def test_hbond_general(self):
traj = pt.iterload(fn('DPDP.nc'), fn('DPDP.parm7'))
dslist = pt.search_hbonds(traj, dtype='dataset')
for key in dslist.keys():
if 'UU' not in key:
assert len(dslist[key].values) == traj.n_frames
mydict = dslist.to_dict()
mydict_np = dslist.to_dict()
assert len(mydict.keys()) == dslist.size
assert len(mydict_np.keys()) == dslist.size
for key in mydict.keys():
mydict[key] = np.asarray(mydict[key])
aa_eq(mydict[key], mydict_np[key])
# raise if dtype='hbond' and series=False
with pytest.raises(ValueError):
pt.hbond(traj, series=False, dtype='hbond')
def test_pmap_hbond(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
hbond_data_serial = pt.hbond(traj, dtype='dict')
hbond_data_pmap = pt.pmap(pt.hbond, traj, n_cores=3)
assert sorted(hbond_data_serial.keys()) == sorted(
hbond_data_pmap.keys())
for key, value in hbond_data_serial.items():
aa_eq(hbond_data_serial[key], hbond_data_pmap[key])
assert value.dtype == np.int32
with pytest.raises(ValueError):
# cpptraj style
# not support yet.
pt.pmap(['radgyr', 'hbond'], traj, n_cores=3)
def test_hbonds_solvent_bridge(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
# find solvent bridge between residue 10 and 11.
hb = pt.hbond(
traj, ':10,11', solvent_donor=':WAT', solvent_acceptor=':WAT')
assert hb._get_bridge() == \
[[('WAT208', 'THR10', 'TRP11')],
[('WAT208', 'THR10', 'TRP11')],
[('WAT208', 'THR10', 'TRP11')],
[('WAT208', 'THR10', 'TRP11')],
[],
[],
[],
[],
[],
[('WAT266', 'THR10', 'TRP11')]]
def test_hbond_general(self):
traj = pt.iterload("./data/DPDP.nc", "./data/DPDP.parm7")
dslist = pt.search_hbonds(traj, dtype='dataset')
for key in dslist.keys():
if 'UU' not in key:
assert len(dslist[key].values) == traj.n_frames
mydict = dslist.to_dict()
mydict_np = dslist.to_dict()
assert len(mydict.keys()) == dslist.size
assert len(mydict_np.keys()) == dslist.size
for key in mydict.keys():
mydict[key] = np.asarray(mydict[key])
aa_eq(mydict[key], mydict_np[key])
# raise if dtype='hbond' and series=False
self.assertRaises(ValueError,
lambda: pt.hbond(traj, series=False, dtype='hbond'))
def test_pmap_hbond_with_solvent_bridge(self):
for trajin_fn, parm_fn in [('tz2.ortho.nc', 'tz2.ortho.parm7'),
('tz2.truncoct.nc', 'tz2.truncoct.parm7')]:
traj = pt.iterload(fn(trajin_fn), fn(parm_fn))
kwargs = dict(solvent_donor=':WAT@O', solvent_acceptor=':WAT')
hbond_data_serial = pt.hbond(traj, dtype='dict', **kwargs)
hbond_data_pmap = pt.pmap(
pt.hbond, traj, dtype='dict', n_cores=3, **kwargs)
assert sorted(hbond_data_serial.keys()) == sorted(
hbond_data_pmap.keys())
for key, value in hbond_data_serial.items():
if key.endswith('HB[ID]'):
assert hbond_data_pmap[key].tolist() == hbond_data_serial[
key].tolist()
print(hbond_data_pmap[key].tolist(),
hbond_data_serial[key].tolist())
else:
aa_eq(hbond_data_serial[key], hbond_data_pmap[key])
assert value.dtype == np.int32
def main(traj):
'''
氢键分析与数据导出
Paramters
----------
traj: MD轨迹 pytraj对象
'''
print('\nStart H-Bond Analysis...')
