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 ""
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
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)
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
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
#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:
