def test(fn):
x=xdrfile(fn)
if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1
for k,f in enumerate(x):
if f.step != step1+k: print "incorrect step",f.step,step1+k,k
if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k
if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1
if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1
for i in range(DIM):
for j in range(DIM):
if fabs(f.box[i][j] - box1[i][j]) > toler: print "box incorrect",f.box[i][j],box1[i][j]
for i in range(x.natoms):
for j in range(DIM):
target = (i+1)*3.7 + (j+1)
if f.x[i][j] - target > toler : print "x incorrect"
print fn,"OK"
def test(fn):
x = xdrfile(fn)
if x.natoms != natoms1: print "natoms != natoms1", x.natoms, natoms1
for k, f in enumerate(x):
if f.step != step1 + k: print "incorrect step", f.step, step1 + k, k
if fabs(f.time - time1 - k) > toler:
print "incorrect time", f.time, time1 + k
if not x.mode & mTrr and fabs(f.prec - prec1) > toler:
print "incorrect precision", f.prec, prec1
if x.mode & mTrr and fabs(f.lam - lam1) > toler:
print "incorrect lambda", f.lam, lam1
for i in range(DIM):
for j in range(DIM):
if fabs(f.box[i][j] - box1[i][j]) > toler:
print "box incorrect", f.box[i][j], box1[i][j]
for i in range(x.natoms):
for j in range(DIM):
target = (i + 1) * 3.7 + (j + 1)
if f.x[i][j] - target > toler: print "x incorrect"
print fn, "OK"
# input: .xtc file specified as the first argument
# output: stdin dump of coordinates in a format suitable for
# piping it into the pitch-n-roll analysis programme
#------------------------------------------------------------
# The .xtc file should contain only the atoms of interest
# (e.g. CA carbons)
# with PBC already REMOVED!!!
#------------------------------------------------------------
from xdrfile import *
import sys
#you have to compile with --enable-shared
#and have libxdrfile.so in the LD_LIBRARY_PATH
if len(sys.argv)!=2:
print "Missing file argument\nUsage: sample.py FILE"
sys.exit()
x=xdrfile(sys.argv[1])
print x.natoms
for f in x: #iterates frames
#print "%8s %8s %8s %8s Step: %8d "%("Atom","X","Y","Z",f.step) #print header
print "%8d" % (f.step),
for atcoor in f.x: #iterate atoms
print "%8.3f %8.3f %8.3f"%(atcoor[0],atcoor[1],atcoor[2]), #print coords one after another (note the comma at the end of the print command)
print
import IPython
import cPickle
# just a shorthand for a long class name
reswtraj = residue_with_traj
nframes = 351194
#nframes = 400 # testing
membrane_resnames=["POPC"]
if len(sys.argv)!=3:
print "Missing file argument\nUsage: sample.py CONF TRAJ"
sys.exit()
#open trajectory
traj_filename = sys.argv[2]
try:
trajectory=xdrfile(traj_filename)
except:
print "Error: Trajectory filename '%s' not right" % (traj_filename,)
sys.exit(1)
print "Opened trajectory with %5d atoms. " % (trajectory.natoms,)
#make neg = Model instance based on configuration in conf_filename
conf_filename = sys.argv[1]
try:
neg = pmx.model.Model(filename=conf_filename)
except:
print "Error: Model filename '%s' not right" % (conf_filename,)
sys.exit(1)
membrane = reswtraj(pmx.molecule.Molecule(),nframes=nframes)
membrane.mol.resname="POPC"
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
#
from xdrfile import *
import sys
# you have to compile with --enable-shared
# and have libxdrfile.so in the LD_LIBRARY_PATH
if len(sys.argv) != 2:
print "Missing file argument\nUsage: sample.py FILE"
sys.exit()
x = xdrfile(sys.argv[1])
for f in x: # iterates frames
print "%8s %8s %8s %8s Step: %8d " % ("Atom", "X", "Y", "Z", f.step) # print header
for i, a in enumerate(f.x): # iterate atoms
print "%8d %8.1f %8.1f %8.1f" % (i + 1, a[0], a[1], a[2]) # print atom number, x, y, z
import IPython
import cPickle
# just a shorthand for a long class name
reswtraj = residue_with_traj
nframes = 351194
#nframes = 400 # testing
membrane_resnames = ["POPC"]
if len(sys.argv) != 3:
print "Missing file argument\nUsage: sample.py CONF TRAJ"
sys.exit()
#open trajectory
traj_filename = sys.argv[2]
try:
trajectory = xdrfile(traj_filename)
except:
print "Error: Trajectory filename '%s' not right" % (traj_filename, )
sys.exit(1)
print "Opened trajectory with %5d atoms. " % (trajectory.natoms, )
#make neg = Model instance based on configuration in conf_filename
conf_filename = sys.argv[1]
try:
neg = pmx.model.Model(filename=conf_filename)
except:
print "Error: Model filename '%s' not right" % (conf_filename, )
sys.exit(1)
membrane = reswtraj(pmx.molecule.Molecule(), nframes=nframes)
membrane.mol.resname = "POPC"
#Изготовление списка пар, соответствующих списку остатков
pairs=map(\
lambda pair:(residues.index(pair[0]),residues.index(pair[1])),\
pairs)
print pairs
#Индексация атомов выбранных плоскостей
planes=[]
for residue in residues:
planes.append((\
topology.index[residue[0]][residue[1]][plane_atoms[residue[0]][0]],\
topology.index[residue[0]][residue[1]][plane_atoms[residue[0]][1]],\
topology.index[residue[0]][residue[1]][plane_atoms[residue[0]][2]]))
#Чтение траектории
xtc=xdrfile(arguments[1][1])
#Анализ стэкинга
stacking=[]
equations=[[] for plane in planes]
residue_quantity=len(residues)
times=[]
#По всем состояниям
count=0
for frame in xtc:
stacking+=[[]]
#stacking[-1]+=[frame.step]
times+=[str(frame.time/1000)]
#По всем остаткам считаем уравнения плоскостей
for i in range(residue_quantity):
try:
atom1=frame.x[planes[i][0]]
