def Move_2_center(top_file, trj_file, trjout_file):
u = Universe(top_file, trj_file)
TRAJ_FRAMES = u.trajectory.numframes
w = Writer(trjout_file, u.trajectory.numatoms)
atoms = Simple_atom.Get_atom_list(top_file)
SOLUTE_COUNT = 0
for atom_ID in atoms:
if atoms[atom_ID].residue_name != "SOL" and atoms[
atom_ID].residue_name != "WAT":
SOLUTE_COUNT += 1
else:
pass
print '''Note: this program will read the pbc condition and use the dimensions \
read from trajectory files. You should make sure the dimensions are right or \
it will create a wrong output trajectory file.'''
START_TIME = Time.time()
NUM_ATOMS = u.trajectory.numatoms
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
dimensions = ts.dimensions
for i in range(SOLUTE_COUNT):
if ts._x[i] > dimensions[0]:
ts._x[i] = ts._x[i] - dimensions[0]
if ts._x[i] < 0:
ts._x[i] = ts._x[i] + dimensions[0]
if ts._y[i] > dimensions[1]:
ts._y[i] = ts._y[i] - dimensions[1]
if ts._y[i] < 0:
ts._y[i] = ts._y[i] + dimensions[1]
if ts._z[i] > dimensions[2]:
ts._z[i] = ts._z[i] - dimensions[2]
if ts._z[i] < 0:
ts._z[i] = ts._z[i] + dimensions[2]
NOW_TIME = Time.time()
BIN_TIME = NOW_TIME - START_TIME
if ts.frame % 100 == 0:
# usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
def Move_2_center(top_file,trj_file,trjout_file):
u=Universe(top_file,trj_file)
TRAJ_FRAMES=u.trajectory.numframes
w = Writer(trjout_file, u.trajectory.numatoms)
atoms=Simple_atom.Get_atom_list(top_file)
SOLUTE_COUNT = 0
for atom_ID in atoms:
if atoms[atom_ID].residue_name != "SOL" and atoms[atom_ID].residue_name != "WAT":
SOLUTE_COUNT +=1
else:
pass
print '''Note: this program will read the pbc condition and use the dimensions \
read from trajectory files. You should make sure the dimensions are right or \
it will create a wrong output trajectory file.'''
START_TIME=Time.time()
NUM_ATOMS = u.trajectory.numatoms
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
dimensions=ts.dimensions
for i in range(SOLUTE_COUNT):
if ts._x[i] > dimensions[0]:
ts._x[i]=ts._x[i]-dimensions[0]
if ts._x[i] <0:
ts._x[i]=ts._x[i]+dimensions[0]
if ts._y[i] > dimensions[1]:
ts._y[i]=ts._y[i]-dimensions[1]
if ts._y[i] <0:
ts._y[i]=ts._y[i]+dimensions[1]
if ts._z[i] > dimensions[2]:
ts._z[i]=ts._z[i]-dimensions[2]
if ts._z[i] < 0:
ts._z[i]=ts._z[i]+dimensions[2]
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
if ts.frame % 100 == 0:
# usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
def Delete_group(self,del_group_id):
'''
Delete a group from the group_list and atom_list.
'''
if del_group_id in range(len(self.group_list)):
delete_list=self.group_list[del_group_id].group_list
atom_serial_list=[self.atom_list[i].atom_serial for i in range(len(self.atom_list))]
for i in delete_list:
usage.echo("remove atom %8d, atom name %6s\r" %(i,self.atom_list[atom_serial_list.index(i)].atom_name))
self.atom_list.remove(self.atom_list[atom_serial_list.index(i)])
'''remove a atom form atom list'''
self.group_list[0].group_list.remove(self.group_list[0].group_list[atom_serial_list.index(i)])
'''remove a atom from group_list[0] which is named system'''
atom_serial_list.remove(i)
print "deleted group %s, %6d atoms" %(self.group_list[del_group_id].group_name,len(delete_list))
self.group_list.remove(self.group_list[del_group_id])
else:
print "you input a number not in the list. %d" %del_group_id
def Move_2_center(top_file,trj_file,trjout_file,skip=1):
u=Universe(top_file,trj_file)
TRAJ_FRAMES=u.trajectory.numframes
atom_l=Simple_atom.Get_Simple_atom_list(top_file)
while True:
fit_residue=Simple_atom.Get_residue(top_file)
if len(fit_residue) > 1:
print "Only 1 residue is aviliable."
continue
else:
break
while True:
fit_atom=Simple_atom.Get_atom(atom_l,fit_residue[0])
if len(fit_atom) > 1:
print "Only 1 atom is aviliable."
continue
else:
break
fitting_group=Simple_atom.Get_residue(top_file)
fit_atom=fit_atom[0]
w = Writer(trjout_file, u.trajectory.numatoms)
NUM_ATOMS=len(atom_l)
print '''Note: this program will read the pbc condition and use the dimensions \
read from trajectory files. You should make sure the dimensions are right or \
it will create a wrong output trajectory file.'''
START_TIME=Time.time()
# loop through the trajectory and write a frame for every step
for ts in u.trajectory:
if ts.frame % skip != 1:
break
if ts.frame==1:
label_coordinate=[ts._x[fit_atom],ts._y[fit_atom],ts._z[fit_atom]]
# origin_list=list()
# for atom in atom_l:
# if atom.residue_serial in fitting_group:
# origin_list.append([\
# ts._x[atom_l.index(atom)],\
# ts._y[atom_l.index(atom)],\
# ts._z[atom_l.index(atom)],\
# ])
else:
shift=[label_coordinate[0]-ts._x[fit_atom],\
label_coordinate[1]-ts._y[fit_atom],\
label_coordinate[2]-ts._z[fit_atom]]
dimensions=ts.dimensions
usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
for i in range(NUM_ATOMS):
ts._x[i] =ts._x[i]+shift[0]
if ts._x[i] > dimensions[0]:
ts._x[i]=ts._x[i]-dimensions[0]
if ts._x[i] <0:
ts._x[i]=ts._x[i]+dimensions[0]
ts._y[i] =ts._y[i]+shift[1]
if ts._y[i] > dimensions[1]:
ts._y[i]=ts._y[i]-dimensions[1]
if ts._y[i] <0:
ts._y[i]=ts._y[i]+dimensions[1]
ts._z[i] =ts._z[i]+shift[2]
if ts._z[i] > dimensions[2]:
ts._z[i]=ts._z[i]-dimensions[2]
if ts._z[i] < 0:
ts._z[i]=ts._z[i]+dimensions[2]
# temp_list=list()
# for atom in atom_l:
# if atom.residue_serial in fitting_group:
# temp_list.append([\
# ts._x[atom_l.index(atom)],\
# ts._y[atom_l.index(atom)],\
# ts._z[atom_l.index(atom)],\
# ])
# # [Rotate,shift]=least_squares_fitting.Fitting(temp_list,origin_list)
# atom_matrix=numpy.array([[ts._x[i],ts._y[i],ts._z[i]]for i in range(NUM_ATOMS)])
# # resu_matrix=numpy.matrix(atom_matrix) * numpy.matrix(Rotate).T
# # resu_matrix=numpy.array(resu_matrix)
# # for i in range(NUM_ATOMS):
# # atom_matrix[i,0]=resu_matrix[i,0]+shift[0]
# # atom_matrix[i,1]=resu_matrix[i,1]+shift[1]
# # atom_matrix[i,2]=resu_matrix[i,2]+shift[2]
# for i in range(NUM_ATOMS):
# ts._x[i]=atom_matrix[i,0]
# ts._y[i]=atom_matrix[i,1]
# ts._z[i]=atom_matrix[i,2]
# w.write(ts)
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)
def pRDF(top_file,trj_file,index_file,trjout_file,solute_index,CUT_OFF=1.0):
'''
Save the WAT_NUMBER closest water molecules to a new trajectory file.
