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// Copyright 2008 Nanorex, Inc. See LICENSE file for details.
#ifndef NX_MOLECULESET_H
#define NX_MOLECULESET_H
#include <list>
#include <string>
using namespace std;
#include <openbabel/mol.h>
using namespace OpenBabel;
#include "Nanorex/Interface/NXMoleculeData.h"
#include "Nanorex/Interface/NXNumbers.h"
namespace Nanorex {
class NXMoleculeSet;
typedef std::list<NXMoleculeSet*>::iterator NXMoleculeSetIterator;
typedef std::list<OBMol*>::iterator OBMolIterator;
/* CLASS: NXMoleculeSet */
/**
* Encapsulates a recursive tree of molecule sets containing molecules.
*
* @ingroup ChemistryDataModel, NanorexInterface
*/
class NXMoleculeSet {
public:
enum GroupClassification {
NONE=0, DNA_GROUP, DNA_SEGMENT, DNA_STRAND,
BLOCK,
NANOTUBE_GROUP, NANOTUBE_SEGMENT,
NUM_GROUP_CLASSIFICATIONS
};
NXMoleculeSet(bool const& deleteOnDestruct = true);
~NXMoleculeSet();
void addChild(NXMoleculeSet* child) { children.push_back(child); }
NXMoleculeSetIterator childrenBegin() { return children.begin(); }
NXMoleculeSetIterator childrenEnd() { return children.end(); }
NXMSInt childCount() { return children.size(); }
//
// Molecules
//
OBMol* newMolecule();
void addMolecule(OBMol* mol) { molecules.push_back(mol); }
OBMolIterator moleculesBegin() { return molecules.begin(); }
OBMolIterator moleculesEnd() { return molecules.end(); }
NXABMInt moleculeCount() { return molecules.size(); }
void getCounts(unsigned int& moleculeCount, unsigned int& atomCount,
unsigned int& bondCount);
/// Does the molecule-set tree have any atoms?
bool empty(void);
void setTitle(std::string const& theTitle) { title = theTitle; }
std::string const& getTitle(void) const { return title; }
void setGroupClassification(GroupClassification const& _classification);
GroupClassification getGroupClassification(void) const;
void setGroupClassificationString(std::string const& _classification);
char const *const getGroupClassificationString(void) const;
private:
static unsigned int NextMoleculeIndex;
bool const deleteInDestructor;
std::list<NXMoleculeSet*> children;
std::list<OBMol*> molecules;
std::string title;
GroupClassification classification;
static char const *const groupClassificationString[NUM_GROUP_CLASSIFICATIONS];
void getCountsHelper(unsigned int& moleculeCount,
unsigned int& atomCount,
unsigned int& bondCount,
NXMoleculeSet* moleculeSet);
};
// --- inline function definitions ---
inline
void
NXMoleculeSet::setGroupClassification(NXMoleculeSet::GroupClassification const& _classification)
{
classification = _classification;
}
inline
NXMoleculeSet::GroupClassification
NXMoleculeSet::getGroupClassification(void) const
{
return classification;
}
inline char const *const NXMoleculeSet::getGroupClassificationString(void) const
{
return groupClassificationString[classification];
}
inline
void
NXMoleculeSet::setGroupClassificationString(std::string const& classificationString)
{
for(int c = (int)NONE; c < (int)NUM_GROUP_CLASSIFICATIONS; ++c) {
if(classificationString == groupClassificationString[c]) {
classification = (GroupClassification) c;
return;
}
}
classification = NONE;
}
} // Nanorex::
#endif
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