#include <GromacsTopFile.h>

Public Member Functions
	GenericMol (const char *theName)

int	getNumAtoms () const

int	getNumBonds () const

int	getNumAngles () const

int	getNumDihedrals () const

int	getNumRes () const

void	addAtom (const char theType, int theTypeNum, int theResNum, const char theResType, const char *theAtomName, Real theCharge, Real theMass)

void	addBond (int atomi, int atomj, int type)

void	addAngle (int atomi, int atomj, int atomk, int type)

void	addDihedral (int atomi, int atomj, int atomk, int atoml, int type)

const char *	getName () const

const GenericAtom *	getAtom (int n) const

const GenericBond *	getBond (int n) const

const GenericAngle *	getAngle (int n) const

const GenericDihedral *	getDihedral (int n) const

Detailed Description

Definition at line 113 of file GromacsTopFile.h.

Constructor & Destructor Documentation

GenericMol::GenericMol ( const char * theName )

Definition at line 916 of file GromacsTopFile.C.

                                           {
   name = strdup(theName);
 }

Member Function Documentation

void GenericMol::addAngle	(	int	atomi,
		int	atomj,
		int	atomk,
		int	type
	)

Definition at line 895 of file GromacsTopFile.C.

References ResizeArray< T >::add().

                                                                    {
   angleList.add(new GenericAngle(atomi, atomj, atomk, type));
 }

void GenericMol::addAtom	(	const char *	theType,
		int	theTypeNum,
		int	theResNum,
		const char *	theResType,
		const char *	theAtomName,
		Real	theCharge,
		Real	theMass
	)

Definition at line 907 of file GromacsTopFile.C.

References ResizeArray< T >::add().

                                                        {
 
   atomList.add(new GenericAtom(theType,theTypeNum,theResNum,theResType,
                            theAtomName,theCharge,theMass));
 }

void GenericMol::addBond	(	int	atomi,
		int	atomj,
		int	type
	)

Definition at line 890 of file GromacsTopFile.C.

References ResizeArray< T >::add().

                                                        {
   bondList.add(new GenericBond(atomi, atomj, type));
 }

void GenericMol::addDihedral	(	int	atomi,
		int	atomj,
		int	atomk,
		int	atoml,
		int	type
	)

Definition at line 900 of file GromacsTopFile.C.

References ResizeArray< T >::add().

                                                   {
   dihedralList.add(new GenericDihedral(atomi, atomj, atomk,
                                              atoml, type));
 }

const GenericAngle * GenericMol::getAngle ( int n ) const

Definition at line 931 of file GromacsTopFile.C.

References ResizeArray< T >::size().

                                                     {
   /* double-check */
   if(n >= angleList.size() || n<0) {
     fprintf(stderr,"Angle index %d out of bounds.\n",n);
     exit(1);
   }
   return angleList[n];
 }

const GenericAtom * GenericMol::getAtom ( int n ) const

Definition at line 951 of file GromacsTopFile.C.

References ResizeArray< T >::size().

                                                   {
   /* double-check */
   if(n >= atomList.size() || n<0) {
     fprintf(stderr,"Atom index %d out of bounds for %s.\n",n,name);
     exit(1);
   }
   return atomList[n];
 }

const GenericBond * GenericMol::getBond ( int n ) const

Definition at line 921 of file GromacsTopFile.C.

References ResizeArray< T >::size().

                                                   {
   /* double-check */
   if(n >= bondList.size() || n<0) {
     fprintf(stderr,"Bond index %d out of bounds.\n",n);
     exit(1);
   }
   return bondList[n];
 }

const GenericDihedral * GenericMol::getDihedral ( int n ) const

Definition at line 941 of file GromacsTopFile.C.

References ResizeArray< T >::size().

                                                           {
   /* double-check */
   if(n >= dihedralList.size() || n<0) {
     fprintf(stderr,"Dihedral index %d out of bounds.\n",n);
     exit(1);
   }
   return dihedralList[n];
 }