APBS 3.0.0
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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 struct sValist Valist
 Declaration of the Valist class as the Valist structure.
 

Functions

VEXTERNC VatomValist_getAtomList (Valist *thee)
 Get actual array of atom objects from the list.
 
VEXTERNC double Valist_getCenterX (Valist *thee)
 Get x-coordinate of molecule center.
 
VEXTERNC double Valist_getCenterY (Valist *thee)
 Get y-coordinate of molecule center.
 
VEXTERNC double Valist_getCenterZ (Valist *thee)
 Get z-coordinate of molecule center.
 
VEXTERNC int Valist_getNumberAtoms (Valist *thee)
 Get number of atoms in the list.
 
VEXTERNC VatomValist_getAtom (Valist *thee, int i)
 Get pointer to particular atom in list.
 
VEXTERNC unsigned long int Valist_memChk (Valist *thee)
 Get total memory allocated for this object and its members.
 
VEXTERNC ValistValist_ctor ()
 Construct the atom list object.
 
VEXTERNC Vrc_Codes Valist_ctor2 (Valist *thee)
 FORTRAN stub to construct the atom list object.
 
VEXTERNC void Valist_dtor (Valist **thee)
 Destroys atom list object.
 
VEXTERNC void Valist_dtor2 (Valist *thee)
 FORTRAN stub to destroy atom list object.
 
VEXTERNC Vrc_Codes Valist_readPQR (Valist *thee, Vparam *param, Vio *sock)
 Fill atom list with information from a PQR file.
 
VEXTERNC Vrc_Codes Valist_readPDB (Valist *thee, Vparam *param, Vio *sock)
 Fill atom list with information from a PDB file.
 
VEXTERNC Vrc_Codes Valist_readXML (Valist *thee, Vparam *param, Vio *sock)
 Fill atom list with information from an XML file.
 
VEXTERNC Vrc_Codes Valist_getStatistics (Valist *thee)
 Load up Valist with various statistics.
 

Detailed Description

Container class for list of atom objects.

Typedef Documentation

◆ Valist

typedef struct sValist Valist

Declaration of the Valist class as the Valist structure.

Definition at line 95 of file valist.h.

Function Documentation

◆ Valist_ctor()

VEXTERNC Valist * Valist_ctor ( )

Construct the atom list object.

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

Definition at line 138 of file valist.c.

◆ Valist_ctor2()

VEXTERNC Vrc_Codes Valist_ctor2 ( Valist * thee)

FORTRAN stub to construct the atom list object.

Author
Nathan Baker, Yong Huang
Returns
Success enumeration
Parameters
theeStorage for new atom list

Definition at line 155 of file valist.c.

◆ Valist_dtor()

VEXTERNC void Valist_dtor ( Valist ** thee)

Destroys atom list object.

Author
Nathan Baker
Parameters
theePointer to storage for atom list

Definition at line 167 of file valist.c.

◆ Valist_dtor2()

VEXTERNC void Valist_dtor2 ( Valist * thee)

FORTRAN stub to destroy atom list object.

Author
Nathan Baker
Parameters
theePointer to atom list object

Definition at line 176 of file valist.c.

◆ Valist_getAtom()

VEXTERNC Vatom * Valist_getAtom ( Valist * thee,
int i )

Get pointer to particular atom in list.

Author
Nathan Baker
Returns
Pointer to atom object i
Parameters
theeAtom list object
iIndex of atom in list

Definition at line 115 of file valist.c.

◆ Valist_getAtomList()

VEXTERNC Vatom * Valist_getAtomList ( Valist * thee)

Get actual array of atom objects from the list.

Author
Nathan Baker
Returns
Array of atom objects
Parameters
theeAtom list object

Definition at line 95 of file valist.c.

◆ Valist_getCenterX()

VEXTERNC double Valist_getCenterX ( Valist * thee)

Get x-coordinate of molecule center.

Author
Nathan Baker
Returns
X-coordinate of molecule center
Parameters
theeAtom list object

Definition at line 66 of file valist.c.

◆ Valist_getCenterY()

VEXTERNC double Valist_getCenterY ( Valist * thee)

Get y-coordinate of molecule center.

Author
Nathan Baker
Returns
Y-coordinate of molecule center
Parameters
theeAtom list object

Definition at line 76 of file valist.c.

◆ Valist_getCenterZ()

VEXTERNC double Valist_getCenterZ ( Valist * thee)

Get z-coordinate of molecule center.

Author
Nathan Baker
Returns
Z-coordinate of molecule center
Parameters
theeAtom list object

Definition at line 85 of file valist.c.

◆ Valist_getNumberAtoms()

VEXTERNC int Valist_getNumberAtoms ( Valist * thee)

Get number of atoms in the list.

Author
Nathan Baker
Returns
Number of atoms in list
Parameters
theeAtom list object

Definition at line 105 of file valist.c.

◆ Valist_getStatistics()

VEXTERNC Vrc_Codes Valist_getStatistics ( Valist * thee)

Load up Valist with various statistics.

Author
Nathan Baker, Yong Huang
Returns
Success enumeration

Definition at line 869 of file valist.c.

◆ Valist_memChk()

VEXTERNC 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
theeAtom list object

Definition at line 129 of file valist.c.

◆ Valist_readPDB()

VEXTERNC Vrc_Codes Valist_readPDB ( Valist * thee,
Vparam * param,
Vio * sock )

Fill atom list with information from a PDB file.

Author
Nathan Baker, Todd Dolinsky, Yong Huang
Returns
Success enumeration
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
theeAtom list object
paramA pre-initialized parameter object
sockSocket read for reading PDB file

Definition at line 515 of file valist.c.

◆ Valist_readPQR()

VEXTERNC Vrc_Codes Valist_readPQR ( Valist * thee,
Vparam * param,
Vio * sock )

Fill atom list with information from a PQR file.

Author
Nathan Baker, Yong Huang
Returns
Success enumeration
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
theeAtom list object
paramA pre-initialized parameter object
sockSocket reading for reading PQR file

Definition at line 606 of file valist.c.

◆ Valist_readXML()

VEXTERNC Vrc_Codes Valist_readXML ( Valist * thee,
Vparam * param,
Vio * sock )

Fill atom list with information from an XML file.

Author
Todd Dolinsky, Yong Huang
Returns
Success enumeration
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
theeAtom list object
paramA pre-initialized parameter object
sockSocket reading for reading PQR file

Definition at line 725 of file valist.c.