# hbond 分析
hb = pt.hbond(
traj,
mask=':*',
distance=4,
options='avgout ./pynalysis/hbond/avg-hbd.dat printatomnum nointramol')
'''
options可填参数与cpptraj一致
输出氢键平均信息文件
打印原子序号
仅计算分子间氢键
distance: 识别氢键cutoff值 默认值3埃
'''
distance_mask = hb.get_amber_mask()[0]
print('Hbond Distance Mask: {} \n '.format(distance_mask))
angle_mask = hb.get_amber_mask()[1]
print('Hbond Hngle Mask: {} \n'.format(angle_mask))
print("\nHbond Data")
print(hb.data) # 1: have hbond; 0: does not have hbond
# 创建excel工作表
hbondxlsx = xlsxwriter.Workbook('./pynalysis/hbond/hbond.xlsx')
distance_sheet = hbondxlsx.add_worksheet('Distance')
angle_sheet = hbondxlsx.add_worksheet('Angle')
# 写入header
col = 0
row = 0
for hbond_mask in distance_mask:
distance_sheet.write(row, col, hbond_mask)
col += 1
col = 0
row = 0
for hbond_mask in angle_mask:
angle_sheet.write(row, col, hbond_mask)
col += 1
# 计算氢键距离
dist = pt.distance(traj, distance_mask)
print('\nAll Hbond Distance: \n', dist, end='\n')
# 计算氢键角度
angle = pt.angle(traj, angle_mask)
print('\nAll Hbond Angle: \n', angle, end='\n')
print('\nSaving Data...', end='\n')
# 写入氢键长度角度数据
row = 1
col = 0
for i in dist[:]:
for j in i[:]:
distance_sheet.write(row, col, j)
row += 1
col += 1
row = 1
row = 1
col = 0
for l in angle[:]:
for k in l[:]:
angle_sheet.write(row, col, k)
row += 1
col += 1
row = 1
hbondxlsx.close()
print('\nDistance and Angle Raw Data(hbond.xlsx) saved.', end='\n')
print('\nH Bond Analysis Complete\n')
print(''.center(80, '*'))
import pytraj as pt
from pytraj.testing import Timer
traj = pt.iterload('GAAC3.1000frames.nc', 'GAAC.parm7', frame_slice=(0, 1000))
hb = pt.hbond(traj, '!:WAT')
masklist = hb._amber_mask()
cpp_cm = ['distance ' + _ for _ in masklist]
cpp_mask = '\n'.join(cpp_cm)
@Timer()
def test_pytraj():
print('pytraj')
traj = pt.iterload('GAAC3.1000frames.nc', 'GAAC.parm7', frame_slice=(0, 1000))
data = pt.distance(traj, masklist)
#print(data)
@Timer()
def test_state():
print('cpptraj')
state = pt.load_cpptraj_state('''
parm GAAC.parm7
trajin GAAC3.1000frames.nc 1 1000
{0}'''.format(cpp_mask))
state.run()
#print(state.data[1:].values)
test_pytraj()
test_state()
# timing output (seconds) with 1000 frames.
import pytraj as pt
from pytraj.testing import Timer
traj = pt.iterload('GAAC3.1000frames.nc', 'GAAC.parm7', frame_slice=(0, 1000))
hb = pt.hbond(traj, '!:WAT')
masklist = hb._amber_mask()
cpp_cm = ['distance ' + _ for _ in masklist]
cpp_mask = '\n'.join(cpp_cm)
@Timer()
def test_pytraj():
print('pytraj')
traj = pt.iterload('GAAC3.1000frames.nc',
'GAAC.parm7',
frame_slice=(0, 1000))
data = pt.distance(traj, masklist)
#print(data)
@Timer()
def test_state():
print('cpptraj')
state = pt.load_cpptraj_state('''
parm GAAC.parm7
trajin GAAC3.1000frames.nc 1 1000
{0}'''.format(cpp_mask))
state.run()
#print(state.data[1:].values)
