HaInterMolMod Class Reference

Class to simulate docking between two molecules. More...

#include <haintermol.h>

Inheritance diagram for HaInterMolMod:

List of all members.

Public Member Functions
	HaInterMolMod (HaMolSet *new_phost_mset)
void	SetStdParams ()
	Set Standard Module parameters.
bool	Initialize ()
	Initialize module.
double	CalculateMMEnergy ()
	Calculate Intermolecular Energy using Molecular Mechanics model.
double	CalcElStaticInter ()
	Calculate intermolecule electrostatic interactions between molecules using Continuum dielectric approach.
double	CalcContElectrEne (vector< AtomList * > inter_groups)
	Calculate electrostatic energy beween two groups of atoms.
bool	CalcEffInterEne ()
	Compute effective interaction energy including ET terms.
int	RunMCDock ()
	Run MC Docking calculations.
int	PauseMCDock ()
	Pause MC Docking calculations.
int	ResumeMCDock ()
	Resume MC Docking calculations.
int	StopMCDock ()
	Stop MC Docking calculations.
int	RunMCDocThread ()
int	BuildNonBondListInterMol ()
	Set Non-bonded interaction list for interacting molecules.
int	InitMolecularFields ()
	Initiate electrostatic and vdW repulsion field around the molecule.
double	CalcChargesInFieldEne ()
	Calculate intermolecular energy using charges(mol 2) in the field(mol 1) approximation.
void	SetElectrModel (int new_elecr_model_idx)
	Set electrostatic energy computation method.
Public Attributes
CWinThread *	mc_dock_thread
int	module_to_init_flag
	flag to reinitiate the module at the next call to its functions
int	build_nb_contact_list
	flag to build atom nonbond interaction list at the call to functions that use it
double	cur_intermol_ene
	current energy or effective energy
double	electr_inter_ene
	electrostatic interaction energy
double	vdw_inter_ene
	van-der-Waals interaction energy
double	add_eff_ene
	effective addition to the intermolecular energy from ET rate
double	MC_temp
	Effective temperature for MC calculations, default = 300.0.
double	ang_ratio
	scale factor to generate random rotation, default = 0.02
double	tr_ratio
	scale factor to generate random translation, default = 0.3
int	delay_time
	delay time between steps in ms
int	stop_calc_flag
	it not zero stop docking caclulations
int	skip_pt_init
	The number of trajectory points to skip in the beginning of the trajectory.
int	skip_pt_between
	The number of trajectory points to skip between points displayed and processed.
int	play_back_flag
	if TRUE playback saved trajectory calculating the effective energy
int	dont_calc_ene_flag
	if TRUE do not calculate intermolecular energy (just display)
int	save_image_seq_gif
	if TRUE save snapshots of trajectory as GIF files
int	save_image_seq_pict
	if TRUE save snapshots of trajectory as PICT files
int	trace_atoms_flag
	if TRUE trace specified atoms;
int	output_rejected_points
	In MC computations output all generated points (including rejected) into file all_mc_pts.dat.
HaString	MC_traj_file_name
	File with MC trajectory.
int	electr_model
int	compute_pk
	flag to compute dynamical changes of pKs of ionizable groups in binding
int	calc_et_rate
	Flag to add to the energy the effective addition from ET rate, default = 0.
int	num_mc_steps
	the maximum number of MC iterations, default = 100
vector< HaMolecule * >	interact_mol
	the collection of interacting molecules
HaField3D	el_pot_field
	Electrostatic field around the immobile molecule.
HaField3D	vdw_pot_field
	Effective VdW 'repulsion' field around the immobile molecule.
AtomList	traced_atoms
	Atoms traced during MC replay.

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Detailed Description

Class to simulate docking between two molecules.

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Member Function Documentation

int HaInterMolMod::RunMCDocThread (   )

function to run MC Docking calculations or play back < a stored trajectory

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Member Data Documentation

int HaInterMolMod::electr_model

method to compute electrostatic energy < (NO_ELECTR=0,CONTINUUM_ELECTR = 1,COULOMB_ELECTR = 2,CHARGES_IN_FIELD_ELECTR = 3)

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The documentation for this class was generated from the following files:

• haintermol.h
• haintermol.cpp

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