#157 better perl bindings for rmsd calculations

[David Koes]

I was trying to use the Perl interface to OpenBabel to do some RMSD calculations and found I couldn't since key functionality seemed to be missing. Specifically, the ability to manipulate SWIG C arrays in perl and access to a couple functions. Here are the changes I made to get things to work:

include/openbabel/obutil.h
156,164d155
< #ifndef __KCC
< extern "C" {
< OBAPI void rotate_coords(double,double m[3][3],unsigned int);
< OBAPI double calc_rms(double,double,unsigned int);
< }
< #else
< OBAPI void rotate_coords(double,double m[3][3],unsigned int);
< OBAPI double calc_rms(double,double,unsigned int);
< #endif
165a157,159

OBAPI void rotate_coords(double,double m[3][3],int);
OBAPI double calc_rms(double,double*,unsigned int);

scripts/openbabel-perl.i
163,188d162
< // Add some helper functions for C arrays
< %inline %{
< double double_array(int size) {
< return (double ) malloc(sizeof(double)size);
< }
< void double_destroy(int a) {
< free(a);
< }
< void double_set(double a, int i, double val) {
< a[i] = val;
< }
< double double_get(double a, int i) {
< return a[i];
< }
<
< double (rotation_matrix())[3] {
< return (double ()[3]) malloc(9sizeof(double));
< }
<
< void rotation_matrix_free(double (m)[3])
< {
< free(m);
< }
<
< %}
<

[Geoff Hutchison]

I don't know what version you've used for the patch -- it's definitely not SVN trunk. Could you e-mail me a patch for SVN trunk?

Thanks very much,
-Geoff

[David Koes]

That was comparing against 2.2.3. Here's the diff for the trunk (note that rotate_coord had the wrong prototype, this is a subtle bug that is also fixed):

Index: include/openbabel/obutil.h

--- include/openbabel/obutil.h (revision 4112)
+++ include/openbabel/obutil.h (working copy)
@@ -153,10 +153,17 @@
};

//RMS helper methods/
+#ifndef __KCC

• extern "C" {
• OBAPI void rotate_coords(double*,double m[3][3],unsigned);
• OBAPI double calc_rms(double,double,unsigned int);
• }
  +#else
• OBAPI void rotate_coords(double*,double m[3][3],unsigned);
• OBAPI double calc_rms(double,double,unsigned int);
  +#endif
• #ifndef SWIG
• OBAPI void rotate_coords(double*,double m[3][3],int);

• OBAPI double calc_rms(double,double,unsigned int);

  
  //! \name String conversion utilities
  //@{
  // Documentation in obutil.cpp
  Index: scripts/openbabel-perl.i
  ===================================================================
  --- scripts/openbabel-perl.i (revision 4112)
  +++ scripts/openbabel-perl.i (working copy)
  @@ -276,6 +276,30 @@
  }
  %}

+// Add some helper functions for C arrays
+%inline %{
+double *double_array(int size) {

• return (double ) malloc(sizeof(double)size);
  +}
  +void double_destroy(int *a) {
• free(a);
  +}
  +void double_set(double *a, int i, double val) {
• a[i] = val;
  +}
  +double double_get(double *a, int i) {
• return a[i];
  +}
  +
  +double (*rotation_matrix())[3] {
• return (double ()[3]) malloc(9sizeof(double));
• }
  +
  +void rotation_matrix_free(double (*m)[3]) {
• free(m);
  +}
  +%}
  +
  %define MAKE_ITER_CLASS(itername, renamediter)
  %rename itername renamediter;
  %perlcode %{