def Traj_2_coor(in_coor_file,traj_file,out_coor_file,atom_list,skip):
'''
Reading a trajectory file. output the frames to files like out_coor_file_1.pdb \n
atom_list : a list of atom serial.\n
out_coor_file: a file name, in pdb or gro format. a list of file based on the name\
will be created for output.\n
skip: a int number like 1,2,3,10.
'''
Alist=Simple_atom.Get_Simple_atom_list(in_coor_file)
Blist=[]
for atom in Alist:
if atom.atom_serial in atom_list:
Blist.append(atom)
'''Get the result atom list in Simple_atom class.'''
u=MDAnalysis.Universe(in_coor_file,traj_file)
for ts in u.trajectory:
if ts.frame % skip ==0 :
a,b=os.path.splitext(out_coor_file)
temp_out_file=a+"_%d" %(int(ts.frame)/skip) + b
if os.path.isfile(temp_out_file):
#print "backup %s to %s" %(temp_out_file,"#"+temp_out_file+"#")
usage.echo("backup %s to %s\r" %(temp_out_file,"#"+temp_out_file+"#"))
try:
os.rename(temp_out_file,"#"+temp_out_file+"#")
except OSError,e:
print e
print "the file %s will be overwrited!" %temp_out_file
pass
fp=open(temp_out_file,'w+')
if temp_out_file.endswith(".gro"):
fp.write("%d\n" %len(Blist))
else:
pass
for atom in Blist:
temp_class=unit_atom.unit_atom(atom_name=atom.atom_name,\
atom_serial=atom.atom_serial,\
residue_name=atom.residue_name,\
residue_serial=atom.residue_serial)
temp_class.atom_coor_x=ts._x[atom.atom_serial-1]/10
temp_class.atom_coor_y=ts._y[atom.atom_serial-1]/10
temp_class.atom_coor_z=ts._z[atom.atom_serial-1]/10
if temp_out_file.endswith(".pdb"):
fp.write(temp_class.atom_2_PDBformat()+"\n")
elif temp_out_file.endswith(".gro"):
fp.write(temp_class.atom_2_GROformat()+"\n")
else:
pass
# print "write frame %5d to %16s" %(ts.frame,temp_out_file)
usage.echo("write frame %5d to %16s\r" %(ts.frame,temp_out_file))
else:
pass
c2.append(result[1])
fp = open(output_name[i], 'a')
if CALCU=="pair":
a=DNA_param.base_pair_parameters(r1[0],r2[0],c1[0],c2[0])
fp.write("%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f\n" %(a[0],a[1],a[2],a[3],a[4],a[5]))
else:
middle_r1,middle_c1=DNA_param.middle_frame(r1[0],r1[1],c1[0],c1[1])
middle_r2,middle_c2=DNA_param.middle_frame(r2[0],r2[1],c2[0],c2[1])
a=DNA_param.base_step_parameters(middle_r1,middle_r2,middle_c1,middle_c2)
fp.write("%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f\n" %(a[0],a[1],a[2],a[3],a[4],a[5]))
if ts.frame % 10 ==0 and i==0:
NOW_TIME=Time.time()
usage.echo(" analysis frame %6d, time %8.1f ps, time used %8.2f s\r" %(ts.frame, time,NOW_TIME-START_TIME))
fp.close()
print "The DNA helical analysis finished"
print "The result are in file: %s" %output_name
def Get_para_fromTOP( coor_file, base_list_1, base_list_2,CALCU="step",PRINT=True):
'''
get pair parameters from coor_file
'''
atom_list=Simple_atom.Get_atom_list(coor_file)
residue_list=Simple_atom.Get_Residue_list(atom_list)
# print residue_list
# atom_list=Simple_atom.Get_atom_list(coor_file)
% (a[0], a[1], a[2], a[3], a[4], a[5]))
else:
middle_r1, middle_c1 = DNA_param.middle_frame(
r1[0], r1[1], c1[0], c1[1])
middle_r2, middle_c2 = DNA_param.middle_frame(
r2[0], r2[1], c2[0], c2[1])
a = DNA_param.base_step_parameters(middle_r1, middle_r2,
middle_c1, middle_c2)
fp.write(
"%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f\n"
% (a[0], a[1], a[2], a[3], a[4], a[5]))
if ts.frame % 10 == 0 and i == 0:
NOW_TIME = Time.time()
usage.echo(
" analysis frame %6d, time %8.1f ps, time used %8.2f s\r"
% (ts.frame, time, NOW_TIME - START_TIME))
fp.close()
print "The DNA helical analysis finished"
print "The result are in file: %s" % output_name
def Get_para_fromTOP(coor_file,
base_list_1,
base_list_2,
CALCU="step",
PRINT=True):
'''
get pair parameters from coor_file
def Get_twist_in_GDNA(traj_file, coor_file, base_list_1, base_list_2,
output_file):
'''
Input the layer 1 (G11,G12,G13,G14) and layer 2 (G21,G22,G23,G24),Calculate the angle
between G1i-G1(i+1) and G2i-G2(i+1). write the result to output_file.\n
B{traj_file:} the GMX trajectory file, in trr or xtc format.\n
B{coor_file:} the GMX coordinate file, in pdb or gro format.\n
B{base_list_1:} the frist group contain four guanine bases.\n
B{base_list_2:} the second group contain four guanine bases.\n
B{output_file:} the output file.
