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macromolecule class

Class representing a generic macromolecule and an interface. More...

Files
file	macromolecule.h
	Data members and function declarations for class macromolecule.
Compounds
struct	macromolecule
	Class for generic representation of macromolecules. More...
Defines
#define	_MACROMOLECULE_H_   1
	Environment variable for 'macromolecule.h'.
Functions
macromolecule *	macromolecule_ctor (char id)
	Constructor for the macromolecule object. More...
void	macromolecule_dtor (macromolecule *thee, char id)
	Destructor for the macromolecule object. More...
double	Born_vol (macromolecule *thee)
	Volume calculation for Born ion. More...
int	Born_is_at (macromolecule *thee, double *xyz, double rad)
	Accessibility check for a specified point (Born ion). More...
double	Born_total_steric (macromolecule *thee, int types, ionlist *ions, char mode)
	Get value for total steric energy due to interaction of Born ion with explicit ions. More...
double	Born_total_steric2 (macromolecule *thee, int types, ionlist *ions, char mode, double *coordsnew[])
	Get value for total steric energy due to interaction of Born ion with explicit ions. More...
double	Born_one_steric (macromolecule *thee, ionlist *ions, int type, int pos, char mode)
	Get value for steric energy due to interaction of Born ion with specified ion. More...
double	Born_total_estatic (macromolecule *thee, int types, ionlist *ions)
	Get value for total electrostatic energy due to interaction of Born ion with explicit ions. More...
double	Born_total_estatic2 (macromolecule *thee, int types, ionlist *ions, double *coordsnew[])
	Get value for total electrostatic energy due to interaction of Born ion with explicit ions. More...
double	Born_point_pot (macromolecule *thee, double *point)
	Get value for electrostatic potential due to Born ion at given point. More...
void	Born_reference (macromolecule *thee, ionlist *ions, int types, double rad, int res, double KB_T, double KB_T_IN_J)
	Writes out some reference knowledge for the Born ion problem based on the work by Debye and Hückel . More...
double	PQR_vol (macromolecule *thee)
	Volume calculation for PQR-file macromolecule. More...
int	PQR_is_at (macromolecule *thee, double *xyz, double rad)
	Accessibility check for a specified point (van-der-Waals surface of a PQR-file macromolecule). More...
void	PQR_rotate (macromolecule *thee)
	Rotates PQR-based macromolecule in case of cylindrical simulation systems. More...
double	PQR_total_steric (macromolecule *thee, int types, ionlist *ions, char mode)
	Get value for total steric energy due to interaction of PQR-based macromolecule with explicit ions. More...
double	PQR_total_steric2 (macromolecule *thee, int types, ionlist *ions, char mode, double *coordsnew[])
	Get value for total steric energy due to interaction of PQR-based macromolecule with explicit ions. More...
double	PQR_one_steric (macromolecule *thee, ionlist *ions, int type, int pos, char mode)
	Get value for steric energy due to interaction of PQR-based macromolecule with specified ion. More...
double	PQR_total_estatic (macromolecule *thee, int types, ionlist *ions)
	Get value for total electrostatic energy due to interaction of PQR-based macromolecule with explicit ions. More...
double	PQR_total_estatic2 (macromolecule *thee, int types, ionlist *ions, double *coordsnew[])
	Get value for total electrostatic energy due to interaction of PQR-based macromolecule with explicit ions. More...
double	PQR_point_pot (macromolecule *thee, double *point)
	Get value for electrostatic potential due to PQR-based macromolecule at given point. More...
double	PQR_sphere_maxradius (macromolecule *thee)
	Gives maximum spherical radius of a PQR-based macromolecule for a sphere centered at {0.0,0.0,0.0}. More...
double	PQR_cylinder_maxradius (macromolecule *thee)
	Gives maximum cylindrical radius of a PQR-based macromolecule for a cylinder centered at {0.0,0.0,0.0}. More...
void	Born_shift (macromolecule *thee, double xshift, double yshift, double zshift)
	Shifts center coordinates of Born ion by specified vector. More...
void	PQR_shift (macromolecule *thee, double xshift, double yshift, double zshift)
	Shifts coordinates in atom list of a PQR-based macromolecule by specified vector. More...
double	CYL_vol (macromolecule *thee)
	Volume calculation for cylinder. More...
int	CYL_is_at (macromolecule *thee, double *xyz, double rad)
	Accessibility check for a specified point (charged cylinder). More...
double	CYL_total_steric (macromolecule *thee, int types, ionlist *ions, char mode)
	Get value for total steric energy due to interaction of charged cylinder with explicit ions. More...
double	CYL_total_steric2 (macromolecule *thee, int types, ionlist *ions, char mode, double *coordsnew[])
	Get value for total steric energy due to interaction of charged cylinder with explicit ions. More...
double	CYL_one_steric (macromolecule *thee, ionlist *ions, int type, int pos, char mode)
	Get value for steric energy due to interaction of charged cylinder with specified ion. More...
double	CYL_total_estatic (macromolecule *thee, int types, ionlist *ions)
	Get value for total electrostatic energy due to interaction of charged cylinder with explicit ions. More...
double	CYL_total_estatic2 (macromolecule *thee, int types, ionlist *ions, double *coordsnew[])
	Get value for total electrostatic energy due to interaction of charged cylinder with explicit ions. More...
double	CYL_point_pot (macromolecule *thee, double *point)
	Get value for electrostatic potential due to charged cylinder at given point. More...

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Detailed Description

Class representing a generic macromolecule and an interface.

To be able to handle different macromolecule types function pointers are used (which replace virtual abstract functions and inheritance in Clean OO-C)

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Function Documentation

int Born_is_at (  macromolecule *    thee, double *    xyz, double    rad )

Accessibility check for a specified point (Born ion). Author: Andreas Vitalis Parameters: thee  Macromolecule object xyz  pointer to coordinate array holding point to be tested (Cartesian in ) rad  Specifies the radius (in ) of 'xyz' (tests if spheres are overlapping or not) Returns: '1' if point is not accessible, '0' otherwise

double Born_one_steric (  macromolecule *    thee, ionlist *    ions, int    type, int    pos, char    mode )

Get value for steric energy due to interaction of Born ion with specified ion. Author: Andreas Vitalis Parameters: thee  Macromolecule object ions  Pointer to array of ionlist objects, indexing starts at '1' type  Integer number specifying the type of the ion (in terms of 'ions'-indexing) pos  Integer number specifying the position of the x-coordinate of the ion within the 'ions'-coordinates array mode  Character indicating the used expression for calculating steric interactions Returns: Value for the contribution to the steric interaction energy in J

double Born_point_pot (  macromolecule *    thee, double *    point )

Get value for electrostatic potential due to Born ion at given point. Author: Andreas Vitalis Parameters: thee  Macromolecule object point  pointer to coordinate array, which specifies the point of interest (Cartesian in ) Returns: Value for the elelctrostatic potential in J/e

void Born_reference (  macromolecule *    thee, ionlist *    ions, int    types, double    rad, int    res, double    KB_T, double    KB_T_IN_J )

Writes out some reference knowledge for the Born ion problem based on the work by Debye and Hückel . Author: Andreas Vitalis Parameters: thee  Macromolecule object ions  Pointer to array of ionlist objects, indexing starts at '1' types  Integer number specifiying the number of different ion types given by 'ions' rad  Radius of the simulation sphere (routine is only used for spherical systems) res  Resolution for distance-dependent calculations KB_T  Thermal energy in kJ/mol KB_T_IN_J  Thermal energy in J

void Born_shift (  macromolecule *    thee, double    xshift, double    yshift, double    zshift )

Shifts center coordinates of Born ion by specified vector. Author: Andreas Vitalis Parameters: thee  Macromolecule object xshift  First component of shift-vector yshift  Second component of shift-vector zshift  Third component of shift-vector

double Born_total_estatic (  macromolecule *    thee, int    types, ionlist *    ions )

Get value for total electrostatic energy due to interaction of Born ion with explicit ions. Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' Returns: Value for the total electrostatic interaction energy in J

double Born_total_estatic2 (  macromolecule *    thee, int    types, ionlist *    ions, double *    coordsnew[] )

Get value for total electrostatic energy due to interaction of Born ion with explicit ions. Coordinates for ions are taken from temporary/VEXTERNCal array Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' coordsnew  Array of pointers used to hold previously modified coordinates to recalculate energy (first index for ion types, second one in form of {x1,y1,z1,x2,y2,z2,...,xn,yn,zn} (starting at '1') for explicit Cartesian coordinates in Returns: Value for the total electrostatic interaction energy in J

double Born_total_steric (  macromolecule *    thee, int    types, ionlist *    ions, char    mode )

Get value for total steric energy due to interaction of Born ion with explicit ions. Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' mode  Character indicating the used expression for calculating steric interactions Returns: Value for the total steric interaction energy in J

double Born_total_steric2 (  macromolecule *    thee, int    types, ionlist *    ions, char    mode, double *    coordsnew[] )

Get value for total steric energy due to interaction of Born ion with explicit ions. Coordinates for ions are taken from temporary/VEXTERNCal array Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' mode  Character indicating the used expression for calculating steric interactions coordsnew  Array of pointers used to hold previously modified coordinates to recalculate energy (first index for ion types, second one in form of {x1,y1,z1,x2,y2,z2,...,xn,yn,zn} (starting at '1') for explicit Cartesian coordinates in Returns: Value for the total steric interaction energy in J

double Born_vol (  macromolecule *    thee )

Volume calculation for Born ion. Author: Andreas Vitalis Parameters: thee  Macromolecule object Returns: Solvent-inaccessible volume in

int CYL_is_at (  macromolecule *    thee, double *    xyz, double    rad )

Accessibility check for a specified point (charged cylinder). Author: Andreas Vitalis Parameters: thee  Macromolecule object xyz  pointer to coordinate array holding point to be tested (Cartesian in ) rad  Specifies the radius (in ) of 'xyz' (tests if xyz-sphere and cylinder are overlapping or not) Returns: '1' if point is not accessible, '0' otherwise

double CYL_one_steric (  macromolecule *    thee, ionlist *    ions, int    type, int    pos, char    mode )

Get value for steric energy due to interaction of charged cylinder with specified ion. Author: Andreas Vitalis Parameters: thee  Macromolecule object ions  Pointer to array of ionlist objects, indexing starts at '1' type  Integer number specifying the type of the ion (in terms of 'ions'-indexing) pos  Integer number specifying the position of the x-coordinate of the ion within the 'ions'-coordinates array mode  Character indicating the used expression for calculating steric interactions (only 'S' is supported for charged cylinders) Returns: Value for the contribution to the steric interaction energy in J

double CYL_point_pot (  macromolecule *    thee, double *    point )

Get value for electrostatic potential due to charged cylinder at given point. Author: Andreas Vitalis Parameters: thee  Macromolecule object point  pointer to coordinate array, which specifies the point of interest (Cartesian in ) Returns: Value for the elelctrostatic potential in J/e

double CYL_total_estatic (  macromolecule *    thee, int    types, ionlist *    ions )

Get value for total electrostatic energy due to interaction of charged cylinder with explicit ions. Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' Returns: Value for the total electrostatic interaction energy in J

double CYL_total_estatic2 (  macromolecule *    thee, int    types, ionlist *    ions, double *    coordsnew[] )

Get value for total electrostatic energy due to interaction of charged cylinder with explicit ions. Coordinates for ions are taken from temporary/external array Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' coordsnew  Array of pointers used to hold previously modified coordinates to recalculate energy (first index for ion types, second one in form of {x1,y1,z1,x2,y2,z2,...,xn,yn,zn} (starting at '1') for explicit Cartesian coordinates in Returns: Value for the total electrostatic interaction energy in J

double CYL_total_steric (  macromolecule *    thee, int    types, ionlist *    ions, char    mode )

Get value for total steric energy due to interaction of charged cylinder with explicit ions. Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' mode  Character indicating the used expression for calculating steric interactions Returns: Value for the total steric interaction energy in J

double CYL_total_steric2 (  macromolecule *    thee, int    types, ionlist *    ions, char    mode, double *    coordsnew[] )

Get value for total steric energy due to interaction of charged cylinder with explicit ions. Coordinates for ions are taken from temporary/external array Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' mode  Character indicating the used expression for calculating steric interactions (only 'S' is supported for charged cylinders) coordsnew  Array of pointers used to hold previously modified coordinates to recalculate energy (first index for ion types, second one in form of {x1,y1,z1,x2,y2,z2,...,xn,yn,zn} (starting at '1') for explicit Cartesian coordinates in Returns: Value for the total steric interaction energy in J

double CYL_vol (  macromolecule *    thee )

Volume calculation for cylinder. Author: Andreas Vitalis Parameters: thee  Macromolecule object Returns: Solvent-inaccessible volume in

macromolecule* macromolecule_ctor (  char    id )

Constructor for the macromolecule object. Assigns function pointers accroding to passed identification character Author: Andreas Vitalis Parameters: id  Character ID specifying the type of macromolecule Returns: Macromolecule object

void macromolecule_dtor (  macromolecule *    thee, char    id )

Destructor for the macromolecule object. Author: Andreas Vitalis Parameters: thee  Macromolecule object id  Character ID specifying the type of macromolecule

double PQR_cylinder_maxradius (  macromolecule *    thee )

Gives maximum cylindrical radius of a PQR-based macromolecule for a cylinder centered at {0.0,0.0,0.0}. Author: Andreas Vitalis Parameters: thee  Macromolecule object Returns: Maximum cylindrical radius in (maximum distance of any atom from z-axis)

int PQR_is_at (  macromolecule *    thee, double *    xyz, double    rad )

Accessibility check for a specified point (van-der-Waals surface of a PQR-file macromolecule). Author: Andreas Vitalis Parameters: thee  Macromolecule object xyz  Pointer to coordinate array holding point to be tested (Cartesian in ) rad  Specifies the radius of 'xyz' (tests if xyz-sphere and PQR-union of spheres are overlapping or not) Returns: '1' if point is not accessible, '0' otherwise

double PQR_one_steric (  macromolecule *    thee, ionlist *    ions, int    type, int    pos, char    mode )

Get value for steric energy due to interaction of PQR-based macromolecule with specified ion. Author: Andreas Vitalis Parameters: thee  Macromolecule object ions  Pointer to array of ionlist objects, indexing starts at '1' type  Integer number specifying the type of the ion (in terms of 'ions'-indexing) pos  Integer number specifying the position of the x-coordinate of the ion within the 'ions'-coordinates array mode  Character indicating the used expression for calculating steric interactions Returns: Value for the contribution to the steric interaction energy in J

double PQR_point_pot (  macromolecule *    thee, double *    point )

Get value for electrostatic potential due to PQR-based macromolecule at given point. Author: Andreas Vitalis Parameters: thee  Macromolecule object point  pointer to coordinate array, which specifies the point of interest (Cartesian in ) Returns: Value for the elelctrostatic potential in J/e

void PQR_rotate (  macromolecule *    thee )

Rotates PQR-based macromolecule in case of cylindrical simulation systems. Simply finds the two atoms, which have the longest distance and aligns the simulation system's z-axis to the resulting vector Parameters: thee  Macromolecule object Author: Andreas Vitalis

void PQR_shift (  macromolecule *    thee, double    xshift, double    yshift, double    zshift )

Shifts coordinates in atom list of a PQR-based macromolecule by specified vector. Author: Andreas Vitalis Parameters: thee  Macromolecule object xshift  First component of shift-vector yshift  Second component of shift-vector zshift  Third component of shift-vector

double PQR_sphere_maxradius (  macromolecule *    thee )

Gives maximum spherical radius of a PQR-based macromolecule for a sphere centered at {0.0,0.0,0.0}. Author: Andreas Vitalis Parameters: thee  Macromolecule object Returns: Maximum spherical radius in (maximum distance of any atom from center)

double PQR_total_estatic (  macromolecule *    thee, int    types, ionlist *    ions )

Get value for total electrostatic energy due to interaction of PQR-based macromolecule with explicit ions. Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' Returns: Value for the total electrostatic interaction energy in J

double PQR_total_estatic2 (  macromolecule *    thee, int    types, ionlist *    ions, double *    coordsnew[] )

Get value for total electrostatic energy due to interaction of PQR-based macromolecule with explicit ions. Coordinates for ions are taken from temporary/VEXTERNCal array Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' coordsnew  Array of pointers used to hold previously modified coordinates to recalculate energy (first index for ion types, second one in form of {x1,y1,z1,x2,y2,z2,...,xn,yn,zn} (starting at '1') for explicit Cartesian coordinates in Returns: Value for the total electrostatic interaction energy in J

double PQR_total_steric (  macromolecule *    thee, int    types, ionlist *    ions, char    mode )

Get value for total steric energy due to interaction of PQR-based macromolecule with explicit ions. Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' mode  Character indicating the used expression for calculating steric interactions Returns: Value for the total steric interaction energy in J

double PQR_total_steric2 (  macromolecule *    thee, int    types, ionlist *    ions, char    mode, double *    coordsnew[] )

Get value for total steric energy due to interaction of PQR-based macromolecule with explicit ions. Coordinates for ions are taken from temporary/VEXTERNCal array Author: Andreas Vitalis Parameters: thee  Macromolecule object types  Integer number specifiying the number of different ion types given by 'ions' ions  Pointer to array of ionlist objects, indexing starts at '1' mode  Character indicating the used expression for calculating steric interactions coordsnew  Array of pointers used to hold previously modified coordinates to recalculate energy (first index for ion types, second one in form of {x1,y1,z1,x2,y2,z2,...,xn,yn,zn} (starting at '1') for explicit Cartesian coordinates in Returns: Value for the total steric interaction energy in J

double PQR_vol (  macromolecule *    thee )

Volume calculation for PQR-file macromolecule. Author: Andreas Vitalis Parameters: thee  Macromolecule object Returns: Solvent-inaccessible volume in

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