def Get_Dihedral_fromTOP(coor_file, base_list_1, PRINT=False):
'''
calculate the dihedral from the top file.
'''
Atom_list = Simple_atom.Get_atom_list(coor_file)
reside_list = Simple_atom.Get_Residue_list(Atom_list)
if PRINT == True:
print "%11s%10s%10s%10s%10s%10s%10s%10s%8s%8s%8s%8s%8s%8s%8s"\
%("baseID","alpha","beta","gamma","delta","epslon","zeta","chi",\
"alpha","beta","gamma","delta","epslon","zeta","chi")
for m in base_list_1:
resu = DNA_param.Get_Dihedral(Atom_list, m)
if PRINT == True:
print "%8d%3s" % (reside_list[m - 1][1], reside_list[m - 1][0]),
for i in range(7):
if resu[i] == "-":
print "%9s" % ("-" * 4),
else:
print "%9.2f" % (resu[i]),
for i in range(7):
if resu[i] == "-":
print "%7s" % ("-" * 4),
else:
print "%7s" % (resu[i + 7]),
print ""
time = float((ts.frame - 1) * dt)
if dt > 0.0:
if time < float(begin):
continue
if time > float(end) and end != -1:
break
if ts.frame % skip == 0:
for atom in Atom_list:
atom.atom_coor_x = ts._x[atom.atom_id - 1]
atom.atom_coor_y = ts._y[atom.atom_id - 1]
atom.atom_coor_z = ts._z[atom.atom_id - 1]
for i in range(len(base_list)):
fp = open(output_name[i], 'a')
resu = DNA_param.Get_Dihedral(Atom_list, base_list[i])
fp.write("%12.4f" % (time / 1000))
for j in range(7):
if resu[j] == "-":
fp.write("%10s" % ("-" * 4))
else:
fp.write("%10.2f" % (resu[j]))
for j in range(7):
if resu[j] == "-":
fp.write("%8s" % ("-" * 4))
else:
fp.write("%8s" % (resu[j + 7]))
fp.write("\n")