How to stringfy a swig matrix object in python

Question

Hi, I am using swig wrapper of openbabel (written in C++, and supply a python wrapper through swig)

Below i just use it to read a molecule structure file and get the unitcell property of it.

import pybel
for molecule in pybel.readfile('pdb','./test.pdb'):
    unitcell = molecule.unitcell
    print unitcell
   |..>     
   |..>     
<openbabel.OBUnitCell; proxy of <Swig Object of type 'OpenBabel::OBUnitCell *' at 0x17b390c0> >

The unitcell has function CellMatrix(),

unitcell.GetCellMatrix()
   <22> <openbabel.matrix3x3; proxy of <Swig Object of type 'OpenBabel::matrix3x3 *' at 0x17b3ecf0> >

the OpenBabel::matrix3x3 is something like :

1 2 3
4 5 6
7 8 9

i am wondering how to print out the contents of the matrix3*3 . I have tried __str__ and __repr__ with it.

Any general way to stringfy the contents of a matrix wrapped by swing in python ?

thanks

Answer 1

Based on this openbabel documentation, it looks like there is a good reason the Python bindings don't come with a nice way to print a matrix3x3 object. The matrix3x3 C++ class overloads the << operator, which SWIG will simply ignore:

http://openbabel.org/api/2.2.0/classOpenBabel_1_1matrix3x3.shtml

This means that you'll need to modify your SWIG interface file (look at http://www.swig.org/Doc1.3/SWIGPlus.html#SWIGPlus_class_extension) to add a __str__ method to openbabel::matrix3x3 in C++ which wraps the << operator. Your method might look a lot like

std::string __str__() {
  //make sure you include sstream in the SWIG interface file
  std::ostringstream oss(std::ostringstream::out);
  oss << (*this);
  return oss.str();
}

I believe that SWIG will properly handle C++ a return type of std::string in this case, but if not you might have to play around with returning a character array.

At this point, you should be able to recompile the bindings, and rerun your Python code. Calling str() on a matrix3x3 object should now display what would be displayed with the << operator in C++.