How to stringfy a swig matrix object in python

Question

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 unit

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++.

Answer 2

Further to the answer from @jhoon, it seems that SWIG doesn't recognise the std::string return type so change the function to return const char*. Also, since it is a function outside the class, you can't use self but you must use SWIG's $self variable.

So, in the SWIG .i file, if you put the following:

%extend OpenBabel::matrix3x3 {
  const char* __str__() {
    std::ostringstream out;
    out << *$self;
    return out.str().c_str();
  }
};

you should get the desired result when calling Python's print on a matrix3x3.

If you find yourself adding this to many classes, consider wrapping it in a macro like:

%define __STR__()
const char* __str__() {
  std::ostringstream out;
  out << *$self;
  return out.str().c_str();
}
%enddef

and then adding it to the class with:

%extend OpenBabel::matrix3x3 {
  __STR__()
};