def parallelParser(
pdbFrameName
): #arg: list with universe, start and stop frame, distance and angle to calculate hbond
sys.stdout = open(outputFolder + "/.temp_RIP-MD/temp_hbond", 'a')
sys.stderr = open(outputFolder + "/.temp_RIP-MD/temp_hbond", 'a')
edges_file = open(outputFolder + "/RIP-MD_Results/Edges/" +
pdbFrameName[0] + ".edges",
"a") #0 contains the frame_number
edges_file.write(
"Hydrogen Bonds\nSource Node\tTarget Node\tEdge Name\tDistance\tAngle\n"
)
u = MDAnalysis.Universe(pdbFrameName[1])
h = hbonds.HydrogenBondAnalysis(u,
"protein",
"protein",
distance=Distance,
angle=Angle)
h.run()
h.generate_table()
for hbond in h.table:
node1 = str(hbond[5]) + ":" + dictAtom[hbond[1]] + ":" + str(hbond[6])
node2 = str(hbond[8]) + ":" + dictAtom[hbond[2]] + ":" + str(hbond[9])
if nodes.has_key(node1) and nodes.has_key(node2):
name = node1 + ":" + str(hbond[7]) + "-(HB)-" + node2 + ":" + str(
hbond[10])
distance = str(round(float(str(hbond[11])), 3))
angle = str(round(float(str(hbond[12])), 3))
edges_file.write(
str(nodes[node1]) + "\t" + str(nodes[node2]) + "\t" + name +
"\t" + distance + "\t" + angle + "\n")
edges_file.write("\n")
edges_file.close()
if len(pdbfile) == 0:
with open('gmx_pdb.log', 'w') as outfile:
p = subProcess.Popen(
'gmx trjconv -f {0} -s {1} -o {2} -conect -pbc mol'.format(
grofile, tprfile, pdbfile),
shell=True,
stdout=outfile,
stderr=outfile)
p.wait()
# Compute hbonds for every tracer and output to a different file
for tracer_index, tracer in enumerate(tracers):
u = mda.Universe(pdbfile)
hbond_analysis = hbonds.HydrogenBondAnalysis(
u,
'resid {}'.format(tracer),
'resname HOH or resname SOL',
distance=2.5,
angle=150)
hbond_analysis.run()
hbond_analysis.generate_table()
hbond_info = pd.DataFrame.from_records(hbond_analysis.table)
hbond_dict = {}
for donor, acceptor in zip(hbond_info['donor_resnm'],
hbond_info['acceptor_resnm']):
key = donor + '-' + acceptor
if key in hbond_dict:
hbond_dict[key] += 1
else:
hbond_dict[key] = 1
file_index = (tracer_index * n_sims) + sim_index
#!/bin/python
import MDAnalysis as mda, sys
from MDAnalysis.analysis import hbonds
from datetime import datetime
now = datetime.now()
traj = 'prot_debug.xtc' #sys.argv[1]
top = 'prot.tpr' #sys.argv[2]
outfile = 'hbond_original.dat' #sys.argv[3]
u = mda.Universe(top,traj)
nframe = len(u.trajectory)
start = 0
for iframe in range(start,nframe):
sys.stdout.flush()
sys.stdout.write('%d\r'%iframe)
h = []
h = hbonds.HydrogenBondAnalysis(u, 'protein or resname NH2', 'protein or resname NH2', distance = 3.0, angle = 120.0, pbc = True)
# h = hbonds.HydrogenBondAnalysis(u, 'resname NH2', 'protein or resname NH2', distance = 3.0, angle = 120.0, pbc = True)
h.run(start = iframe, stop = iframe+1)
h.generate_table()
outf = open(outfile,'a')
for hbond in h.table:
outf.write('%d %d %d %s %d %s %s %d %s %.8f %.8f\n'%(hbond[0],hbond[1],hbond[2],hbond[3],hbond[4],hbond[5],hbond[6],hbond[7],hbond[8],hbond[9],hbond[10]))
outf.close()
print(datetime.now()-now)
]))
}
if __name__ == '__main__':
argparser = argparse.ArgumentParser(
description="Script to count hydrogen bonds")
argparser.add_argument('-f', '--file', help="the trajectory file.")
argparser.add_argument('-s', '--struct', help="a structure file")
args = argparser.parse_args()
u = MDAnalysis.Universe(args.struct, args.file)
h_all = hbonds.HydrogenBondAnalysis(u,
"protein",
"protein",
update_selection1=False,
update_selection2=False)
results_all = h_all.run()
cnt = h_all.count_by_time().count
print "All:\t%.3f\t%.3f" % (cnt.mean(), cnt.std())
h_main = HydrogenBondAnalysis_mainchain(u,
"protein",
"protein",
update_selection1=False,
update_selection2=False)
results_main = h_main.run()
cnt = h_main.count_by_time().count
print "Main:\t%.3f\t%.3f" % (cnt.mean(), cnt.std())
us.append(u17)
us.append(u18)
us.append(u19)
us.append(u20)
us.append(u21)
ns = []
dists = []
ave_dists = []
tabs = []
ind = 0
for i in us:
print(ind)
h = hb.HydrogenBondAnalysis(i, 'resid 1-6', 'resid 8-12', distance = 3)
h.run()
h.generate_table()
tab = h.table
tabs.append(tab)
ns.append(len(tab))
ds = np.empty(len(tab))
for j in range(len(tab)):
bonds = tab[j]
ds[j] = bonds[-2]
ave = np.sum(ds)/len(ds)
dists.append(ds)
ave_dists.append(ave)
ind += 1
#!/bin/python
import MDAnalysis as mda, sys
from MDAnalysis.analysis import hbonds
traj = sys.argv[1]
top = sys.argv[2]
outfile = sys.argv[3]
u = mda.Universe(traj, top)
nframe = len(u.trajectory)
start = 0
#for iframe in range(start,nframe):
# sys.stdout.flush()
# sys.stdout.write('%d\r'%iframe)
# h = []
h = hbonds.HydrogenBondAnalysis(u,
'protein',
'resname SOL',
distance=3.0,
angle=120.0,
pbc=True,
verbose=True)
h.run(verbose=True)
print h.count_by_time()
local_hbonds_array = np.zeros((local_n, timesteps), dtype=np.float)
## Do smth
folder = 'data/charmm36m/2us/'
for i, j in enumerate(range(ind_start, ind_end)):
struct = folder + 'chain.pdb'
traj = folder + 'chain_{}.xtc'.format(j + 1)
print(traj)
sys.stdout.flush()
#local_hbonds_array[i] = np.zeros(timesteps, dtype=np.float) + rank
system = md.Universe(struct, traj)
## compute information about hbonds and write it to the 'hb.timeseries'
hb = hbonds.HydrogenBondAnalysis(system)
hb.run(step=step)
## go through the 'hb.timeseries' file and calculate number of bonds for each time frame
## (it's the length of array frame)
hb_number = []
for frame in hb.timeseries:
hb_number.append(len(frame))
hb_number = np.array(hb_number)
local_hbonds_array[i] = hb_number
comm.barrier()
## Gather data
comm.Gather(local_hbonds_array, hbonds_array, root=0)
