Builder test codes

calc_rmsd.cpp

#include <iostream>
#include <sstream>

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/builder.h>
#include <openbabel/math/align.h>

using namespace std;
using namespace OpenBabel;
int main(int argc, char **argv) {
  if (argc != 3) {
    cerr << "Usage: " << argv[0] << "<target> <reference>" << endl;
    exit(EXIT_FAILURE);
  }

  OBMol mol1, mol2;
  OBConversion conv;
  ifstream ifs1, ifs2;
  string s, s1, s2;
  stringstream ss;

  for(int i = 1; i <= 2; ++i) {
    OBFormat *inFormat = conv.FormatFromExt(argv[i]);
    if(inFormat==NULL || !conv.SetInFormat(inFormat)) {
      cerr << " Cannot read file format for " << argv[i] << endl;
      exit(EXIT_FAILURE);
    }
  }
  ifs1.open(argv[1]);
  ifs2.open(argv[2]);
  conv.SetOutFormat("can");
  if (!ifs1 || !ifs2 ) {
    cerr << "Cannot read input file" << endl;
      exit(EXIT_FAILURE);
  }
  while(ifs1.peek() != EOF && ifs1.good() && ifs2.peek() != EOF && ifs2.good()) {
    conv.Read(&mol1, &ifs1);
    conv.Read(&mol2, &ifs2);
    s1 = conv.WriteString(&mol1, true);
    s2 = conv.WriteString(&mol2, true);
    ss.str(s1);
    ss >> s;
    OBAlign aln(mol1, mol2);
    aln.Align();
    cout << s << "," << aln.GetRMSD() << endl;
  }
}

test.cpp

#include <iostream>

#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/builder.h>

using namespace std;
using namespace OpenBabel;
int main(int argc, char **argv) {
  OBMol mol;
  OBBuilder builder;

  ifstream ifs;
  OBConversion conv;
  conv.SetOutFormat("SDF");

  for (int i=1; i < argc; i++) {
    OBFormat *inFormat = conv.FormatFromExt(argv[i]);
    if(inFormat==NULL || !conv.SetInFormat(inFormat))
    {
      cerr << " Cannot read file format for " << argv[i] << endl;
      continue; // try next file
    }
    ifs.open(argv[i]);
    if (!ifs) {
      cerr << "Cannot read input file: " << argv[i] << endl;
      continue;
    }
    while(ifs.peek() != EOF && ifs.good()) {
      conv.Read(&mol, &ifs);
      builder.Build(mol);
      mol.AddHydrogens();
      conv.Write(&mol, &cout);
    }
  }
}