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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

VatomValist_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.

VatomValist_getAtom (Valist *thee, int i)
 Get pointer to particular atom in list.

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, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Fill atom list with information from a PQR file.

int Valist_readPDB (Valist *thee, Vparam *param, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Fill atom list with information from a PDB file.

void Valist_buildMesh (Valist *thee, double size, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Build rectangular prismatic finite element mesh which surrounds molecule contained in Valist object.


Detailed Description

Container class for list of atom objects.


Function Documentation

void Valist_buildMesh Valist   thee,
double    size,
const char *    iodev,
const char *    iofmt,
const char *    thost,
const char *    fname
 

Build rectangular prismatic finite element mesh which surrounds molecule contained in Valist object.

The mesh will have rectangular sides and consist of 6 simplices and 8 vertices will all boundaries Dirichlet. The mesh will be written to the sock specified by the parameters below.

Bug:
This routine has not been tested.
Author:
Nathan Baker (mesh topology based on MCSF file by Mike Holst)
Parameters:
thee  Valist object to use as reference for the mesh
size  The factor by which the mesh is larger than the biomolecule. In other words, if the smallest box containing the biomolecule is dx x dy x dz, then the mesh built by this routine will have dimensions (size*dx) x (size*dy) x (size*dz).
iodev  Output device type (FILE/BUFF/UNIX/INET)
iofmt  Output device format (ASCII/XDR)
thost  Output hostname (for sockets)
fname  Output FILE/BUFF/UNIX/INET name

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
Parameters:
thee  Storage for new atom list
Returns:
1 if successful, 0 otherwise

void Valist_dtor Valist **    thee
 

Destroys atom list object.

Author:
Nathan Baker
Parameters:
thee  Pointer to memory location for atom list object

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
Parameters:
thee  Valist object
i  Index of atom of interest
Returns:
Pointer to atom object i

Vatom* Valist_getAtomList Valist   thee
 

Get actual array of atom objects from the list.

Author:
Nathan Baker
Parameters:
thee  Valist object
Returns:
Array of atom objects

double Valist_getCenterX Valist   thee
 

Get x-coordinate of molecule center.

Author:
Nathan Baker
Parameters:
thee  Valist object
Returns:
X-coordinate of molecule center

double Valist_getCenterY Valist   thee
 

Get y-coordinate of molecule center.

Author:
Nathan Baker
Parameters:
thee  Valist object
Returns:
Y-coordinate of molecule center

double Valist_getCenterZ Valist   thee
 

Get z-coordinate of molecule center.

Author:
Nathan Baker
Parameters:
thee  Valist object
Returns:
Z-coordinate of molecule center

int Valist_getNumberAtoms Valist   thee
 

Get number of atoms in the list.

Author:
Nathan Baker
Parameters:
thee  Valist object
Returns:
Number of atoms in list

int Valist_memChk Valist   thee
 

Get total memory allocated for this object and its members.

Author:
Nathan Baker
Parameters:
thee  Valist object
Returns:
Total memory in bytes

int Valist_readPDB Valist   thee,
Vparam   param,
const char *    iodev,
const char *    iofmt,
const char *    thost,
const char *    fname
 

Fill atom list with information from a PDB file.

Author:
Nathan Baker
Parameters:
thee  Valist object to be filled
param  A pre-initialized parameter object
iodev  Input device type (FILE/BUFF/UNIX/INET)
iofmt  Input device format (ASCII/XDR)
thost  Input hostname (for sockets)
fname  Input FILE/BUFF/UNIX/INET name
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.

int Valist_readPQR Valist   thee,
const char *    iodev,
const char *    iofmt,
const char *    thost,
const char *    fname
 

Fill atom list with information from a PQR file.

Author:
Nathan Baker
Parameters:
thee  Valist object to be filled
iodev  Input device type (FILE/BUFF/UNIX/INET)
iofmt  Input device format (ASCII/XDR)
thost  Input hostname (for sockets)
fname  Input FILE/BUFF/UNIX/INET name
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.


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