def extract_frames_from_trajectory(options):
#create a temporary directory to run the model
cmsfile=os.path.abspath(options.cmsfile)
trjfile=os.path.abspath(options.trjfile)
tmp_folder = "/tmp/extractmd_%s/" % (os.getpid())
if not os.path.exists(tmp_folder) :
os.mkdir(tmp_folder)
os.chdir(tmp_folder)
asl_expr = options.asl
basename=os.path.basename(trjfile).split('_trj')[0]
csim = create_simulation(cmsfile, trjfile)
# hardcode basename
basename = 'solute-%s' % basename
frames='::5'
total_frame = csim.total_frame
slice_list = _parse_frames(frames)
frames = get_indices(slice_list, total_frame)
# only extract PDBs
extract_func = extract_pdb
for i in frames:
filename = "%s/%s_%05d.%s"%(tmp_folder, basename, i, 'pdb')
extract_func(csim, i, filename, asl = asl_expr )
print "wrote %s pdbfiles" % i
print "trajectories are in analysis/ directory"
return tmp_folder, basename
def __init__(self, input_cmsname, input_trjname, clustercenter_file):
"""
Data members
"""
self.cmsname = input_cmsname
self.dsim = create_simulation(input_cmsname, input_trjname)
self._indexGenerator()
self.hsa_data = self._initializeHSADict(clustercenter_file)
self.box = self._initializePBC()
def __init__(self, input_cmsname, input_trjname, clustercenter_file):
"""
Data members
"""
self.cmsname = input_cmsname
self.dsim = create_simulation(input_cmsname, input_trjname)
self._indexGenerator()
self.hsa_data = self._initializeHSADict(clustercenter_file)
self.box = self._initializePBC()
def __init__(self, start_frame, n_frame, input_cmsname, input_trjname, center, resolution, dimensions):
"""
Data members
"""
self.cmsname = input_cmsname
self.dsim = create_simulation(input_cmsname, input_trjname)
self.start_frame = start_frame
self.n_frame = n_frame
self._indexGenerator()
self._initializeGrid(center, resolution, dimensions)
self.voxeldata, self.voxeldict = self._initializeVoxelDict()
self.chg, self.vdw = self._getNonbondedParams()
self.box = self._initializePBC()
def __init__(self, start_frame, n_frame, input_cmsname, input_trjname,
center, resolution, dimensions):
"""
Data members
"""
self.cmsname = input_cmsname
self.dsim = create_simulation(input_cmsname, input_trjname)
self.start_frame = start_frame
self.n_frame = n_frame
self._indexGenerator()
self._initializeGrid(center, resolution, dimensions)
self.voxeldata, self.voxeldict = self._initializeVoxelDict()
self.chg, self.vdw = self._getNonbondedParams()
self.box = self._initializePBC()
for l in ene_data[10:]:
#print l
float_converted_data = [float(x) for x in l.strip("\n").split()[1:]]
traj_data[l.strip("\n").split()[0]] = float_converted_data
vol_list = []
print "Calculating distribution of volumes from the trajectory excluding first %.1f picosecond" % options.exclude_region
for k in traj_data.keys():
#print k, traj_data[k][7]
if float(k) > options.exclude_region:
vol_list.append(traj_data[k][7])
mean_vol = np.mean(np.asarray(vol_list))
sd_vol = np.std(np.asarray(vol_list))
print "Mean system volume is %.2f with fluctuations %.3f" % (mean_vol, sd_vol)
chemical_time_of_frame = 0
"WARNING: Current version of the script assumes that both energies and coordinates are stored at the same time interval."
min_diff = 999999999
for k in traj_data.keys():
#print k, traj_data[k][7]
if float(k) > options.exclude_region:
frame_vol = traj_data[k][7]
if abs(frame_vol - mean_vol) < min_diff:
min_diff = abs(frame_vol - mean_vol)
#print k, int((float(k)/1002)*1000), frame_vol, min_diff
chemical_time_of_frame = int((float(k) / 1002) * 1000)
print "The frame corresponding to mean volume %i, writing into a cms file ..." % chemical_time_of_frame
dsim = create_simulation(options.cms_file, options.trj)
dsim.cst.writeCms("test_mean_vol_config.cms",
dsim.getFrame(chemical_time_of_frame))
print "Reading data from ene file..."