'''
START_TIME =Time.time()
Atoms =Simple_atom.Get_atom_list(top_file)
atom_list =copy.deepcopy(Atoms)
index_list =Index.Read_index_to_Inclass(index_file)
solute_atom_list =index_list[solute_index].group_list
solute_rest_set = set(solute_atom_list)
solvent_list =Get_solvent_list(atom_list)
WAT_NUMBER =0.0
if len(solvent_list) < WAT_NUMBER:
print "Error: The number of water molecules (%d) is less than the critical number (%d)." \
%(len(solvent_list),WAT_NUMBER)
sys.exit()
natoms = libxdrfile.read_xtc_natoms(trj_file)
x = numpy.zeros((natoms, libxdrfile.DIM), dtype=numpy.float32)
box = numpy.zeros((libxdrfile.DIM,libxdrfile.DIM), dtype=numpy.float32)
XTC = libxdrfile.xdrfile_open(trj_file, 'r')
# OUTPUT_ATOMS =len(solute_atom_list)+3*WAT_NUMBER
XTC_write =libxdrfile.xdrfile_open(trjout_file,'w')
# x_out =numpy.zeros((OUTPUT_ATOMS,libxdrfile.DIM),dtype=numpy.float32)
# loop through file until return status signifies end or a problem
# (it should become exdrENDOFFILE on the last iteration)
status = libxdrfile.exdrOK
FIRST_FRAME =True
TEST_SET = True
test_count =0
solu_set =set()
OFF =0.0
while status == libxdrfile.exdrOK:
status,step,time,prec = libxdrfile.read_xtc(XTC, box, x)
# do something with x
sol_dict=dict()
sol_dist=list()
# ###############
for i in atom_list:
# u_atom = MDPackage.Coor.unit_atom.unit_atom(atom_coor_x=x[i-1,0],atom_coor_y=x[i-1,1],atom_coor_z=x[i-1,2])
atom_list[i].atom_coor_x=x[i-1,0]
atom_list[i].atom_coor_y=x[i-1,1]
atom_list[i].atom_coor_z=x[i-1,2]
###############
if FIRST_FRAME == True:
# FIRST_FRAME = False
#this cut-off is used to cut the water molecules which are far away from solute molecule.
# and defined as cut-off = 1.2 *(max-dist from center of solute to WAT_NUMBER of closest
# water molecules)
for solvent in solvent_list:
usage.echo("Checking solvent atom: %d\r" %(solvent))
min_dist,solu_temp=Min_dist(atom_list,solute_atom_list,solvent)
sol_dist.append(min_dist)
sol_dict[min_dist]=solvent
solu_set.add(solu_temp)
try:
solute_rest_set.remove(solu_temp)
except:
pass
# print solu_set
elif TEST_SET == True:
_tmp_count =0
SOLUTE_CENTER = Get_solute_center(atom_list,solu_set)
for solvent in solvent_list:
if Dist(atom_list,SOLUTE_CENTER,solvent) > OFF :
# SKIP_COUNT +=1
continue
# _dist_1,_solu_1 = Min_dist(atom_list,solute_rest_set,solvent)
_dist_2,_solu_2 = Min_dist(atom_list,solute_atom_list,solvent)
# if _dist_1 < _dist_2:
# print "%d: %d %d; size: %d" %(solvent, _solu_1, _solu_2, len(solu_set))
# solu_set.add(_solu_1)
# sol_dist.append(_dist_1)
# sol_dict[_dist_1]=solvent
# _tmp_count += 1
# else:
sol_dist.append(_dist_2)
sol_dict[_dist_2]=solvent
# if _tmp_count ==0:
# test_count += 1
# if test_count >=20:
# TEST_SET = False
# else:
# SOLUTE_CENTER = Get_solute_center(atom_list,solu_set)
# for solvent in solvent_list:
# if Dist(atom_list,SOLUTE_CENTER,solvent) > OFF :
# # SKIP_COUNT +=1
# continue
# _dist_2,_solu_2 = Min_dist(atom_list,solu_set,solvent)
# sol_dist.append(_dist_2)
# sol_dict[_dist_2]=solvent
sorted_sol_dist=sorted(sol_dist)
if FIRST_FRAME == True:
for xx,item in enumerate(sorted_sol_dist):
if item > CUT_OFF:
WAT_NUMBER = xx+1
break
OUTPUT_ATOMS =len(solute_atom_list)+3*WAT_NUMBER
x_out =numpy.zeros((OUTPUT_ATOMS,libxdrfile.DIM),dtype=numpy.float32)
print "WAT_NUMBER: %d ;" %(WAT_NUMBER)
SOLUTE_CENTER=Get_solute_center(atom_list,solute_atom_list)
# print SOLUTE_CENTER
OFF = Get_Cutoff(atom_list,SOLUTE_CENTER,sorted_sol_dist,sol_dict,WAT_NUMBER)
#########################################
for i in range(len(solute_atom_list)):
x_out[i,0] =x[solute_atom_list[i]-1,0]
x_out[i,1] =x[solute_atom_list[i]-1,1]
x_out[i,2] =x[solute_atom_list[i]-1,2]
for i in range(WAT_NUMBER):
for j in range(3):
x_out[len(solute_atom_list)+3*i+j,0] =x[sol_dict[sorted_sol_dist[i]]-1+j,0]
x_out[len(solute_atom_list)+3*i+j,1] =x[sol_dict[sorted_sol_dist[i]]-1+j,1]
x_out[len(solute_atom_list)+3*i+j,2] =x[sol_dict[sorted_sol_dist[i]]-1+j,2]
status2=libxdrfile.write_xtc(XTC_write,step,time,box,x_out,prec)
if FIRST_FRAME == True:
new_list=[atom_list[i] for i in solute_atom_list]
for i in range(WAT_NUMBER):
new_list.append(atom_list[sol_dict[sorted_sol_dist[i]]])
new_list.append(atom_list[sol_dict[sorted_sol_dist[i]]+1])
new_list.append(atom_list[sol_dict[sorted_sol_dist[i]]+2])
out_file=string.split(trjout_file,'.')[0]+".pdb"
Simple_atom.Save_file(out_file,new_list)
FIRST_FRAME = False
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
# if step % 10 == 0:
# print ""
sys.stderr.write("step %10d, time %10.2f ps, time used: %6.2f s\r" %(step,time,BIN_TIME))
sys.stderr.flush()
# finally close file
print ""
libxdrfile.xdrfile_close(XTC)
def Move_2_center(top_file,trj_file,index_file,trjout_file):
u=Universe(top_file,trj_file)
TRAJ_FRAMES=u.trajectory.numframes
w = Writer(trjout_file, u.trajectory.numatoms)
atoms=Simple_atom.Get_Simple_atom_list(top_file)
index = Index.Read_index_to_Inclass(index_file)
Index.Print_Index(index)
while True:
try:
solute_index=int(raw_input("Choosing the group for centering:"))
# solvent_index = int(raw_input("Choosing the solvent group:"))
break
except:
print "You should input a number."
continue
solute_group = index[solute_index].group_list
# solvent_group = index[solvent_index].group_list
solute_atoms =len(solute_group)
NUM_ATOMS = u.trajectory.numatoms
# print "\t Reading %d frames from trajectory file: %s" %(nframes,traj_file)
START_TIME=Time.time()
for ts in u.trajectory:
ref_com =np.zeros((3),dtype=np.float32)
# sys.stderr.write("\t Reading frame %8d\r" %ts.frame)
# sys.stderr.flush()
for i,ai in list(enumerate(solute_group)):
ref_com[0] += ts._x[ai-1]
ref_com[1] += ts._y[ai-1]
ref_com[2] += ts._z[ai-1]
ref_com = ref_com/solute_atoms
dimensions=ts.dimensions
ref_com = ref_com - np.array([dimensions[0]/2, dimensions[1]/2, dimensions[2]/2])
# ref_com = np.array([sum(traj_data[:,0])/solute_atoms - dimensions[0]/2,\
# sum(traj_data[:,1])/solute_atoms - dimensions[1]/2,\
# sum(traj_data[:,2])/solute_atoms - dimensions[2]/2])
for i in range(NUM_ATOMS):
ts._x[i] = ts._x[i] - ref_com[0]
ts._y[i] = ts._y[i] - ref_com[1]
ts._z[i] = ts._z[i] - ref_com[2]
if (i+1) in solute_group:
continue
if ts._x[i] > dimensions[0] or ts._x[i] <0:
ts._x[i]=ts._x[i]%dimensions[0]
if ts._y[i] > dimensions[1] or ts._y[i] <0:
ts._y[i]=ts._y[i]%dimensions[1]
if ts._z[i] > dimensions[2] or ts._z[i] < 0:
ts._z[i]=ts._z[i]%dimensions[2]
NOW_TIME=Time.time()
BIN_TIME=NOW_TIME-START_TIME
# if ts.frame % 10 == 0:
# usage.echo("%8.4f %8.4f %8.4f\r" %(dimensions[0],dimensions[1],dimensions[2]))
usage.echo(" "*40+"Converted frame %d, time used: %8.2f s, time left: %8.2f s \r" \
% (ts.frame,BIN_TIME,BIN_TIME*(float(TRAJ_FRAMES)/ts.frame-1) ))
# for ts in u.trajectory:
w.write(ts)
# del traj_data
# usage.echo("Writting frame %d\r" %ts.frame)
w.close_trajectory()
print "Converted %r --> %r" % (intrj, outtrj)