#include <Actin.h>

Public Member Functions
void	import_config (vector< string > configlines)

void	Elastic_Force_Calculator (void)

void	export_for_resume (int MD_step)

void	export_for_resume (int MD_step, MyAtomInfo atoms[], int atom_count)

void	set_state (MyAtomInfo all_atoms[], int atom_count)
	Set the current state (OpenMM) of the class. More...

void	set_label (std::string lab)
	Assigns the label(pdb) used to write to the trajectory files. More...

int	get_num_of_nodes (void)
	public access to total number of ECM nodes. More...

std::string	get_label (void)
	return the label(pdb) used to write to the trajectory files. More...

double	get_node_pair_Nominal_Length_in_Nm (int bond_number)

double	get_abp_relaxlength (int bond_number)

double	get_MT_relaxlength (int bond_number)

double	get_node_position (int node_number, int node_coordinate)

double	get_node_mass (void)
	Return the node mass. More...

double	get_node_radius (int index)

void	shift_position (double x, double y, double z)
	This function shifts the whole actin. More...

void	shift_velocity (double vx, double vy, double vz)

double	get_node_velocity (int node_number, int node_coordinate)
	Returns the x (0), y (1), and z (2) velocities of the node index (number). More...

int	get_num_of_node_pairs (void)
	Return the number of bonds between membrane nodes. More...

int	get_num_of_abp_pairs (void)
	Return the number of bonds between membrane nodes. More...

int	get_num_of_MT_pairs (void)

int	get_spring_model (void)
	Return input spring model, used to setup the openmm system for the bonds. More...

int	get_abp_spring_model (void)
	Return input abp spring model, used to setup the openmm system for the bonds. More...

int	get_MT_spring_model (void)

int	get_node_pair (int bond_num, int node_id)
	Return the id(int) of the nodes in the bonds. More...

int	get_abp_pair (int bond_num, int node_id)
	Return the id(int) of the nodes in the bonds. More...

int	get_MT_pair (int bond_num, int node_id)

double	get_avg_node_dist (void)
	Return the average distance of the nodes as calculated from the mesh. More...

double	get_avg_abp_dist (void)
	Return the average distance of the nodes as calculated from the mesh. More...

double	get_avg_MT_dist (void)

double	get_abp_r0factor (void)
	Return the abp r0 factor for rest length of bond. More...

double	get_MT_r0factor (void)

double	get_act_r0factor (void)
	Return the actin r0 factor for rest length of bond. More...

double	get_spring_stiffness_coefficient (void)
	Return spring stiffness coefficient. More...

double	get_abp_spring_stiffness_coefficient (void)
	Return abp spring stiffness coefficient. More...

double	get_MT_spring_stiffness_coefficient (void)

double	get_contractile_force (void)
	Return contractile constant force. More...

double	get_contractile_k1 (void)
	Return contractile stiffness_1. More...

double	get_contractile_k2 (void)
	Return contractile stiffness_2. More...

double	get_contractile_rmin (void)
	Return contractile r_min. More...

double	get_contractile_rmax (void)
	Return contractile r_max. More...

double	get_abp_hill_co (void)
	Return hill coefficient. More...

double	get_MT_hill_co (void)

double	get_contractile_hill_co (void)
	Return hill coefficient. More...

int	get_contractile_model (void)
	Return contractile type. More...

int	get_abp_model (void)
	Return abp type. More...

int	get_MT_model (void)

double	get_abp_force (void)
	Return contractile constant force. More...

double	get_MT_force (void)

double	get_abp_k1 (void)
	Return contractile stiffness_1. More...

double	get_MT_k1 (void)

double	get_abp_k2 (void)
	Return contractile stiffness_2. More...

double	get_MT_k2 (void)

double	get_abp_rmin (void)
	Return contractile r_min. More...

double	get_MT_rmin (void)

double	get_abp_rmax (void)
	Return contractile r_max. More...

double	get_MT_rmax (void)

double	get_kelvin_damping_coefficient (void)
	Return kelvin damping coefficient. More...

int	get_ext_force_model (void)
	Return external force model. More...

double	get_kx (void)

double	get_ky (void)

double	get_kz (void)

void	check (void)

void	check_2 (void)

void	check_3 (void)

void	set_file_time (char *buffer)

void	set_index (int ind)

int	return_num_of_actin_membrane_shared_nodes (int j)

int	return_ActMem_shared_act_atom (int mem, int bond)

int	return_ActMem_shared_mem_atom (int mem, int bond)

void	add_to_force (double force, int index, int coor)

void	update_COM_velocity (void)

void	update_COM_position (void)

	Actin ()

std::map< string, vector< string > >	get_map ()

vector< string >	get_insertOrder ()

void	assign_key_value (string key, string value)

void	assign_parameters (void)

void	consistancy_check (void)

Public Attributes
vector< vector< vector< int > > >	Actin_Membrane_shared_Node_list

vector< int >	Num_of_Actin_Membrane_shared_Nodes

std::map< string, vector< string > >	Params

vector< string >	insertOrder

vector< string >	values

Private Member Functions
void	read_actin_file (void)

void	Node_neighbour_list_constructor ()
	Construct a vector that lists all the neighbours of each node and their respective index in the 'Node_Bond_list'. More...

void	initialise (std::string Mesh_file_name)

void	read_gmesh_file (std::string gmesh_file)

void	read_gmesh_file_2 (std::string gmesh_file)

void	Node_Bond_identifier (void)

void	Node_Bond_identifier_2 (void)

void	Node_Bond_identifier_3 (void)

double	Hookian (double distance, double initial_distance)

double	Kelvin (double distance, int bond_index)

void	set_bond_nominal_length (void)

void	set_node_radius (void)

void	initialise_node_bond_relaxed_length (void)

void	initialise_abp_bond_relaxed_length (void)

void	initialise_MT_bond_relaxed_length (void)

double	Maxwell (double distance, int bond_index)

Private Attributes
std::string	file_time

int	index

std::string	label

std::string	Mesh_file_name

std::string	MeshType

std::map< std::string, double >	param_map

double	Node_Mass =1

string	Node_radius_stat

vector< double >	Node_radius

int	spring_model =2

double	Spring_coefficient =100

double	Contractile_force =10

int	contractile_model = 1

double	contractile_hill_co = 0

double	Contractile_k1 =50

double	Contractile_k2 =25

double	Contractile_rmin =0

double	Contractile_rmax =1000000

double	act_r0factor = 1

double	abp_force =0

double	abp_k1 =0

double	abp_k2 =0

double	abp_rmin =0

double	abp_rmax =1000000

double	abp_r0factor = 1

double	abp_hill_co = 100

double	abp_model = 1

double	abp_spring_model =2

double	abp_Spring_coefficient =0

double	MT_force =0

double	MT_k1 =0

double	MT_k2 =0

double	MT_rmin =0

double	MT_rmax =1000000

double	MT_r0factor = 1

double	MT_hill_co = 100

double	MT_model = 1

double	MT_spring_model =2

double	MT_Spring_coefficient =0

double	rescale_factor =1

double	Damping_coefficient =0.5

vector< double >	Shift_position_xyzVector

vector< double >	Shift_velocities_xyzVector

int	ext_force_model =0

double	kx =10

double	ky =10

double	kz =10

vector< vector< int > >	Node_neighbour_list
	This list is used to store all the neighbours of nodes: Example: If node i has 4 neighbours: m, n, o, p Then we find these neighbours in the 'Node_neighbour_list' as follows: Node_neighbour_list [ i ][0] = m Node_neighbour_list [ i ][1] = n Node_neighbour_list [ i ][2] = o Node_neighbour_list [ i ][3] = p. More...

vector< vector< int > >	Node_neighbour_list_respective_bond_index
	This list is used to cross reference the neighbouring nodes to their respective index in the 'Node_neighbour_list'. More...

string	mesh_format

int	Num_of_Nodes =0

vector< vector< double > >	Node_Position

vector< vector< double > >	Node_Velocity

vector< vector< double > >	Node_Force

vector< vector< int > >	Pyramid_Nodes

vector< vector< int > >	filaments

vector< vector< int > >	abps

vector< vector< int > >	MTs

std::string	output_file_neme

vector< vector< int > >	Node_Bond_list

int	Num_of_Node_Pairs =0

vector< vector< int > >	abp_Bond_list

int	Num_of_abp_Pairs =0

vector< vector< int > >	MT_Bond_list

int	Num_of_MT_Pairs =0

string	Node_Bond_Nominal_Length_stat

double	Node_Bond_user_defined_Nominal_Length_in_Nm

vector< double >	Node_Bond_Nominal_Length_in_Nm

vector< double >	abp_Bond_relaxed_length

vector< double >	MT_Bond_relaxed_length

double	Total_Potential_Energy =0

double	Kelvin_Damping_Coefficient =100

double	Total_Kinetic_Energy =0

double	COM_velocity [3] ={0}

double	COM_position [3] ={0}

double	Dashpot_Viscosity

double	tau_Maxwell_relax =0

double	exp_tau =0

double	Min_node_pair_length =1000

double	Max_node_pair_length =0

double	Average_node_pair_length =0

double	Min_abp_pair_length =1000

double	Max_abp_pair_length =0

double	Average_abp_pair_length =0

double	Min_MT_pair_length =1000

double	Max_MT_pair_length =0

double	Average_MT_pair_length =0

Constructor & Destructor Documentation

◆ Actin()

Actin::Actin ( )

inline

Member Function Documentation

◆ add_to_force()

void Actin::add_to_force	(	double	force,
		int	index,
		int	coor
	)

inline

◆ assign_key_value()

void Actin::assign_key_value	(	string	key,
		string	value
	)

inline

◆ assign_parameters()

void Actin::assign_parameters ( void )

◆ check()

void Actin::check ( void )

◆ check_2()

void Actin::check_2 ( void )

◆ check_3()

void Actin::check_3 ( void )

◆ consistancy_check()

void Actin::consistancy_check ( void )

◆ Elastic_Force_Calculator()

void Actin::Elastic_Force_Calculator ( void )

◆ export_for_resume() [1/2]

void Actin::export_for_resume ( int MD_step )

◆ export_for_resume() [2/2]

void Actin::export_for_resume	(	int	MD_step,
		MyAtomInfo	atoms[],
		int	atom_count
	)

◆ get_abp_force()

double Actin::get_abp_force ( void )

inline

Return contractile constant force.

◆ get_abp_hill_co()

double Actin::get_abp_hill_co ( void )

inline

Return hill coefficient.

◆ get_abp_k1()

double Actin::get_abp_k1 ( void )

inline

Return contractile stiffness_1.

◆ get_abp_k2()

double Actin::get_abp_k2 ( void )

inline

Return contractile stiffness_2.

◆ get_abp_model()

int Actin::get_abp_model ( void )

inline

Return abp type.

◆ get_abp_pair()

int Actin::get_abp_pair	(	int	bond_num,
		int	node_id
	)

inline

Return the id(int) of the nodes in the bonds.

The id of each node in the bond list is stored in the first (0) and the second (1) id slot.

◆ get_abp_r0factor()

double Actin::get_abp_r0factor ( void )

inline

Return the abp r0 factor for rest length of bond.

◆ get_abp_relaxlength()

double Actin::get_abp_relaxlength ( int bond_number )

inline

◆ get_abp_rmax()

double Actin::get_abp_rmax ( void )

inline

Return contractile r_max.

◆ get_abp_rmin()

double Actin::get_abp_rmin ( void )

inline

Return contractile r_min.

◆ get_abp_spring_model()

int Actin::get_abp_spring_model ( void )

inline

Return input abp spring model, used to setup the openmm system for the bonds.

◆ get_abp_spring_stiffness_coefficient()

double Actin::get_abp_spring_stiffness_coefficient ( void )

inline

Return abp spring stiffness coefficient.

◆ get_act_r0factor()

double Actin::get_act_r0factor ( void )

inline

Return the actin r0 factor for rest length of bond.

◆ get_avg_abp_dist()

double Actin::get_avg_abp_dist ( void )

inline

Return the average distance of the nodes as calculated from the mesh.

◆ get_avg_MT_dist()

double Actin::get_avg_MT_dist ( void )

inline

◆ get_avg_node_dist()

double Actin::get_avg_node_dist ( void )

inline

Return the average distance of the nodes as calculated from the mesh.

◆ get_contractile_force()

double Actin::get_contractile_force ( void )

inline

Return contractile constant force.

◆ get_contractile_hill_co()

double Actin::get_contractile_hill_co ( void )

inline

Return hill coefficient.

◆ get_contractile_k1()

double Actin::get_contractile_k1 ( void )

inline

Return contractile stiffness_1.

◆ get_contractile_k2()

double Actin::get_contractile_k2 ( void )

inline

Return contractile stiffness_2.

◆ get_contractile_model()

int Actin::get_contractile_model ( void )

inline

Return contractile type.

◆ get_contractile_rmax()

double Actin::get_contractile_rmax ( void )

inline

Return contractile r_max.

◆ get_contractile_rmin()

double Actin::get_contractile_rmin ( void )

inline

Return contractile r_min.

◆ get_ext_force_model()

int Actin::get_ext_force_model ( void )

inline

Return external force model.

◆ get_insertOrder()

vector<string > Actin::get_insertOrder ( )

inline

◆ get_kelvin_damping_coefficient()

double Actin::get_kelvin_damping_coefficient ( void )

inline

Return kelvin damping coefficient.

◆ get_kx()

double Actin::get_kx ( void )

inline

◆ get_ky()

double Actin::get_ky ( void )

inline

◆ get_kz()

double Actin::get_kz ( void )

inline

◆ get_label()

std::string Actin::get_label ( void )

inline

return the label(pdb) used to write to the trajectory files.

◆ get_map()

std::map<string, vector<string> > Actin::get_map ( )

inline

◆ get_MT_force()

double Actin::get_MT_force ( void )

inline

◆ get_MT_hill_co()

double Actin::get_MT_hill_co ( void )

inline

◆ get_MT_k1()

double Actin::get_MT_k1 ( void )

inline

◆ get_MT_k2()

double Actin::get_MT_k2 ( void )

inline

◆ get_MT_model()

int Actin::get_MT_model ( void )

inline

◆ get_MT_pair()

int Actin::get_MT_pair	(	int	bond_num,
		int	node_id
	)

inline

◆ get_MT_r0factor()

double Actin::get_MT_r0factor ( void )

inline

◆ get_MT_relaxlength()

double Actin::get_MT_relaxlength ( int bond_number )

inline

◆ get_MT_rmax()

double Actin::get_MT_rmax ( void )

inline

◆ get_MT_rmin()

double Actin::get_MT_rmin ( void )

inline

◆ get_MT_spring_model()

int Actin::get_MT_spring_model ( void )

inline

◆ get_MT_spring_stiffness_coefficient()

double Actin::get_MT_spring_stiffness_coefficient ( void )

inline

◆ get_node_mass()

double Actin::get_node_mass ( void )

inline

Return the node mass.

At the current stage of this code all membrane nodes have the same mass.

◆ get_node_pair()

int Actin::get_node_pair	(	int	bond_num,
		int	node_id
	)

inline

Return the id(int) of the nodes in the bonds.

The id of each node in the bond list is stored in the first (0) and the second (1) id slot.

◆ get_node_pair_Nominal_Length_in_Nm()

double Actin::get_node_pair_Nominal_Length_in_Nm ( int bond_number )

inline

◆ get_node_position()

double Actin::get_node_position	(	int	node_number,
		int	node_coordinate
	)

inline

◆ get_node_radius()

double Actin::get_node_radius ( int index )

inline

◆ get_node_velocity()

double Actin::get_node_velocity	(	int	node_number,
		int	node_coordinate
	)

inline

Returns the x (0), y (1), and z (2) velocities of the node index (number).

◆ get_num_of_abp_pairs()

int Actin::get_num_of_abp_pairs ( void )

inline

Return the number of bonds between membrane nodes.

◆ get_num_of_MT_pairs()

int Actin::get_num_of_MT_pairs ( void )

inline

◆ get_num_of_node_pairs()

int Actin::get_num_of_node_pairs ( void )

inline

Return the number of bonds between membrane nodes.

◆ get_num_of_nodes()

int Actin::get_num_of_nodes ( void )

inline

public access to total number of ECM nodes.

Returns: integer number of nodes in the ECM.

◆ get_spring_model()

int Actin::get_spring_model ( void )

inline

Return input spring model, used to setup the openmm system for the bonds.

◆ get_spring_stiffness_coefficient()

double Actin::get_spring_stiffness_coefficient ( void )

inline

Return spring stiffness coefficient.

◆ Hookian()

double Actin::Hookian	(	double	distance,
		double	initial_distance
	)

private

◆ import_config()

void Actin::import_config ( vector< string > configlines )

◆ initialise()

void Actin::initialise ( std::string Mesh_file_name )

private

◆ initialise_abp_bond_relaxed_length()

void Actin::initialise_abp_bond_relaxed_length ( void )

private

◆ initialise_MT_bond_relaxed_length()

void Actin::initialise_MT_bond_relaxed_length ( void )

private

◆ initialise_node_bond_relaxed_length()

void Actin::initialise_node_bond_relaxed_length ( void )

private

◆ Kelvin()

double Actin::Kelvin	(	double	distance,
		int	bond_index
	)

private

◆ Maxwell()

double Actin::Maxwell	(	double	distance,
		int	bond_index
	)

private

◆ Node_Bond_identifier()

void Actin::Node_Bond_identifier ( void )

private

◆ Node_Bond_identifier_2()

void Actin::Node_Bond_identifier_2 ( void )

private

◆ Node_Bond_identifier_3()

void Actin::Node_Bond_identifier_3 ( void )

private

◆ Node_neighbour_list_constructor()

void Actin::Node_neighbour_list_constructor ( )

private

Construct a vector that lists all the neighbours of each node and their respective index in the 'Node_Bond_list'.

◆ read_actin_file()

void Actin::read_actin_file ( void )

private

◆ read_gmesh_file()

void Actin::read_gmesh_file ( std::string gmesh_file )

private

◆ read_gmesh_file_2()

void Actin::read_gmesh_file_2 ( std::string gmesh_file )

private

◆ return_ActMem_shared_act_atom()

int Actin::return_ActMem_shared_act_atom	(	int	mem,
		int	bond
	)

inline

◆ return_ActMem_shared_mem_atom()

int Actin::return_ActMem_shared_mem_atom	(	int	mem,
		int	bond
	)

inline

◆ return_num_of_actin_membrane_shared_nodes()

int Actin::return_num_of_actin_membrane_shared_nodes ( int j )

inline

◆ set_bond_nominal_length()

void Actin::set_bond_nominal_length ( void )

private

◆ set_file_time()

void Actin::set_file_time ( char * buffer )

inline

◆ set_index()

void Actin::set_index ( int ind )

inline

◆ set_label()

void Actin::set_label ( std::string lab )

inline

Assigns the label(pdb) used to write to the trajectory files.

It is also used to identify the class object throught the programme

◆ set_node_radius()

void Actin::set_node_radius ( void )

private

◆ set_state()

void Actin::set_state	(	MyAtomInfo	all_atoms[],
		int	atom_count
	)

Set the current state (OpenMM) of the class.