for l in ene_data[10:]:
#print l
float_converted_data = [float(x) for x in l.strip("\n").split()[1:]]
traj_data[l.strip("\n").split()[0]] = float_converted_data
vol_list = []
print "Calculating distribution of volumes from the trajectory excluding first %.1f picosecond" % options.exclude_region
for k in traj_data.keys():
#print k, traj_data[k][7]
if float(k) > options.exclude_region:
vol_list.append(traj_data[k][7])
mean_vol = np.mean(np.asarray(vol_list))
sd_vol = np.std(np.asarray(vol_list))
print "Mean system volume is %.2f with fluctuations %.3f" % (mean_vol, sd_vol)
chemical_time_of_frame = 0
"WARNING: Current version of the script assumes that both energies and coordinates are stored at the same time interval."
min_diff = 999999999
for k in traj_data.keys():
#print k, traj_data[k][7]
if float(k) > options.exclude_region:
frame_vol = traj_data[k][7]
if abs(frame_vol - mean_vol) < min_diff:
min_diff = abs(frame_vol - mean_vol)
#print k, int((float(k)/1002)*1000), frame_vol, min_diff
chemical_time_of_frame = int((float(k)/1002)*1000)
print "The frame corresponding to mean volume %i, writing into a cms file ..." % chemical_time_of_frame
dsim = create_simulation(options.cms_file, options.trj)
dsim.cst.writeCms("test_mean_vol_config.cms", dsim.getFrame(chemical_time_of_frame))
mean_frame_index = 0
for k in traj_data.keys():
#print k, traj_data[k][7]
if float(k) > 400:
frame_vol = traj_data[k][7]
if (frame_vol - mean_vol)**2 < min_diff:
min_diff = abs(frame_vol - mean_vol)
#print k, float(k)/1000, frame_vol, min_diff
mean_frame_time = k
mean_frame_index = int(float(k))
mean_frame_vol = frame_vol
mean_cms_name = "mean_vol_config.cms"
print "Frame %i has the closest volume (%f) to the mean." % (mean_frame_index, mean_frame_vol)
print "Writing frame %i to %s." % (mean_frame_index, mean_cms_name)
dsim = create_simulation(sys.argv[2], sys.argv[3])
dsim.cst.writeCms(mean_cms_name, dsim.getFrame(mean_frame_index))
"""
comp_cts = []
for ffst in dsim.cst.ffsts:
comp_cts.append(copy.copy(ffst.parent_structure))
oxygen_atids = self._water_oxygen_atoms[0:self._nwater]
atids = self._getCombinedAtids(oxygen_atids)
new_ct = mm.mmct_ct_duplicate(dsim.cst.handle)
full_ct = Structure(new_ct, True )
full_ct = full_ct.extract(atids, copy_props=True)
sys.exit(1)
asl_expr = None
if options.asl:
asl_expr = options.asl
elif options.asl_file:
try:
asl_expr = ''.join(open(options.asl_file).readlines())
asl_expr = asl_expr.strip()
except Exception, e:
print "Fail to parse ASL from %s: %s"%(options.asl_file, e)
sys.exit(1)
cmsfile = args[0]
trjfile = args[1]
csim = create_simulation(cmsfile, trjfile)
basename = options.basename
if not basename:
base_filename = os.path.basename(cmsfile)
t = base_filename.split('.')
if len(t) >= 2:
basename = '.'.join(t[:-1])
else:
# cmsfile does not contain suffix
basename = base_filename
total_frame = csim.total_frame
if options.frames == None:
frames = range(total_frame)
else:
sys.exit(1)
asl_expr = None
if options.asl:
asl_expr = options.asl
elif options.asl_file:
try:
asl_expr = ''.join(open(options.asl_file).readlines())
asl_expr = asl_expr.strip()
except Exception, e:
print "Fail to parse ASL from %s: %s" % (options.asl_file, e)
sys.exit(1)
cmsfile = args[0]
trjfile = args[1]
csim = create_simulation(cmsfile, trjfile)
basename = options.basename
if not basename:
base_filename = os.path.basename(cmsfile)
t = base_filename.split('.')
if len(t) >= 2:
basename = '.'.join(t[:-1])
else:
# cmsfile does not contain suffix
basename = base_filename
total_frame = csim.total_frame
if options.frames == None:
frames = range(total_frame)
else: