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)
base_name_list_1=list()
base_name_list_2=list()
base_atom_list_1=list()
base_atom_list_2=list()
for m in base_list_1:
# for n in residue_list:
# if n[1]==m:
base_name_list_1.append(residue_list[m-1])
# print base_name_list_1
for m in base_list_2:
base_name_list_2.append(residue_list[m-1])
base_atom_list_1=[DNA_matrix.Get_baseID_list(atom_list,j) for j in base_list_1]
base_atom_list_2=[DNA_matrix.Get_baseID_list(atom_list,j) for j in base_list_2]
r1=[]
'''the group 1 rotate list'''
r2=[]
'''the group 2 rotate list'''
c1=[]
'''the group 1 coordinate list'''
c2=[]
'''the group 2 coordinate list'''
for m in range(len(base_name_list_1)):
temp_list = [ [atom_list[x-1].atom_coor_x*10, atom_list[x-1].atom_coor_y*10,atom_list[x-1].atom_coor_z*10] \
for x in base_atom_list_1[m] ]
# print temp_list
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), base_name_list_1[m][0])
r1.append(result[0])
c1.append(result[1])
for m in range(len(base_name_list_2)):
temp_list = [ [atom_list[x-1].atom_coor_x*10, atom_list[x-1].atom_coor_y*10,atom_list[x-1].atom_coor_z*10] \
for x in base_atom_list_2[m] ]
# print temp_list
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), base_name_list_2[m][0])
r2.append(result[0])
c2.append(result[1])
if CALCU=="pair":
a=DNA_param.base_pair_parameters(r1[0],r2[0],c1[0],c2[0])
if PRINT:
print " shear stretch stagger buckle propeller opening"
print "%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f" %(a[0],a[1],a[2],a[3],a[4],a[5])
return a
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)
if PRINT:
print " shift slide rise tilt roll twist"
print "%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f" %(a[0],a[1],a[2],a[3],a[4],a[5])
return a
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)
base_name_list_1 = list()
base_name_list_2 = list()
base_atom_list_1 = list()
base_atom_list_2 = list()
for m in base_list_1:
# for n in residue_list:
# if n[1]==m:
base_name_list_1.append(residue_list[m - 1])
# print base_name_list_1
for m in base_list_2:
base_name_list_2.append(residue_list[m - 1])
base_atom_list_1 = [
DNA_matrix.Get_baseID_list(atom_list, j) for j in base_list_1
]
base_atom_list_2 = [
DNA_matrix.Get_baseID_list(atom_list, j) for j in base_list_2
]
r1 = []
'''the group 1 rotate list'''
r2 = []
'''the group 2 rotate list'''
c1 = []
'''the group 1 coordinate list'''
c2 = []
'''the group 2 coordinate list'''
for m in range(len(base_name_list_1)):
temp_list = [ [atom_list[x-1].atom_coor_x*10, atom_list[x-1].atom_coor_y*10,atom_list[x-1].atom_coor_z*10] \
for x in base_atom_list_1[m] ]
# print temp_list
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list),
base_name_list_1[m][0])
r1.append(result[0])
c1.append(result[1])
for m in range(len(base_name_list_2)):
temp_list = [ [atom_list[x-1].atom_coor_x*10, atom_list[x-1].atom_coor_y*10,atom_list[x-1].atom_coor_z*10] \
for x in base_atom_list_2[m] ]
# print temp_list
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list),
base_name_list_2[m][0])
r2.append(result[0])
c2.append(result[1])
if CALCU == "pair":
a = DNA_param.base_pair_parameters(r1[0], r2[0], c1[0], c2[0])
if PRINT:
print " shear stretch stagger buckle propeller opening"
print "%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f" % (
a[0], a[1], a[2], a[3], a[4], a[5])
return a
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)
if PRINT:
print " shift slide rise tilt roll twist"
print "%8.2f %8.2f %8.2f %8.2f %8.2f %8.2f" % (
a[0], a[1], a[2], a[3], a[4], a[5])
return a
temp_list = [ [ts._x[x-1], ts._y[x-1], ts._z[x-1]] for x in base_atom_list_1[i][m] ]
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), base_name_list_1[i][m][0])
#base_name_list_1[index of the groups][index of the base of group 1][base_name,base_serial]
r1.append(result[0])
c1.append(result[1])
for m in range(len(base_name_list_2[i])):
temp_list = [ [ts._x[x-1], ts._y[x-1], ts._z[x-1]] for x in base_atom_list_2[i][m] ]
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), base_name_list_2[i][m][0])
r2.append(result[0])
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
#base_name_list_1[index of the groups][index of the base of group 1][base_name,base_serial]
r1.append(result[0])
c1.append(result[1])
for m in range(len(base_name_list_2[i])):
temp_list = [[ts._x[x - 1], ts._y[x - 1], ts._z[x - 1]]
for x in base_atom_list_2[i][m]]
result = DNA_matrix.Get_rotate_matrix(
numpy.array(temp_list), base_name_list_2[i][m][0])
r2.append(result[0])
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:
