def test_HydrogenBondLifetimes(self, universe, selection):
hbonds = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(universe,
selection,
selection,
distance=3.5,
angle=120.0)
hbonds.run(start=0, stop=4)
hbonds.autocorrelation(tau_max=3)
assert_almost_equal(hbonds.acf_timeseries[3], 0.75)
def test_HydrogenBondLifetimes_growing_continuous(self, universe, selection):
hbonds = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(universe,
selection,
selection,
distance=3.5,
angle=120.0)
hbonds.run(start=0, stop=9)
hbonds.autocorrelation(tau_max=5)
assert all([frame >= framePlus1 for frame, framePlus1 in zip(hbonds.acf_timeseries, hbonds.acf_timeseries[1:])])
def get_hbonds(self, distance=3.0, angle=160.0):
sys.path.insert(0, "/home/joe/git/md_analysis/")
import joe_hbonds as joe
self.hbond_distance = distance
self.hbond_angle = angle
hbonds = joe.HydrogenBondAnalysis(self.universe,
'protein',
'protein',
update_selection1=True,
update_selection2=True,
detect_hydrogens='distance',
distance=self.hbond_distance,
angle=self.hbond_angle,
distance_type="heavy")
hbonds.run()
hbonds_occupancy = hbonds.count_by_type()
hbonds_occupancy_list = hbonds_occupancy.tolist()
fp = open(self.out_path + self.out_file + "_hbonds.dat", 'w')
for i in range(len(hbonds_occupancy_list)):
fp.write("{0}\n".format(hbonds_occupancy_list[i]))
fp.close()
def GetTimeSeries(psf, dcd, outname, libpath):
"""
Get time series data for Hbond (MDanalysis)
:param psf: PSF file
:param dcd: trajectory file (DCD)
:param outname: output name
:return: times series results (Pandas dataframe)
"""
donor, acceptor, head, glycerol, phos = CollectHbondCandInfo(libpath)
universe = mda.Universe(psf, dcd)
hbonds = mda.analysis.hbonds.HydrogenBondAnalysis(universe,
"segid MEMB",
"segid PROA",
donors=donor,
acceptors=acceptor)
hbonds.run()
hbonds.generate_table()
hbonds_data = pd.DataFrame.from_records(hbonds.table)
hbonds_data.to_csv("%s_hbonds_analysis_raw_data.csv" % outname)
return hbonds_data
# This code computes the H-bond occupancy
# Here we are considering only the H-bonds from the
# Has to be upgraded to use pandas
import MDAnalysis
import MDAnalysis.analysis.hbonds
var1 = '/Users/keshavpatil/Desktop/BRAF/100ns_unbiased/active_braf/unb100.xtc'
var2 = '/Users/keshavpatil/Desktop/BRAF/100ns_unbiased/active_braf/unb100.gro'
u = MDAnalysis.Universe(var2, var1)
hbonds = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u,
'protein',
'protein',
distance=3.0,
angle=120.0)
hbonds.run()
hbonds_occupancy = hbonds.count_by_type()
hbonds_occupancy_list = hbonds_occupancy.tolist()
# get the specific H-bonds:
# By specific I mean: the H-bonds whose either the
# donor_atom or the acceptor_atom or both belong to
# alpha-helix or the activation loop
# This is ofcourse dependent on the
# type of kinase. The github repository which
# has the info on this for somewhere around hundreds of
# kinases is: https://github.com/ejjordan/mutator/blob/master/all_kinase.csv
# Take this input from the user
print('Enter the threshold for the h-bond occupany')
threshold = input()