'''
C1_list_1 = []
C1_list_2 = []
print " init......"
fp = open(output_file, "w")
fp.write("#Group 1: ")
for i in base_list_1:
fp.write("%d\t " % i)
fp.write("\n")
fp.write("#Group 2: ")
for i in base_list_2:
fp.write("%d\t " % i)
fp.write("\n")
fp.write("#time\t angle_1 \t angle _2 \t angle _3 \t angle_4\n")
Atom_list = Simple_atom.Get_Simple_atom_list(coor_file)
for base in base_list_1:
atom_list = Simple_atom.Get_Atom_in_residue(Atom_list, base)
for atom in atom_list:
if atom.atom_name == "C1'":
C1_list_1.append(atom.atom_serial)
for base in base_list_2:
atom_list = Simple_atom.Get_Atom_in_residue(Atom_list, base)
for atom in atom_list:
if atom.atom_name == "C1'":
C1_list_2.append(atom.atom_serial)
# print C1_list_1
# print C1_list_2
u = MDAnalysis.Universe(coor_file, traj_file)
for ts in u.trajectory:
angle = []
for i in range(4):
vector1=[ts._x[C1_list_1[(i+1)%4]-1]-ts._x[C1_list_1[i]-1],\
ts._y[C1_list_1[(i+1)%4]-1]-ts._y[C1_list_1[i]-1],\
ts._z[C1_list_1[(i+1)%4]-1]-ts._z[C1_list_1[i]-1]]
vector2=[ts._x[C1_list_2[(i+1)%4]-1]-ts._x[C1_list_2[i]-1],\
ts._y[C1_list_2[(i+1)%4]-1]-ts._y[C1_list_2[i]-1],\
ts._z[C1_list_2[(i+1)%4]-1]-ts._z[C1_list_2[i]-1]]
vector1 = numpy.array(vector1)
vector2 = numpy.array(vector2)
# print vector1,vector2
gamma = numpy.dot(vector1, vector2) / (math.sqrt(
numpy.dot(vector1, vector1) * numpy.dot(vector2, vector2)))
angle.append(math.acos(gamma) / 3.1416 * 180)
fp.write("%6.3f \t %6.3f \t %6.3f \t %6.3f \t %6.3f\n" \
%(ts.time/1000,angle[0],angle[1],angle[2],angle[3]))
#if ts.frame % 100 ==0:
# print " analysis frame %6d......" %ts.frame
usage.echo(" analysis frame %6d......\r" % ts.frame)
fp.close()
print "The result are in the file: ", output_file
ts._y[C1_list_1[(k+1)%4]-1]-ts._y[C1_list_1[k]-1],\
ts._z[C1_list_1[(k+1)%4]-1]-ts._z[C1_list_1[k]-1]]
vector2=[ts._x[C1_list_2[(k+1)%4]-1]-ts._x[C1_list_2[k]-1],\
ts._y[C1_list_2[(k+1)%4]-1]-ts._y[C1_list_2[k]-1],\
ts._z[C1_list_2[(k+1)%4]-1]-ts._z[C1_list_2[k]-1]]
vector1 = numpy.array(vector1)
vector1_1 = numpy.cross(
numpy.cross(orient_group_1, vector1), orient_group_1)
vector2 = numpy.array(vector2)
vector2_2 = numpy.cross(
numpy.cross(orient_group_2, vector2), orient_group_2)
# print vector1_1,vector2_2
gamma = numpy.dot(vector1_1, vector2_2) / (math.sqrt(
numpy.dot(vector1_1, vector1_1) *
numpy.dot(vector2_2, vector2_2)))
angle.append(math.acos(abs(gamma)) / 3.1416 * 180)
fp = open(output_name[i], 'a')
fp.write("%6.3f \t %6.3f \t %6.3f \t %6.3f \t %6.3f\n" \
%(ts.time/1000,angle[0],angle[1],angle[2],angle[3]))
if ts.frame % 100 == 0 and i == 0:
usage.echo(" analysis frame %6d\r" % ts.frame)
fp.close()
print "The result are in the file: ", output_name
def Get_twist_in_GDNA(traj_file,coor_file,base_list_1,base_list_2,output_file):
'''
Input the layer 1 (G11,G12,G13,G14) and layer 2 (G21,G22,G23,G24),Calculate the angle
between G1i-G1(i+1) and G2i-G2(i+1). write the result to output_file.\n
B{traj_file:} the GMX trajectory file, in trr or xtc format.\n
B{coor_file:} the GMX coordinate file, in pdb or gro format.\n
B{base_list_1:} the frist group contain four guanine bases.\n
B{base_list_2:} the second group contain four guanine bases.\n
B{output_file:} the output file.
