Data Structures | Files | Typedefs | Functions

Valist class

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

Data Structures

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

Files

file  valist.h
 

Contains declarations for class Valist.


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.


Function Documentation

VEXTERNC Valist* Valist_ctor (  )

Construct the atom list object.

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

Definition at line 131 of file valist.c.

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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 148 of file valist.c.

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VEXTERNC void Valist_dtor ( Valist **  thee )

Destroys atom list object.

Author:
Nathan Baker
Parameters:
theePointer to storage for atom list

Definition at line 160 of file valist.c.

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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 169 of file valist.c.

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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 108 of file valist.c.

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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 88 of file valist.c.

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 59 of file valist.c.

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 69 of file valist.c.

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 78 of file valist.c.

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 98 of file valist.c.

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VEXTERNC Vrc_Codes Valist_getStatistics ( Valist thee )

Load up Valist with various statistics.

Author:
Nathan Baker, Yong Huang
Returns:
Success enumeration

Definition at line 851 of file valist.c.

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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 122 of file valist.c.

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 508 of file valist.c.

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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 599 of file valist.c.

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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 707 of file valist.c.

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