MOLGEOM.CPP

Description : Molecular geometry member functions of Atom and Molecule classes

Header files called upon : fstream.h, iomanip.h, strstream.h, string.h, math.h, stdlib.h , VECTOR.H , MATRIX.H , MOLECULE.H

Class details are as follows:

Further class member definitions : Atom

Member functions (public)

float Atom::distance(Atom *atomPt[2])

Returns the bond distance between two atoms specified by an atom pointer

eg Atom *atm_ptr[2];

assign atm_ptr to atoms

cout << Atom::distance(atm_ptr);

NB function declared in MOLECULE.H

float Atom::angle(Atom *atomPt[3])

Returns the bond angle (in degrees) between three atoms specified by an atom pointer

eg Atom *atm_ptr[3];

assign atm_ptr to atoms

cout << Atom::angle(atm_ptr);

NB function declared in MOLECULE.H

float Atom::torsion(Atom *atomPt[4])

Returns the torsion angle (in degrees) between four atoms specified by an atom pointer

eg Atom *atm_ptr[4];

assign atm_ptr to atoms

cout << Atom::torsion(atm_ptr);

NB function declared in MOLECULE.H

Further class member definitions : Molecule

Member functions (public)

void Molecule::findBonds(const float& maxBondLength, int oneDirection)

Checks distance between all atoms and assigns a bond between atoms with distance less than that defined by parameter 'maxBondLength'. If 'oneDirection' is given value 0 then reciprocative arrangement occurs ie if atom1 assigned bond to atom2, then atom2 assigned bond to atom1; if 'oneDirection' assigned non-zero then non-reciprocative arrangement occurs, which is adequate for function 'calcGeometry' (see below)

eg mol1.findbonds(2.2, 1);

NB function declared in MOLECULE.H

void Molecule::calcGeometry()

Steps through bond connection network for every atom in a molecule using 'traverse' function (see below) in order to calculate and write out bond distances, bond angles and torsion angles

eg mol1.calcGeometry();

NB1 bond connectivities must alreay have been allocated before using this function ie use function 'findbonds' (see above)

NB2 function declared in MOLECULE.H

void Molecule::traverse(Atom *pt)

Recursive function that steps through the bond connection network of a molecule on order to calculate and write out bond distances, bond angles and torsion angles. This function is called using function 'calcGeometry()' (see above)

NB funtion declared in MOLECULE.H

Further class member definitions : ProteinMainChain (derived from class Molecule)

Member functions (public)

void ProteinMainChain::torsionList()

calculates and writes out torsion angles for protein main-chain

eg protmc1.torsionList();

NB function declared in MOLECULE.H