计算DNA中两个碱基的中点

最新推荐文章于 2024-07-30 17:22:42 发布

rogerzhanglijie

最新推荐文章于 2024-07-30 17:22:42 发布

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分类专栏： Python 文章标签： list distance float up file import

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import math
#up_sticky_end is the up strand where the sequence is split
#bottom_sticky_end is the bottom strand where the sequence is split
def Calculate_distance(file_pdb,up_strand_list,bottom_strand_list,up_sticky_end,bottom_sticky_end):
   file_pdb_data=open(file_pdb,'r')
   lines_data=file_pdb_data.readlines()
   file_pdb_data.close()
   up_point_list=[]
   bottom_point_list=[]
   for i in range(0,len(up_strand_list)):
       for line_data in lines_data:
           line_data_list=line_data.split()
           if up_strand_list[i]!=up_sticky_end:
               if up_strand_list[i] in line_data_list[4:] and "P" in line_data_list[2:]:
                   up_point_list.append(line_data_list[-5:-2])
                   break
           elif up_strand_list[i]==up_sticky_end:
               if up_strand_list[i] in line_data_list[4:] and "O5'" in line_data_list[2:]:
                   up_point_list.append(line_data_list[-5:-2])
                   break
   for j in range(0,len(bottom_strand_list)):
       for line_data in lines_data:
           line_data_list=line_data.split()
           if bottom_strand_list[j]!=bottom_sticky_end:
               if bottom_strand_list[j] in line_data_list[4:] and "P" in line_data_list[2:]:
                   bottom_point_list.append(line_data_list[-5:-2])
                   break
           elif bottom_strand_list[j]==bottom_sticky_end:
               if bottom_strand_list[j] in line_data_list[4:] and "O5'" in line_data_list[2:]:
                   bottom_point_list.append(line_data_list[-5:-2])
                   break
   print up_point_list[1:],bottom_point_list[:-1]
   return up_point_list[1:],bottom_point_list[:-1]
def distance(list1,list2,i):
   x_avg=(float(list1[i][0])+float(list2[i][0]))/2
   y_avg=(float(list1[i][1])+float(list2[i][1]))/2
   z_avg=(float(list1[i][2])+float(list2[i][2]))/2
   return x_avg,y_avg,z_avg
def extract_resdue_list(file):
   resdue_file=open(file,"r")
   all_resdue_list=[]
   for line in resdue_file.readlines():
       line_list=line.split()[1:]
       all_resdue_list.append(line_list)
   resdue_file.close()
   return all_resdue_list
if __name__=="__main__":
   #resdue_lists=extract_resdue_list("sequence.txt")

#The following is the test data

L1=["756","757","530"]

   L2=["52","12","11"]
   list_one,list_two=Calculate_distance("0.pdb",L1,L2,"93","-1")
   distance(list_one,list_two)