Valist class

Container class for list of atom objects. More...

Files
file	valist.h
	Contains declarations for class Valist.
Data Structures
struct	sValist
	Container class for list of atom objects. More...
Typedefs
typedef sValist	Valist
	Declaration of the Valist class as the Valist structure.
Functions
Vatom *	Valist_getAtomList (Valist *thee)
	Get actual array of atom objects from the list.
double	Valist_getCenterX (Valist *thee)
	Get x-coordinate of molecule center.
double	Valist_getCenterY (Valist *thee)
	Get y-coordinate of molecule center.
double	Valist_getCenterZ (Valist *thee)
	Get z-coordinate of molecule center.
int	Valist_getNumberAtoms (Valist *thee)
	Get number of atoms in the list.
Vatom *	Valist_getAtom (Valist *thee, int i)
	Get pointer to particular atom in list.
unsigned long int	Valist_memChk (Valist *thee)
	Get total memory allocated for this object and its members.
Valist *	Valist_ctor ()
	Construct the atom list object.
int	Valist_ctor2 (Valist *thee)
	FORTRAN stub to construct the atom list object.
void	Valist_dtor (Valist **thee)
	Destroys atom list object.
void	Valist_dtor2 (Valist *thee)
	FORTRAN stub to destroy atom list object.
int	Valist_readPQR (Valist *thee, Vio *sock)
	Fill atom list with information from a PQR file.
int	Valist_readPDB (Valist *thee, Vparam *param, Vio *sock)
	Fill atom list with information from a PDB file.

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Detailed Description

Container class for list of atom objects.

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Function Documentation

Valist* Valist_ctor (   )

Construct the atom list object. Author: Nathan Baker Returns: Pointer to newly allocated (empty) atom list

int Valist_ctor2 (  Valist *  thee  )

FORTRAN stub to construct the atom list object. Author: Nathan Baker Returns: 1 if successful, 0 otherwise Parameters: thee  Storage for new atom list

void Valist_dtor (  Valist **  thee  )

Destroys atom list object. Author: Nathan Baker Parameters: thee  Pointer to storage for atom list

void Valist_dtor2 (  Valist *  thee  )

FORTRAN stub to destroy atom list object. Author: Nathan Baker Parameters: thee  Pointer to atom list object

Vatom* Valist_getAtom (  Valist *  thee, int  i )

Get pointer to particular atom in list. Author: Nathan Baker Returns: Pointer to atom object i Parameters: thee  Atom list object i  Index of atom in list

Vatom* Valist_getAtomList (  Valist *  thee  )

Get actual array of atom objects from the list. Author: Nathan Baker Returns: Array of atom objects Parameters: thee  Atom list object

double Valist_getCenterX (  Valist *  thee  )

Get x-coordinate of molecule center. Author: Nathan Baker Returns: X-coordinate of molecule center Parameters: thee  Atom list object

double Valist_getCenterY (  Valist *  thee  )

Get y-coordinate of molecule center. Author: Nathan Baker Returns: Y-coordinate of molecule center Parameters: thee  Atom list object

double Valist_getCenterZ (  Valist *  thee  )

Get z-coordinate of molecule center. Author: Nathan Baker Returns: Z-coordinate of molecule center Parameters: thee  Atom list object

int Valist_getNumberAtoms (  Valist *  thee  )

Get number of atoms in the list. Author: Nathan Baker Returns: Number of atoms in list Parameters: thee  Atom list object

unsigned long int Valist_memChk (  Valist *  thee  )

Get total memory allocated for this object and its members. Author: Nathan Baker Returns: Total memory in bytes Parameters: thee  Atom list object

int Valist_readPDB (  Valist *  thee, Vparam *  param, Vio *  sock )

Fill atom list with information from a PDB file. Author: Nathan Baker, Todd Dolinsky Returns: 1 if successful, 0 otherwise Note: We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999. Parameters: thee  Atom list object param  A pre-initialized parameter object sock  Socket read for reading PDB file

int Valist_readPQR (  Valist *  thee, Vio *  sock )

Fill atom list with information from a PQR file. Author: Nathan Baker Returns: 1 if successful, 0 otherwise Note: A PQR file has PDB structure with charge and radius in the last two columns instead of weight and occupancy We don't actually respect PDB format; instead recognize whitespace- or tab-delimited fields which allows us to deal with structures with coordinates > 999 or < -999. Parameters: thee  Atom list object sock  Socket reading for reading PQR file

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