◆ shift_position()

void Actin::shift_position	(	double	x,
		double	y,
		double	z
	)

inline

This function shifts the whole actin.

◆ shift_velocity()

void Actin::shift_velocity	(	double	vx,
		double	vy,
		double	vz
	)

inline

◆ update_COM_position()

void Actin::update_COM_position ( void )

inline

◆ update_COM_velocity()

void Actin::update_COM_velocity ( void )

inline

Member Data Documentation

◆ abp_Bond_list

vector<vector<int> > Actin::abp_Bond_list

private

◆ abp_Bond_relaxed_length

vector<double> Actin::abp_Bond_relaxed_length

private

◆ abp_force

double Actin::abp_force =0

private

◆ abp_hill_co

double Actin::abp_hill_co = 100

private

◆ abp_k1

double Actin::abp_k1 =0

private

◆ abp_k2

double Actin::abp_k2 =0

private

◆ abp_model

double Actin::abp_model = 1

private

◆ abp_r0factor

double Actin::abp_r0factor = 1

private

◆ abp_rmax

double Actin::abp_rmax =1000000

private

◆ abp_rmin

double Actin::abp_rmin =0

private

◆ abp_Spring_coefficient

double Actin::abp_Spring_coefficient =0

private

◆ abp_spring_model

double Actin::abp_spring_model =2

private

◆ abps

vector<vector<int> > Actin::abps

private

◆ act_r0factor

double Actin::act_r0factor = 1

private

◆ Actin_Membrane_shared_Node_list

vector<vector<vector<int> > > Actin::Actin_Membrane_shared_Node_list

◆ Average_abp_pair_length

double Actin::Average_abp_pair_length =0

private

◆ Average_MT_pair_length

double Actin::Average_MT_pair_length =0

private

◆ Average_node_pair_length

double Actin::Average_node_pair_length =0

private

◆ COM_position

double Actin::COM_position[3] ={0}

private

◆ COM_velocity

double Actin::COM_velocity[3] ={0}

private

◆ Contractile_force

double Actin::Contractile_force =10

private

◆ contractile_hill_co

double Actin::contractile_hill_co = 0

private

◆ Contractile_k1

double Actin::Contractile_k1 =50

private

◆ Contractile_k2

double Actin::Contractile_k2 =25

private

◆ contractile_model

int Actin::contractile_model = 1

private

◆ Contractile_rmax

double Actin::Contractile_rmax =1000000

private

◆ Contractile_rmin

double Actin::Contractile_rmin =0

private

◆ Damping_coefficient

double Actin::Damping_coefficient =0.5

private

◆ Dashpot_Viscosity

double Actin::Dashpot_Viscosity

private

◆ exp_tau

double Actin::exp_tau =0

private

◆ ext_force_model

int Actin::ext_force_model =0

private

◆ filaments

vector<vector<int> > Actin::filaments

private

◆ file_time

std::string Actin::file_time

private

◆ index

int Actin::index

private

◆ insertOrder

vector<string> Actin::insertOrder

◆ Kelvin_Damping_Coefficient

double Actin::Kelvin_Damping_Coefficient =100

private

◆ label

std::string Actin::label

private

◆ Max_abp_pair_length

double Actin::Max_abp_pair_length =0

private

◆ Max_MT_pair_length

double Actin::Max_MT_pair_length =0

private

◆ Max_node_pair_length

double Actin::Max_node_pair_length =0

private

◆ Mesh_file_name

std::string Actin::Mesh_file_name

private

◆ mesh_format

string Actin::mesh_format

private

◆ MeshType

std::string Actin::MeshType

private

