# load data
# pdb file from: http://www.rcsb.org/pdb/explore/explore.do?pdbId=1l2y
import warnings
warnings.filterwarnings('ignore', category=DeprecationWarning)

import pytraj as pt

traj = pt.iterload('1L2Y.pdb', top='1L2Y.pdb')
traj

pytraj.TrajectoryIterator, 38 frames: 
Size: 0.000258 (GB)
<Topology: 304 atoms, 20 residues, 1 mols, PBC with box type = ortho>

# search hbonds for all residues
# dump data to `dataset` (similiar to python'list and dict)
dataset = pt.search_hbonds(traj, dtype='dataset')
print(dataset)
# 0: no hbond
# 1: there is hbond

<pytraj.DatasetList with 32 datasets>
total_solute_hbonds
[6 7 8 ..., 7 6 6]

ASN1_O-GLN5_N-H
[1 0 0 ..., 0 0 0]

ARG16_O-TRP6_NE1-HE1
[1 1 1 ..., 1 1 1]
...

ASP9_OD2-SER14_OG-HG
[0 0 0 ..., 0 0 0]

ASP9_OD2-ARG16_NH1-HH11
[0 0 0 ..., 0 0 0]

# get total solute hbonds
print(dataset['total_solute_hbonds'])

<pytraj.array.DataArray: size=38, key=total_solute_hbonds, dtype=int32, ndim=1> 
values:
[6 7 8 ..., 7 6 6]

# take data for specific hbond
print(dataset['ARG16_O-TRP6_NE1-HE1'])

<pytraj.array.DataArray: size=38, key=ARG16_O-TRP6_NE1-HE1, dtype=int32, ndim=1> 
values:
[1 1 1 ..., 1 1 1]

# take hbond for only ASP9
glu5 = dataset.filter(lambda x: 'ASP9' in x.key)
print(glu5.keys())

['ASP9_O-SER14_OG-HG', 'ASP9_OD2-ARG16_NH1-HH12', 'ASP9_OD2-ARG16_NH2-HH22', 'ASP9_OD2-ARG16_NE-HE', 'ASP9_OD1-LYS8_NZ-HZ1', 'ASP9_OD2-ARG16_NH2-HH21', 'ASP9_OD1-SER14_OG-HG', 'GLN5_O-ASP9_N-H', 'ASP9_OD2-SER14_OG-HG', 'ASP9_OD2-ARG16_NH1-HH11']

glu5_val = glu5.values
print(glu5_val)

print('total hbonds for GLU5 per frame')
import numpy as np
glu5_total = np.sum(glu5_val, axis=0)
print(glu5_total)

[[1 1 1 ..., 0 0 0]
 [0 1 0 ..., 0 0 0]
 [0 1 0 ..., 0 0 0]
 ..., 
 [0 0 0 ..., 0 0 0]
 [0 0 0 ..., 0 0 0]
 [0 0 0 ..., 0 0 0]]
total hbonds for GLU5 per frame
[1 3 1 ..., 0 0 0]

# plot
%matplotlib inline

from matplotlib import pyplot as plt
plt.plot(glu5_total, 'ro')

[<matplotlib.lines.Line2D at 0x1072b06d8>]

Hbond¶