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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.

unsigned long int Valist_memChk (Valist *thee)
 Get total memory allocated for this object and its members.

ValistValist_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, Vparam *param, 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.

int Valist_readXML (Valist *thee, Vparam *param, Vio *sock)
 Fill atom list with information from an XML file.

int Valist_getStatistics (Valist *thee)
 Load up Valist with various statistics.


Detailed Description

Container class for list of atom objects.


Function Documentation

Valist* Valist_ctor  ) 
 

Construct the atom list object.

Author:
Nathan Baker
Returns:
Pointer to newly allocated (empty) atom list

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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

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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

int Valist_getStatistics Valist thee  ) 
 

Load up Valist with various statistics.

Author:
Nathan Baker
Returns:
1 if successful, 0 otherwise

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

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int Valist_readPQR Valist thee,
Vparam param,
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
param  A pre-initialized parameter object
sock  Socket reading for reading PQR file

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int Valist_readXML Valist thee,
Vparam param,
Vio *  sock
 

Fill atom list with information from an XML file.

Author:
Todd Dolinsky
Returns:
1 if successful, 0 otherwise
Note:
  • The XML file must adhere to some guidelines, notably the presence of an <atom> tag with all other useful information (x, y, z, charge, and radius) as nested elements.
Parameters:
thee  Atom list object
param  A pre-initialized parameter object
sock  Socket reading for reading PQR file

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