◆ Min_abp_pair_length

double Actin::Min_abp_pair_length =1000

private

◆ Min_MT_pair_length

double Actin::Min_MT_pair_length =1000

private

◆ Min_node_pair_length

double Actin::Min_node_pair_length =1000

private

◆ MT_Bond_list

vector<vector<int> > Actin::MT_Bond_list

private

◆ MT_Bond_relaxed_length

vector<double> Actin::MT_Bond_relaxed_length

private

◆ MT_force

double Actin::MT_force =0

private

◆ MT_hill_co

double Actin::MT_hill_co = 100

private

◆ MT_k1

double Actin::MT_k1 =0

private

◆ MT_k2

double Actin::MT_k2 =0

private

◆ MT_model

double Actin::MT_model = 1

private

◆ MT_r0factor

double Actin::MT_r0factor = 1

private

◆ MT_rmax

double Actin::MT_rmax =1000000

private

◆ MT_rmin

double Actin::MT_rmin =0

private

◆ MT_Spring_coefficient

double Actin::MT_Spring_coefficient =0

private

◆ MT_spring_model

double Actin::MT_spring_model =2

private

◆ MTs

vector<vector<int> > Actin::MTs

private

◆ Node_Bond_list

vector<vector<int> > Actin::Node_Bond_list

private

◆ Node_Bond_Nominal_Length_in_Nm

vector<double> Actin::Node_Bond_Nominal_Length_in_Nm

private

◆ Node_Bond_Nominal_Length_stat

string Actin::Node_Bond_Nominal_Length_stat

private

◆ Node_Bond_user_defined_Nominal_Length_in_Nm

double Actin::Node_Bond_user_defined_Nominal_Length_in_Nm

private

◆ Node_Force

vector<vector<double> > Actin::Node_Force

private

◆ Node_Mass

double Actin::Node_Mass =1

private

◆ Node_neighbour_list

vector<vector<int> > Actin::Node_neighbour_list

private

This list is used to store all the neighbours of nodes: Example: If node i has 4 neighbours: m, n, o, p Then we find these neighbours in the 'Node_neighbour_list' as follows: Node_neighbour_list [ i ][0] = m Node_neighbour_list [ i ][1] = n Node_neighbour_list [ i ][2] = o Node_neighbour_list [ i ][3] = p.

◆ Node_neighbour_list_respective_bond_index

vector<vector<int> > Actin::Node_neighbour_list_respective_bond_index

private

This list is used to cross reference the neighbouring nodes to their respective index in the 'Node_neighbour_list'.

Example: Suppose node i has 4 neighbours: m, n, o, p Then we find these neighbours in the 'Node_neighbour_list' as follows: Node_neighbour_list [ i ][0] = m Node_neighbour_list [ i ][1] = n Node_neighbour_list [ i ][2] = o Node_neighbour_list [ i ][3] = p

Then the i'th index of the 'Node_neighbour_list_respective_bond_index' will also contain 4 elements: Node_neighbour_list_respective_bond_index [ i ][0] = index_1 Node_neighbour_list_respective_bond_index [ i ][1] = index_2 Node_neighbour_list_respective_bond_index [ i ][2] = index_3 Node_neighbour_list_respective_bond_index [ i ][3] = index_4

The index_::s will point to the index in the 'Node_Bond_list' that has stored the respective nodes as pairs: Node_Bond_list [ index_1 ][ 0 ] and Node_Bond_list [ index_1 ][ 1 ] = i, m Node_Bond_list [ index_2 ][ 0 ] and Node_Bond_list [ index_2 ][ 1 ] = i, n Node_Bond_list [ index_3 ][ 0 ] and Node_Bond_list [ index_3 ][ 1 ] = i, o Node_Bond_list [ index_4 ][ 0 ] and Node_Bond_list [ index_4 ][ 1 ] = i, p