'''
C1_list_1=[]
C1_list_2=[]
print " init......"
fp=open(output_file,"w")
fp.write("#Group 1: ")
for i in base_list_1:
fp.write("%d\t " %i)
fp.write("\n")
fp.write("#Group 2: ")
for i in base_list_2:
fp.write("%d\t " %i)
fp.write("\n")
fp.write("#time\t angle_1 \t angle _2 \t angle _3 \t angle_4\n")
Atom_list=Simple_atom.Get_Simple_atom_list(coor_file)
for base in base_list_1:
atom_list=Simple_atom.Get_Atom_in_residue(Atom_list,base)
for atom in atom_list:
if atom.atom_name =="C1'":
C1_list_1.append(atom.atom_serial)
for base in base_list_2:
atom_list=Simple_atom.Get_Atom_in_residue(Atom_list,base)
for atom in atom_list:
if atom.atom_name =="C1'":
C1_list_2.append(atom.atom_serial)
# print C1_list_1
# print C1_list_2
u=MDAnalysis.Universe(coor_file,traj_file)
for ts in u.trajectory:
angle=[]
for i in range(4):
vector1=[ts._x[C1_list_1[(i+1)%4]-1]-ts._x[C1_list_1[i]-1],\
ts._y[C1_list_1[(i+1)%4]-1]-ts._y[C1_list_1[i]-1],\
ts._z[C1_list_1[(i+1)%4]-1]-ts._z[C1_list_1[i]-1]]
vector2=[ts._x[C1_list_2[(i+1)%4]-1]-ts._x[C1_list_2[i]-1],\
ts._y[C1_list_2[(i+1)%4]-1]-ts._y[C1_list_2[i]-1],\
ts._z[C1_list_2[(i+1)%4]-1]-ts._z[C1_list_2[i]-1]]
vector1=numpy.array(vector1)
vector2=numpy.array(vector2)
# print vector1,vector2
gamma=numpy.dot(vector1,vector2)/(math.sqrt(numpy.dot(vector1,vector1)*numpy.dot(vector2,vector2)))
angle.append(math.acos(gamma)/3.1416*180)
fp.write("%6.3f \t %6.3f \t %6.3f \t %6.3f \t %6.3f\n" \
%(ts.time/1000,angle[0],angle[1],angle[2],angle[3]))
#if ts.frame % 100 ==0:
# print " analysis frame %6d......" %ts.frame
usage.echo(" analysis frame %6d......\r" %ts.frame)
fp.close()
print "The result are in the file: ",output_file
ts._y[C1_list_1[(k+1)%4]-1]-ts._y[C1_list_1[k]-1],\
ts._z[C1_list_1[(k+1)%4]-1]-ts._z[C1_list_1[k]-1]]
vector2=[ts._x[C1_list_2[(k+1)%4]-1]-ts._x[C1_list_2[k]-1],\
ts._y[C1_list_2[(k+1)%4]-1]-ts._y[C1_list_2[k]-1],\
ts._z[C1_list_2[(k+1)%4]-1]-ts._z[C1_list_2[k]-1]]
vector1=numpy.array(vector1)
vector1_1=numpy.cross(numpy.cross(orient_group_1,vector1),orient_group_1)
vector2=numpy.array(vector2)
vector2_2=numpy.cross(numpy.cross(orient_group_2,vector2),orient_group_2)
# print vector1_1,vector2_2
gamma=numpy.dot(vector1_1,vector2_2)/(math.sqrt(numpy.dot(vector1_1,vector1_1)*numpy.dot(vector2_2,vector2_2)))
angle.append(math.acos(abs(gamma))/3.1416*180)
fp=open(output_name[i],'a')
fp.write("%6.3f \t %6.3f \t %6.3f \t %6.3f \t %6.3f\n" \
%(ts.time/1000,angle[0],angle[1],angle[2],angle[3]))
if ts.frame % 100 ==0 and i ==0:
usage.echo(" analysis frame %6d\r" %ts.frame)
fp.close()
print "The result are in the file: ",output_name