class PE

PE - potential energy class

Public Methods

PE()

~PE()

void init_struct(int i_num_atom, int i_num_h, int i_num_c, int i_num_n, int i_num_o, int i_num_s)

init the data structs used in PE from given protein info

double calculate_pe(Vec i_at1, Vec i_at2, string i_name_at1, string i_name_at2, int i_type_res1, int i_type_res2, long i_id_at1, long i_id_at2)

calculate forces acting on each pair of atom in the protein

double get_tot_pe()

return the pe of the whole protein currently

void clear_force_vec()

clear the force vectors associated with each atom

Private Fields

Vec* force_vec

stores the cumulated force vector on a atom

float** pairwise_force

force as a scalar value between each pair of atoms

float* force

force as a scalar value on each atom

int num_atoms

number of atoms in residue

float ave_12

averaged out lennard jones 12 parameter

float ave_6

averaged out lennard jones 6 parameter

float ave_equil_dist

averaged out 0 energy distance for getting cut off point

float ave_min_ener_dist

for computing distance from force

float cut_off_dist

cut off distance

double max_force

calculated from cut off dist

bool* start

Private Methods

double calculate_vDW(Vec i_atom1, Vec i_atom2, int i_type_at1, int i_type_at2)

calculate the vDW forces between 2 atoms using the lennard-jones 6-12 potential

Documentation

PE - potential energy class

PE()

~PE()

void init_struct(int i_num_atom, int i_num_h, int i_num_c, int i_num_n, int i_num_o, int i_num_s)

init the data structs used in PE from given protein info

double calculate_pe(Vec i_at1, Vec i_at2, string i_name_at1, string i_name_at2, int i_type_res1, int i_type_res2, long i_id_at1, long i_id_at2)

calculate forces acting on each pair of atom in the protein

double get_tot_pe()

return the pe of the whole protein currently

void clear_force_vec()

clear the force vectors associated with each atom

double calculate_vDW(Vec i_atom1, Vec i_atom2, int i_type_at1, int i_type_at2)

calculate the vDW forces between 2 atoms using the lennard-jones 6-12 potential

Vec* force_vec

stores the cumulated force vector on a atom

float** pairwise_force

force as a scalar value between each pair of atoms

float* force

force as a scalar value on each atom

int num_atoms

number of atoms in residue

float ave_12

averaged out lennard jones 12 parameter

float ave_6

averaged out lennard jones 6 parameter

float ave_equil_dist

averaged out 0 energy distance for getting cut off point

float ave_min_ener_dist

for computing distance from force

float cut_off_dist

cut off distance

double max_force

calculated from cut off dist

bool* start

This class has no child classes.

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