当前，我的代码在TINKER输入坐标文件中读取我的原子。
定义了一个计算距离的函数，如下所示：
def getdist(at1,at2):
''' Calculate distance between two particles
'''
dist_at=sqrt((at2[0]-at1[0])**2+(at2[1]-at1[1])**2+(at2[2]-at1[2])**2)
return dist_at
这将传递到主脚本，该主脚本根据在命令行中传递的两个参数执行计算：
def parsecmd():
description="Calculate distances, angles, torsions and quota in periodic or\
non-periodic molecular structures.\n\
See documentation for further information."
usage="usage: %prog [options] input_file"
#updtate this when new formats are added
list_of_formats="XYZ/XMOL, TINKER XYZ/ARC"
#parse command line
parser=OP(version='%prog 1.1',description=description,usage=usage)
parser.add_option('-c','--credits',dest='credits',action='store_true',
default=False,help='display credits')
parser.add_option('-f','--format',dest='fformat', default="arc",
help='specify the format of the input structure, [default: %default]')
parser.add_option('-e','--filedata',dest='filedata',nargs=1,
help='specify that input file is setup file')
parser.add_option('-d','--distance',dest='distance',nargs=2,type='int',
help='require a distance calculation on the specified couple of atoms')
parser.add_option('-a','--angle',dest='angle',nargs=3,type='int',
help='require angle calculation on the specified three atoms')
parser.add_option('-i','--dih',dest='dih',nargs=4,type='int',
help='dihedral angle four atoms')
parser.add_option('-t','--torsion',dest='torsion',nargs=5,type='int',
help='require torsions calculation on the specified dihedral angle combination pair and periodicity (i.e. 360 deg)')
parser.add_option('-T','--torsion1',dest='torsion1',nargs=5,type='int',
help='require torsions calculation on the specified four atoms and periodicity (i.e. 360 deg)')
parser.add_option('-u','--unitcell',dest='periodicity',nargs=6,type='float',
help='define periodic unit cell (a,b,c in angstrom; alpha,beta,gamma in degrees)')
parser.add_option('-l','--listformats',dest='listformats',action='store_true',
default=False, help='list the available formats')
(options, args) = parser.parse_args(argv[1:])
while 1:
#get format file structure
if lower(fformat) == "arc":
retdata=read_arc(structfile,offset)
elif lower(fformat) == "xyz":
retdata=read_xyz(structfile,offset)
else:
pass
if retdata=="EOF":
break
else:
coordinates=retdata[0] #always in 1st position if not EOF
offset=retdata[1] #always in 2nd position if not EOF
for index,task in enumerate(tasklist):
if task != None:
if index == 0: #get distances
tmplist=[]
for element in task: #scan over the lists of distances
for i in range(3):
at1[i]=coordinates[element[0]-1][i] #1st atom
at2[i]=coordinates[element[1]-1][i] #2nd atom
if pbc == None:
dist=getdist(at1,at2)
else:
dist=getpbcdist(at1,at2,pbc)
tmplist.append('%12.4f' % dist)
F_DISTS.write(join(tmplist,'')+"\n") #write out the list of
distances as string
def main():
'''
#===============================================================================
# MAIN MAIN MAIN MAIN
#===============================================================================
'''
(options,args)=parsecmd()
print('test')
infile=args[0]
outfiles=[]
#tasklist contain the list of task.the list in the 1st element is
#for the distances, that in the 2nd is for angle and in the 3rd for torsions and 4th is torsion combination
tasklist=[]
fformat=options.fformat #get format input file
if options.periodicity: #get periodicity
pbc=options.periodicity
else:
pbc=None
if options.filedata: #read data from file
filedata=safeopen(options.filedata,'r')
if filedata:
(tasklist,outfiles)=read_filedata(filedata)
else:
print ("Cannot find "+options.filedata)
else:
if options.distance: #distance
junk=[]
junk.append(list(options.distance)) #convert the tuple from the cml to a list
tasklist.append(junk)
tasklist.append(None) #no angle to calculate
tasklist.append(None) #no torsion to calculate
#create list outfiles in the form [['file'],None,None]
outfiles.append('distcml.dat')
outfiles.append(None)
outfiles.append(None)
我想让at2遍历文件中的多个原子，而不是通过命令行at1和at2传递两个参数，而我想用这些原子数的列来计算距离at1的距离。
我在寻找什么
at1 = 26
at2 = 26,27,28,29,30,31,32,33,34,45（这些值保存在一个名为atoms.dat的文件中，所有内容都由新行分隔开）
我想要at1和at2中所有元素之间的距离。
我尝试过的事情：
我尝试在代码内使用for循环打开文件，因此at2被迭代了文件中的每一行，但发生了此错误：
文件“ distances_reference_atom_to_other_atoms.py”，第839行，位于主目录中 junk.append（list（options.distance））＃将元组从cml转换为列表 TypeError：“ int”对象不可迭代
然后，我尝试通过命令行传递参数，并且发生了类似的错误。