5.7 Looping over subsets of Atoms or Bonds

It can sometimes be useful to loop over a subset of the atoms or bonds of a molecule. Traditionally this can be done with "if" statements inside a loop, but it can sometimes be cleaner and more convenient to subset the members being looped over inside the iterator. To do this, many of OEChem's iterator generation functions (such as OEMolBase::GetAtoms) can take an argument which determines which subset of the object to loop over (these functions are called predicates as detailed in the chapter "Predicate Functions" below). The details of these functions are not important here. Instead, a programmer can simply use the predefined functors to control their loops.

The following example shows the use of the predicate OEHasAtomicNum() to loop over only carbon atoms in a molecule.

#include "oechem.h"
#include <iostream>

using namespace OESystem;
using namespace OEChem;
using namespace std;

int main()
{
  OEMol mol;
  OEParseSmiles(mol, "c1cc(O)c(O)cc1CCN");

  OEIter<OEAtomBase> atom;
  cerr << "Carbon Atoms:" << endl;
  for (atom=mol.GetAtoms(OEHasAtomicNum(6));atom;++atom)
  {
    cerr << "Atom: " << atom->GetIdx() << " ";
  }
  return 0;
}

Some of the common predefined functors in OEChem are listed below. Predicate functions can be trivial, such as OEIsHydrogen(), or quite complex, such as Match(const char*), which returns atoms which match the SMARTS string passed to the constructor. For a complete listing, please see the chapter on predicate functions or the API manual. Many predicates take intuitive construction arguments. For instance, OEHasAtomName has a const char* argument which is the atom's name (e.g. mol.GetAtoms(OEHasAtomName("CA"))).

Atoms

OEHasAtomName(const char *)
OEHasAtomicNum(unsigned int)
OEIsHalogen
OEIsAromaticAtom
OEAtomIsInRing
OEIsChiralAtom
OEHasResidueNumber(unsigned int)
OEMatchFunc(const char*)

Bonds

OEHasBondIdx(unsigned int)
OEHasOrder(unsigned int)
OEBondIsInRing
OEIsRotor

Conformers

OEHasConfIdx(unsigned int)

These predicates can be particularly helpful when used in conjunction with functions which take OEIters as arguments as seen in the example below. This use of predicates allows factorization of the loop in a way not easily possible with if statements.

#include "oechem.h"

#include <iostream>

using namespace OESystem;
using namespace OEChem;
using namespace std;

void PrintAtoms(OEIter<OEAtomBase> &atom,const char *title)
{
  cerr << title << ":" << endl;
  for (atom.ToFirst();atom;++atom)
  {
    cerr << atom->GetIdx() << " ";
  }
  cerr << endl;
}

int main()
{
  OEMol mol;
  OEParseSmiles(mol, "c1c(O)c(O)c(Cl)cc1CCCBr");

  OEIter<OEAtomBase> atom;
  atom = mol.GetAtoms(OEAtomIsInRing());
  PrintAtoms(atom,"Ring Atoms");

  atom = mol.GetAtoms(OEHasAtomicNum(8));
  PrintAtoms(atom,"Oxygens");

  atom = mol.GetAtoms(OEIsHalogen());
  PrintAtoms(atom,"Halogens");

  return 0;
}

While this introduction can help you get some use from predicates, details on more complex predicates and how to write your own predicates can be found in the chapter entitled Predicate Functions (see below).

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1