<commit_before>#include <iostream>
#include <fstream>

#include "openeye.h"
#include "oesystem.h"
#include "oechem.h"
#include "oedocking.h"

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

int main(int numOfArg, char* argv[])
{
	OEGraphMol receptor;
	OEReadReceptorFile(receptor, argv[3]);
    	unsigned int dockMethod = atoi(argv[1]);
	unsigned int dockResolution = atoi(argv[2]);
	OEDock dock(dockMethod, dockResolution);
	dock.Initialize(receptor);

	oemolistream imstr;
	oemolostream omstr;

	imstr.SetFormat(OEFormat::SDF);
	omstr.SetFormat(OEFormat::SDF);

	OEMol mcmol;
	//Scoring the molecules in SDF File
	         while (OEReadMolecule(imstr, mcmol))
	         {
	           OEGraphMol dockedMol;
	           dock.DockMultiConformerMolecule(dockedMol,mcmol);
	           string sdtag = OEDockMethodGetName(dockMethod);
	           OESetSDScore(dockedMol, dock, sdtag);
	           dock.AnnotatePose(dockedMol);
	           //Writing moles to the SDF File with Scores
	           OEWriteMolecule(omstr, dockedMol);
	         }
    return 0;
}<commit_msg>Update dockingstd.cpp<commit_after>#include <iostream>
#include <fstream>

#include "openeye.h"
#include "oesystem.h"
#include "oechem.h"
#include "oedocking.h"

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

int main(int numOfArg, char* argv[])
{
	OEGraphMol receptor;
	OEReadReceptorFile(receptor, argv[3]);
    	unsigned int dockMethod = atoi(argv[1]);
	unsigned int dockResolution = atoi(argv[2]);
	OEDock dock(dockMethod, dockResolution);
	dock.Initialize(receptor);

	oemolistream imstr;
	oemolostream omstr;

	imstr.SetFormat(OEFormat::SDF);
	omstr.SetFormat(OEFormat::SDF);

	OEMol mcmol;
	//Scoring the molecules in SDF File
	while (OEReadMolecule(imstr, mcmol))
	{
	 	OEGraphMol dockedMol;
	       	dock.DockMultiConformerMolecule(dockedMol,mcmol);
	      	string sdtag = OEDockMethodGetName(dockMethod);
	    	OESetSDScore(dockedMol, dock, sdtag);
	      	dock.AnnotatePose(dockedMol);
	      	//Writing moles to the SDF File with Scores
	      	OEWriteMolecule(omstr, dockedMol);
	}
    	return 0;
}
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