Example #1
0
 def getAtomsInSameFragment(self, a1, a2=0):
     if not is_int(a1) or not is_int(a2): raise ValueError
     if a2 != 0: raise ValueError
     tmp = openbabel.vectorInt()
     self.mol.FindChildren(tmp, a2, a1)
     fragment = sorted(toList(tmp) + [a1])
     return fragment
Example #2
0
 def getAtomsInSameFragment(self, a1, a2 = 0):
     if not is_int(a1) or not is_int(a2): raise ValueError
     if a2 != 0: raise ValueError
     tmp = openbabel.vectorInt()
     self.mol.FindChildren(tmp, a2, a1)
     fragment = sorted(toList(tmp) + [a1])
     return fragment
Example #3
0
File: recap3.py Project: rbelew/mgl
  def fragment_size(self, a, b):
	# size of fragment b if a-b were broken
	c1 = ob.vectorInt()
	self.mol.FindChildren(c1,a.GetIdx(),b.GetIdx())
	#for atom in c1:
	#  if self.mol.GetAtom(atom).GetValence() == 1:
	return 1+len(c1)
Example #4
0
    def getAtomsInSameFragment(self, a1, a2 = 0):
        """ The heart of FragIt.

            This method determines fragments in a system.
            It works by finding all possible atoms between
            two end-points in the molecular graph by calling
            the FindChildren method of OBMol.

            Note: There is some dark art going on here since
                  a2 is apparently always zero.
        """
        if not isinstance(a1, int) or not isinstance(a2, int):
            raise ValueError
        if a2 != 0:
            raise ValueError
        tmp = openbabel.vectorInt()
        self.mol.FindChildren(tmp, a2, a1)
        fragment = sorted(toList(tmp) + [a1])
        return fragment
Example #5
0
    def getAtomsInSameFragment(self, a1, a2=0):
        """ The heart of FragIt.

            This method determines fragments in a system.
            It works by finding all possible atoms between
            two end-points in the molecular graph by calling
            the FindChildren method of OBMol.

            Note: There is some dark art going on here since
                  a2 is apparently always zero.
        """
        if not isinstance(a1, int) or not isinstance(a2, int):
            raise ValueError
        if a2 != 0:
            raise ValueError
        tmp = openbabel.vectorInt()
        self.mol.FindChildren(tmp, a2, a1)

        fragment = [value for value in tmp] + [a1]
        return sorted(fragment)
Example #6
0
 def fragment_size(self, a, b):
     # size of fragment b if a-b were broken
     c1 = openbabel.vectorInt()
     self.mol.OBMol.FindChildren(c1,a.GetIdx(),b.GetIdx())
     return len(c1) + 1
Example #7
0
 def fragment_size(self, a, b):
     # size of fragment b if a-b were broken
     c1 = openbabel.vectorInt()
     self.mol.OBMol.FindChildren(c1, a.GetIdx(), b.GetIdx())
     return len(c1) + 1