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我正在做一些关于蛋白质建模的教程，方法是使用多个模板对相同的蛋白质进行建模。我目前正在尝试运行 align_all.py 但是输出变成这样

rmsd_list.sort(key=lambda x,y: cmp(x[1],y[1]))

TypeError：（）缺少1个必需的位置参数：'y'

我尝试了很多方法来纠正它，但仍然没有得到解决方案。我希望有人可以帮助我解决这个问题。我目前正在使用 Python 2.7。

以下是完整代码

from pymol import cmd

def align_all(target=None,mobile_selection='name ca',target_selection='name ca',cutoff=2, cycles=5,cgo_object=0,method='align'):

cutoff = int(cutoff)
  cycles = int(cycles)
  cgo_object = int(cgo_object)

  object_list = cmd.get_names()
  object_list.remove(target)

  rmsd = {}
  rmsd_list = []
  for i in range(len(object_list)):
    if cgo_object:
      objectname = 'align_%s_on_%s' % (object_list[i],target)
      if method == 'align':
        rms = cmd.align('%s & %s'%(object_list[i],mobile_selection),'%s & %s'%(target,target_selection),cutoff=cutoff,cycles=cycles,object=objectname)
      elif method == 'super':
        rms = cmd.super('%s & %s'%(object_list[i],mobile_selection),'%s & %s'%(target,target_selection),cutoff=cutoff,cycles=cycles,object=objectname)
      elif method == 'cealign':
        rmsdict = cmd.cealign('%s & %s' % (target,target_selection),'%s & %s' % (object_list[i],mobile_selection))
        rms = [rmsdict['RMSD'],rmsdict['alignment_length'],1,0,0]
      else:
        print ("only 'align', 'super' and 'cealign' are accepted as methods")
        sys.exit(-1)
    else:
      if method == 'align':
        rms = cmd.align('%s & %s'%(object_list[i],mobile_selection),'%s & %s'%(target,target_selection),cutoff=cutoff,cycles=cycles)
      elif method == 'super':
        rms = cmd.super('%s & %s'%(object_list[i],mobile_selection),'%s & %s'%(target,target_selection),cutoff=cutoff,cycles=cycles)
      elif method == 'cealign':
        rmsdict = cmd.cealign('%s & %s' % (target,target_selection),'%s & %s' % (object_list[i],mobile_selection))
        rms = [rmsdict['RMSD'],rmsdict['alignment_length'],1,0,0]
      else:
        print ("only 'align', 'super' and 'cealign' are accepted as methods")
        sys.exit(-1)

    rmsd[object_list[i]] = (rms[0],rms[1])
    rmsd_list.append((object_list[i],rms[0],rms[1]))


  rmsd_list.sort(key=lambda x,y: cmp(x[1],y[1]))
# loop over dictionary and print out matrix of final rms values
  print ("Aligning against:",target)
  for object_name in object_list:
    print ("%s: %6.3f using %d atoms" % (object_name,rmsd[object_name][0],rmsd[object_name][1]))

  print ("\nSorted from best match to worst:")
  for r in rmsd_list:
    print ("%s: %6.3f using %d atoms" % r)

cmd.extend('align_all',align_all)

谢谢你。

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1 回答 1

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排序函数 key 关键字被传递给对象，并期望返回该对象的比较键。旧版本的 python 排序使用 cmp 关键字来比较要排序的两个元素。

你要rmsd_list.sort(key=lambda e: e[1])我怀疑。

于 2021-03-03T05:53:38.800 回答