def create_hcstrings_states(Assignments, outfile='HCstrings_states.txt'):
SA = hct.get_StatesAssignments(Assignments)
states = SA.keys()
HCstrings_states = {}
n = 0
for state in states:
n += 1
print "Get HC strings for state %d/%d" % (n, len(states))
TrajID = SA[state].keys()
numhelix_state = []
HCstrings_states[state] = []
for trajid in TrajID:
TrajFile = '/Users/tud51931/projects/MSM/msm/ff03-hybridkcenter/sourcedata/Trajectories/trj%s_hc.lh5' % trajid
Traj = Trajectory.LoadFromLHDF(TrajFile)
HCstrings_states[state] += [
Traj['HCs'][i] for i in SA[state][trajid]
]
fn = outfile
if os.path.exists(fn):
newfn = fn + '.bck'
os.system('mv %s %s' % (fn, newfn))
print "Write HCstings of states into %s" % fn
HCfile = open(fn, 'w')
pickle.dump(HCstrings_states, HCfile)
HCfile.close()
print "Done."
def test1():
"""
This test shows how to get the number of helix from a trajectory.
"""
traj = Trajectory.LoadFromLHDF('/Users/tud51931/projects/MSM/msm/ff03-hybridkcenter/sourcedata/Trajectories/trj34.lh5')
numhelix = compute_numhelix_trajectory(traj)
print len(numhelix)
def LoadTrajectory(trajectory):
if isinstance(trajectory, str):
try:
t = Trajectory.LoadFromLHDF(trajectory)
return t
except IOError:
raise IOError("Can not find %s" % trajectory)
elif isinstance(trajectory, Trajectory):
return trajectory
def test2():
"""
This test shows how to create new trj files with hc strings.
"""
path ="/Users/tud51931/projects/MSM/msm/ff03-hybridkcenter/sourcedata/Trajectories"
for i in range(0,100):
Trajfile = "%s/trj%d.lh5"%(path,i)
if os.path.exists(Trajfile):
T = Trajectory.LoadFromLHDF(Trajfile)
CreateTrajFileWithHCstrings(T)
print "Done."
def calculatedistance(AtomName1, ResidueID1, AtomName2, ResidueID2, trajfile,
LongestTrajLength):
""" Calculate the distance between given two atoms in given trajectory"""
t = Trajectory.LoadFromLHDF(trajfile)
Atom1 = (t['AtomNames'] == AtomName1) * (t['ResidueID'] == ResidueID1)
Atom2 = (t['AtomNames'] == AtomName2) * (t['ResidueID'] == ResidueID2)
distance = []
for i in range(len(t['XYZList'])):
x = (t['XYZList'][i, Atom1, :] - t['XYZList'][i, Atom2, :])[0]
x = x.tolist()
distance.append(np.dot(x, x)**0.5)
distance += [-1] * (LongestTrajLength - len(t['XYZList']))
return distance
def FixGenFile(Mapping, GenFile, Outfile='./Gens.Fixed.lh5'):
"""
Use Mapping.dat file get a fixed(mapped) generator file.
New generator file will be Gens.Fixed.lh5
"""
gen = Trajectory.LoadFromLHDF(GenFile)
newgen = copy.deepcopy(gen)
mapping = loadtxt(Mapping)
GeneratorStateID = np.arange(len(gen['XYZList']))
newgen['StateID'] = GeneratorStateID[mapping >= 0]
newgen['XYZList'] = gen['XYZList'][mapping >= 0, :, :]
print "Save to %s" % Outfile
newgen.SaveToLHDF(Outfile)
def Reference_Rg(trajfile):
"""
Compute the Rg from single trajfile.
"""
t = Trajectory.LoadFromLHDF(trajfile)
Rg = []
for i in range(len(t['XYZList'])):
XYZ = t['XYZList'][i, :, :]
mu = XYZ.mean(0)
mu = mu.tolist()
XYZ2 = XYZ - np.tile(mu, (len(XYZ), 1))
Rg.append(((XYZList**2).sum() / n_atoms)**(0.5))
return Rg
import os, sys
import numpy as np
from msmbuilder import Trajectory
sys.path.append('~/scripts/gfzhou/')
import HelixCoilTools as hct
from scipy import savetxt
"""
This script is to get the number of helix from trajectories.
"""
datafile = "./numhelix_alltraj.txt"
if os.path.exists(datafile):
print "%s already exists!" % datafile
print "quit."
sys.exit()
path = "/Users/tud51931/projects/MSM/msm/ff03-hybridkcenter/sourcedata/Trajectories"
numhelix_alltraj = -1 * np.ones((100, 8000), dtype=int)
for i in range(100):
Trajfile = "%s/trj%d.lh5" % (path, i)
if os.path.exists(Trajfile):
T = Trajectory.LoadFromLHDF(Trajfile)
print "Compute number of helix for %s" % Trajfile
numhelix = hct.compute_numhelix_trajectory(T)
numhelix_alltraj[i][:len(numhelix)] = numhelix[:]
print "Save data to %s" % datafile
savetxt(datafile, numhelix_alltraj)
print "Done."
def GetHCStringsforTrajectory(trajectory):
if isinstance(trajectory, str):
gens = Trajectory.LoadFromLHDF(trajectory)
dihedrals = hct.ComputeDihedralsFromTrajectory(gens)
HCs = hct.ConvertDihedralsToHCStrings(dihedrals)
print HCs
