32.9.3 Molecule parameters

Parameters holding objects of type OEChem::OEGraphMol and OEChem::OEMol are supported by OEInterface, but they require that the function OESystem::RegisterMolParameters() be called before OEConfigure is called. (Note that OESystem::RegisterMolParameters() is defined in the OEChem public headers).

Chapter 32 - Example 12 : cpp file

#include "oeplatform.h"
#include "oesystem.h"

//RegisterMolParameters is defined here
#include "oechem.h"

//Defines static const unsigned char* array InterfaceData
#include "ch32-12.itf"

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

int main(int argc, char** argv)
{
  OEInterface itf;
  RegisterMolParameters();
  OEConfigure(itf,InterfaceData);
  if (OECheckHelp(itf,argc,argv)) return 0;
  OEParseCommandLineLW(itf,argc,argv);

  oeout << "Molecule has " << itf.Get<OEGraphMol>("-mol").NumAtoms() << " atoms " << oeendl;

  return 0;
}

Chapter 32 - Example 12 : OEConfigure txt configuration file

!PARAMETER -mol
  !TYPE OEGraphMol
  !KEYLESS 1
  !REQUIRED yes
  !BRIEF Molecule to count atoms off
!END

If we have a molecule file hexane.smi with the following contents

CCCCCC

This program returns the following

> ch32-12 hexane.smi
Molecule has 6 atoms
>

Note that every time the OEInterface Get command is called it returns a copy of the requested object or POD, not a reference. In this example program the Get function was integrated into the output stream line. Since we only needed to access this object once this is not inefficient, however if we wished to accesses it multiple times it would have been more efficient to make a local copy and access it several times.

Also not that this method of loading a molecule will only every return the first molecule in a file. If you wish to load multiple molecules from a file you should use the OEChem molstream's.

				OEChem - C++ Theory Manual Version 1.3.1

				OEChem - C++ Theory Manual Version 1.3.1