◆ Node_Position

vector<vector<double> > Actin::Node_Position

private

◆ Node_radius

vector<double> Actin::Node_radius

private

◆ Node_radius_stat

string Actin::Node_radius_stat

private

◆ Node_Velocity

vector<vector<double> > Actin::Node_Velocity

private

◆ Num_of_abp_Pairs

int Actin::Num_of_abp_Pairs =0

private

◆ Num_of_Actin_Membrane_shared_Nodes

vector<int> Actin::Num_of_Actin_Membrane_shared_Nodes

◆ Num_of_MT_Pairs

int Actin::Num_of_MT_Pairs =0

private

◆ Num_of_Node_Pairs

int Actin::Num_of_Node_Pairs =0

private

◆ Num_of_Nodes

int Actin::Num_of_Nodes =0

private

◆ output_file_neme

std::string Actin::output_file_neme

private

◆ param_map

std::map<std::string, double> Actin::param_map

private

◆ Params

std::map<string, vector<string> > Actin::Params

◆ Pyramid_Nodes

vector<vector<int> > Actin::Pyramid_Nodes

private

◆ rescale_factor

double Actin::rescale_factor =1

private

◆ Shift_position_xyzVector

vector<double> Actin::Shift_position_xyzVector

private

◆ Shift_velocities_xyzVector

vector<double> Actin::Shift_velocities_xyzVector

private

◆ Spring_coefficient

double Actin::Spring_coefficient =100

private

◆ spring_model

int Actin::spring_model =2

private

◆ tau_Maxwell_relax

double Actin::tau_Maxwell_relax =0

private

◆ Total_Kinetic_Energy

double Actin::Total_Kinetic_Energy =0

private

◆ Total_Potential_Energy

double Actin::Total_Potential_Energy =0

private

◆ values

vector<string> Actin::values

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

/Users/ali/Documents/Dr Ejtehadi/Programming/Latest Tiam/Ali/Membrane_OBJ/include/Actin.h

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ Actin()

Member Function Documentation

◆ add_to_force()

◆ assign_key_value()

◆ assign_parameters()

◆ check()

◆ check_2()

◆ check_3()

◆ consistancy_check()

◆ Elastic_Force_Calculator()

◆ export_for_resume() [1/2]

◆ export_for_resume() [2/2]

◆ get_abp_force()

◆ get_abp_hill_co()

◆ get_abp_k1()

◆ get_abp_k2()

◆ get_abp_model()

◆ get_abp_pair()

◆ get_abp_r0factor()

◆ get_abp_relaxlength()

◆ get_abp_rmax()

◆ get_abp_rmin()

◆ get_abp_spring_model()

◆ get_abp_spring_stiffness_coefficient()

◆ get_act_r0factor()

◆ get_avg_abp_dist()

◆ get_avg_MT_dist()

◆ get_avg_node_dist()

◆ get_contractile_force()

◆ get_contractile_hill_co()

◆ get_contractile_k1()

◆ get_contractile_k2()

◆ get_contractile_model()

◆ get_contractile_rmax()

◆ get_contractile_rmin()

◆ get_ext_force_model()

◆ get_insertOrder()

◆ get_kelvin_damping_coefficient()

◆ get_kx()

◆ get_ky()

◆ get_kz()

◆ get_label()

◆ get_map()

◆ get_MT_force()

◆ get_MT_hill_co()

◆ get_MT_k1()

◆ get_MT_k2()

◆ get_MT_model()

◆ get_MT_pair()

◆ get_MT_r0factor()

◆ get_MT_relaxlength()

◆ get_MT_rmax()

◆ get_MT_rmin()

◆ get_MT_spring_model()

◆ get_MT_spring_stiffness_coefficient()

◆ get_node_mass()

◆ get_node_pair()

◆ get_node_pair_Nominal_Length_in_Nm()

◆ get_node_position()

◆ get_node_radius()

◆ get_node_velocity()

◆ get_num_of_abp_pairs()

◆ get_num_of_MT_pairs()

◆ get_num_of_node_pairs()

◆ get_num_of_nodes()

◆ get_spring_model()

◆ get_spring_stiffness_coefficient()

◆ Hookian()

◆ import_config()

◆ initialise()

◆ initialise_abp_bond_relaxed_length()

◆ initialise_MT_bond_relaxed_length()

◆ initialise_node_bond_relaxed_length()

◆ Kelvin()

◆ Maxwell()