75 for (i = 0; i <
nAtom(); ++i) {
80 for (i = 0; i <
nBond(); ++i) {
87 for (i = 0; i <
nAngle(); ++i) {
void setAtomType(int atomId, int atomType)
Set the type for one atom in a generic molecule of this Species.
virtual int calculateDihedralTypeId(int index) const =0
Return the dihedral type id for a specific dihedral.
int nAtom() const
Get number of atoms per molecule for this Species.
virtual int calculateAngleTypeId(int index) const =0
Return the angle type id for a specific angle.
Classes used by all simpatico molecular simulations.
virtual int calculateBondTypeId(int index) const =0
Return the bond type id for a specific bond.
int hasAngles_
Does this chain have angle potentials (0 = false, 1 = true).
int nDihedral() const
Get number of dihedrals per molecule for this Species.
#define UTIL_THROW(msg)
Macro for throwing an Exception, reporting function, file and line number.
void makeDihedral(int dihedralId, int atomId1, int atomId2, int atomId3, int atomId4, int dihedralType)
Add a dihedral to the chemical structure of a generic molecule.
Utility classes for scientific computation.
void makeBond(int bondId, int atomId1, int atomId2, int bondType)
Add a bond to the chemical structure of a generic molecule.
void makeAngle(int angleId, int atomId1, int atomId2, int atomId3, int angleType)
Add an angle to the chemical structure of a generic molecule.
int hasDihedrals_
Does this chain have dihedral potentials (0 = false, 1 = true).
void buildLinear()
Build the chemical structure for a linear molecule.
virtual int calculateAtomTypeId(int index) const =0
Return the atom type id for a specific atom.
void allocate()
Allocate chemical structure arrays.
A Species represents a set of chemically similar molecules.
int nBond() const
Get number of bonds per molecule for this Species.
int nAngle() const
Get number of angles per molecule for this Species.
virtual ~Linear()
Destructor.