def Get_pls_fromTOP( coor_file, base_list_1, base_list_2, output_name):
'''
get parameters from coor_file, for rigidity (perstence length) calculations
'''
START_TIME=Time.time()
if len(base_list_1)==len(base_list_2):
LIST_NUM=len(base_list_1)
else:
print "ERROR: The length of the base list not match."
return -1
if len(output_name)!=LIST_NUM:
print "ERROR: The number of the output file not match the size of the base list."
Atom_list=Simple_atom.Get_atom_list(coor_file)
residue_list=Simple_atom.Get_Residue_list(Atom_list)
chain=[]
for ii,reside in enumerate(residue_list):
if reside[0] in atomlib.RESIDUE_NAME_LIST:
chain.append([ii+1,reside])
else:
pass
# for ca in chain:
# print "%4d\t ( %6d %8s )" % (ca[0], ca[1][1],ca[1][0])
if (len(chain) % 2) == 0:
pass
else:
print "-the base number of nucleic acid segment is not even, so..."
print "-please check it!"
#####
# construct the lists for bp of nucleic acids
chain_bpList=list()
chain_bpAtomList=list()
##
# chain_bpList -> save the bp iformation in a list
# format: [ [[[residue_name, residue_serial], [residue_name, residue_serial]], [[], []], ... ]
##
num_nuc=len(chain)
for ii in range(num_nuc/2):
chain_bpList.append([chain[ii][1], chain[num_nuc-ii-1][1]])
if len(chain_bpList) == num_nuc/2:
chainLIST_NUM=len(chain_bpList)
else :
print "- number of base pairs in chain_bpList: %d" %(len(chain_bpList_1))
print "- total base pairs in system: %d" %(num_nuc/2)
sys.exit()
# print the base pair list of DNA chain
# for ii, bp_1 in enumerate(chain_bpList):
# print ii, bp_1
#build the atom list for each base pair in the LIST of chain_bpList\
for i in range(chainLIST_NUM):
chain_bpAtomList.append([DNA_matrix.Get_baseID_list(Atom_list,j[1]) for j in chain_bpList[i]])
#########################################
L_stepList=list()
R_middle_LIST=list()
O_middle_LIST=list()
for i in range(chainLIST_NUM):
# print i+1,
# 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(chain_bpList_1[i])):
# temp_list = [ [ts._x[x-1], ts._y[x-1], ts._z[x-1]] for x in chain_bpAtomList_1[i][m] ]
# result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), chain_bpList_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(chain_bpList_2[i])):
# temp_list = [ [ts._x[x-1], ts._y[x-1], ts._z[x-1]] for x in chain_bpAtomList_2[i][m] ]
# result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), chain_bpList_2[i][m][0])
# r2.append(result[0])
# c2.append(result[1])
# 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])
# R_middle_LIST_1.append(middle_r1)
# R_middle_LIST_2.append(middle_r2)
# O_middle_LIST_1.append(middle_c1)
# O_middle_LIST_2.append(middle_c2)
# a=DNA_param.persistence_length_parameters(middle_r1,middle_r2,middle_c1,middle_c2)
# L_stepList.append(a[1])
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(chain_bpList[i])):
# temp_list = [ [ts._x[x-1], ts._y[x-1], ts._z[x-1]] for x in chain_bpAtomList[i][m] ]
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 chain_bpAtomList[i][m] ]
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), chain_bpList[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])
middle_r,middle_c=DNA_param.middle_frame(r1[0],r1[1],c1[0],c1[1])
R_middle_LIST.append(middle_r)
O_middle_LIST.append(middle_c)
for i in range(chainLIST_NUM-1):
a=DNA_param.persistence_length_parameters(R_middle_LIST[i], R_middle_LIST[i+1], O_middle_LIST[i], O_middle_LIST[i+1])
L_stepList.append(a[1])
# print
# print len(R_middle_LIST)==len(O_middle_LIST)==chainLIST_NUM
# print L_stepList
##########################################
#construct list for base_list_1 and base_list_2
base_name_list_1=list()
base_name_list_2=list()
# base_atom_list_1=list()
# base_atom_list_2=list()
for i in range(LIST_NUM):
if os.path.isfile(output_name[i]):
print "backup %s to %s" %(output_name[i],"#"+output_name[i]+"#")
try:
os.rename(output_name[i],"#"+output_name[i]+"#")
except OSError,e:
print e
print "the file %s will be overwrited!" %output_name[i]
fp = open(output_name[i], 'w')
fp.write("#Group 1: ")
for j in base_list_1[i]:
fp.write("%d\t " %j)
fp.write("\n")
fp.write("#Group 2: ")
for j in base_list_2[i]:
fp.write("%d\t " %j)
fp.write("\n")
fp.write("#skip: no skip, only for one frame coordinate (.gro or .pdb) \n" )
fp.write("# L0 L cos(theta) theta\n")
fp.close()
# base_name_list_1.append( [residue_list[j-1] for j in base_list_1[i]])
# base_name_list_2.append( [residue_list[j-1] for j in base_list_2[i]])
temp_list=list()
for m in base_list_1[i]:
temp_list.append(residue_list[m-1])
base_name_list_1.append(temp_list)
# base_name_list_1.append(residue_list[m-1])
temp_list=list()
for m in base_list_2[i]:
temp_list.append(residue_list[m-1])
base_name_list_2.append(temp_list)
'''the group 1 coordinate list'''
c2=[]
'''the group 2 coordinate list'''
for m in range(len(chain_bpList[i])):
temp_list = [ [ts._x[x-1], ts._y[x-1], ts._z[x-1]] for x in chain_bpAtomList[i][m] ]
result = DNA_matrix.Get_rotate_matrix(numpy.array(temp_list), chain_bpList[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])
middle_r,middle_c=DNA_param.middle_frame(r1[0],r1[1],c1[0],c1[1])
# print middle_c
R_middle_LIST.append(middle_r)
O_middle_LIST.append(middle_c)
for i in range(chainLIST_NUM-1):
a=DNA_param.persistence_length_parameters(R_middle_LIST[i], R_middle_LIST[i+1], O_middle_LIST[i], O_middle_LIST[i+1])
L_stepList.append(a[1])
# print
# print len(R_middle_LIST)==len(O_middle_LIST)==chainLIST_NUM
# print L_stepList
####
for i in range(LIST_NUM):
L0=0.0
fp = open(output_name[i], 'a')
# print output_name[i]
bp_INDEX0=0
bp_INDEX1=0
# print base_name_list_1[0], base_name_list_2[0]
# print chain_bpList[1], chain_bpList[2]
