[Open Babel] stereochem "patch"

[Eugen L. <eu...@le...>]

I've made a simple hack to do stereochem
conservation for

babel -imol blah.mol -omol blahout.mol

Not tested much, and I don't know how you
submit patches.=20

All changes are to mdl.cpp, relatively
to today's cvs checkout, and do build
on cygwin cleanly. Regression tests are
not more broken than usual.

Right at beginning of the file mdl.cpp insert the
function wedgeorhatch:

=2E...
#include "mol.h"

using namespace std;
namespace OpenBabel {

extern OBAtomTyper atomtyper; //CM

int wedgeorhatch(int flag) {

	if (flag & OB_WEDGE_BOND) return 1;
	if (flag & OB_HASH_BOND ) return 6;
	return 0;
}
=2E...
ReadSDFFile already does what it should, so no changes there.

In WriteSDFile:
=2E...
  vector<OBEdgeBase*>::iterator j;
  for (atom =3D mol.BeginAtom(i);atom;atom =3D mol.NextAtom(i))
    for (nbr =3D atom->BeginNbrAtom(j);nbr;nbr =3D atom->NextNbrAtom(j))
      if (atom->GetIdx() < nbr->GetIdx()) {
        bond =3D (OBBond*) *j;
        sprintf(buff,"%3d%3d%3d%3d%3d%3d%3d%3d", // probably one %3d too ma=
ny
                bond->GetBeginAtomIdx(),
                bond->GetEndAtomIdx(),
                (bond->GetBO() =3D=3D 5) ? 4 : bond->GetBO(),
		wedgeorhatch(bond->GetFlags()),  // this is the change
		0,0,0,0);
        ofs << buff << endl;
      }
=2E...


I'm using isopentan.mol mit sterochem as input:


  -ISIS-  11100315272D

  5  4  0  0  0  0  0  0  0  0999 V2000
   -2.9792    0.9542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1647    1.4667    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5002    0.8750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4272    2.2458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5042    2.0542    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  4  1  1  0  0  0
  2  5  1  6  0  0  0
M  END

and get the following as output:


 OpenBabel          2D

  5  4  0  0  0  0  0  0  0  0  1
   -2.9792    0.9542    0.0000 C   0  0  0  0  0
   -2.1647    1.4667    0.0000 C   0  0  0  0  0
   -1.5002    0.8750    0.0000 C   0  0  0  0  0
   -2.4272    2.2458    0.0000 C   0  0  0  0  0
   -1.5042    2.0542    0.0000 C   0  0  0  0  0
  1  2  1  0  0  0  0  0
  2  3  1  0  0  0  0  0
  2  4  1  1  0  0  0  0
  2  5  1  6  0  0  0  0
M  END
$$$$

Oops, I notice that there's an extra zero columnt. Just remove
one superfluous %3d from sprintf, and get rid of one of the zeros below
wedgeorhatch(bond->GetFlags()),=20

I haven't tidied it all up, because I'm not a programmer,
and you will probably add the functionality using equivalent
but different code.

I can supply some test cases for the regression tests, though,
if you need them.

I don't have time nor the skills to work on cml.cpp, so I leave
that to Peter.=20

-- Eugen* Leitl <a href=3D"http://leitl.org">leitl</a>
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