandran(self, universe, rama_ref_array):
rama = Ramachandran(universe.select_atoms("protein")).run()
assert_almost_equal(rama.angles,
rama_ref_array,
5,
err_msg="error: dihedral angles should "
"match test values")
def test_ramachandran_single_frame(self, universe, rama_ref_array):
rama = Ramachandran(universe.select_atoms("protein")).run(start=5,
stop=6)
assert_almost_equal(rama.angles[0],
rama_ref_array[5],
5,
err_msg="error: dihedral angles should "
"match test values")
def test_ramachandran_residue_selections(self, universe):
rama = Ramachandran(universe.select_atoms("resname GLY")).run()
test_rama = np.load(GLYRamaArray)
assert_almost_equal(rama.angles,
test_rama,
5,
err_msg="error: dihedral angles should "
"match test values")
def angle_to_list(u):
from MDAnalysis.analysis.dihedrals import Ramachandran
r = u.select_atoms("resid 2")
R = Ramachandran(r).run()
phi = []
psi = []
for line in list(R.angles):
phi.append(line.tolist()[0][0])
psi.append(line.tolist()[0][1])
return phi, psi
def ramachandran(u):
Ramachandran(u.select_atoms("protein")).run()
import pdb
import numpy as np
import MDAnalysis as mda
u = mda.Universe('prot.psf', 'out.xtc')
# selection of atomgroups
ags = [res.phi_selection() for res in u.residues[4:9]]
from MDAnalysis.analysis.dihedrals import Dihedral
from MDAnalysis.analysis.dihedrals import Ramachandran
#R = Dihedral(ags).run()
r = u.select_atoms("resid 5-10")
R = Ramachandran(r).run()
#R = Dihedral(ags).run()
np.save('out2.npy', R.angles)
#R.save()
#import matplotlib.pyplot as plt
#fig, ax = plt.subplots(figsize=plt.figaspect(1))
#R.plot(ax=ax, color='k', marker='s')
#pdb.set_trace()
def ramachandran(u: mda.Universe, label: str, output_filepath: str):
sel = u.select_atoms(STANDARD_SELECTION)
R = Ramachandran(sel).run()
mdplots.plot_ramachandran(R, label, output_filepath)
import matplotlib.pyplot as plt
import MDAnalysis as mda
from MDAnalysis.analysis.dihedrals import Ramachandran
u = mda.Universe("pro.gro", "test.xtc")
r = u.select_atoms("protein")
R = Ramachandran(r).run()
fig, ax = plt.subplots()
R.plot(ax=ax, color='k', marker='s', ref=True)
plt.show()
# UCSF Biophysics Bootcamp
# Ramachandran Project Assistance
# August 27, 2020
"""
This is an alternate method for generating Ramachandran plots
that uses the MDAnalysis package to calculate dihedral angles.
"""
# Import useful modules
import sys, re, math
import numpy as np
import matplotlib.pyplot as plt
import MDAnalysis as mda
from MDAnalysis.analysis.dihedrals import Ramachandran
## 1. Read in PDB file
read_3emn = mda.Universe("/home/yessica/VDAC_project/bin/pdbs/3emn_noalt.pdb")
## 2. For every residue, extract the desired atoms with the corresponding Names
pol_atoms = read_3emn.select_atoms("protein")
## 4. Calculate the phi and psi angles
angles = Ramachandran(pol_atoms).run()
## 5. Make a scatter plot of phi and psi values
fig, ax = plt.subplots(figsize=plt.figaspect(1))
angles.plot(ax=ax, color='k')
plt.show()
def test_plot(self, universe):
ax = Ramachandran(
universe.select_atoms("resid 5-10")).run().plot(ref=True)
assert isinstance(ax, matplotlib.axes.Axes), \
"Ramachandran.plot() did not return and Axes instance"
def test_None_removal(self):
with pytest.warns(UserWarning):
u = mda.Universe(PDB_rama)
rama = Ramachandran(u.select_atoms("protein").residues[1:-1])
def test_protein_ends(self, universe):
with pytest.warns(UserWarning):
rama = Ramachandran(universe.select_atoms("protein")).run()
def test_outside_protein_length(self, universe):
with pytest.raises(ValueError):
rama = Ramachandran(universe.select_atoms("resid 220")).run()