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Vparam class

Reads and assigns charge/radii parameters. More...


Files

file  vparam.c
 Class Vparam methods.

file  vparam.h
 Contains declarations for class Vparam.


Data Structures

struct  sVparam_AtomData
 AtomData sub-class; stores atom data. More...

struct  Vparam
 Reads and assigns charge/radii parameters. More...

struct  Vparam_ResData
 ResData sub-class; stores residue data. More...


Typedefs

typedef sVparam_AtomData Vparam_AtomData
 Declaration of the Vparam_AtomData class as the sVparam_AtomData structure.

typedef Vparam_ResData Vparam_ResData
 Declaration of the Vparam_ResData class as the Vparam_ResData structure.

typedef Vparam Vparam
 Declaration of the Vparam class as the Vparam structure.


Functions

unsigned long int Vparam_memChk (Vparam *thee)
 Get number of bytes in this object and its members.

Vparam_AtomDataVparam_AtomData_ctor ()
 Construct the object.

int Vparam_AtomData_ctor2 (Vparam_AtomData *thee)
 FORTRAN stub to construct the object.

void Vparam_AtomData_dtor (Vparam_AtomData **thee)
 Destroy object.

void Vparam_AtomData_dtor2 (Vparam_AtomData *thee)
 FORTRAN stub to destroy object.

void Vparam_AtomData_copyTo (Vparam_AtomData *thee, Vparam_AtomData *dest)
 Copy current atom object to destination.

void Vparam_ResData_copyTo (Vparam_ResData *thee, Vparam_ResData *dest)
 Copy current residue object to destination.

void Vparam_AtomData_copyFrom (Vparam_AtomData *thee, Vparam_AtomData *src)
 Copy current atom object from another.

Vparam_ResDataVparam_ResData_ctor (Vmem *mem)
 Construct the object.

int Vparam_ResData_ctor2 (Vparam_ResData *thee, Vmem *mem)
 FORTRAN stub to construct the object.

void Vparam_ResData_dtor (Vparam_ResData **thee)
 Destroy object.

void Vparam_ResData_dtor2 (Vparam_ResData *thee)
 FORTRAN stub to destroy object.

VparamVparam_ctor ()
 Construct the object.

int Vparam_ctor2 (Vparam *thee)
 FORTRAN stub to construct the object.

void Vparam_dtor (Vparam **thee)
 Destroy object.

void Vparam_dtor2 (Vparam *thee)
 FORTRAN stub to destroy object.

Vparam_ResDataVparam_getResData (Vparam *thee, char resName[VMAX_ARGLEN])
 Get residue data.

Vparam_AtomDataVparam_getAtomData (Vparam *thee, char resName[VMAX_ARGLEN], char atomName[VMAX_ARGLEN])
 Get atom data.

int Vparam_readFlatFile (Vparam *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Read a flat-file format parameter database.

int Vparam_readXMLFile (Vparam *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Read an XML format parameter database.

VPRIVATE int readFlatFileLine (Vio *sock, Vparam_AtomData *atom)
 Read a single line of the flat file database.

VPRIVATE int readXMLFileAtom (Vio *sock, Vparam_AtomData *atom)
 Read atom information from an XML file.


Variables

VPRIVATE char * MCwhiteChars = " =,;\t\n\r"
 Whitespace characters for socket reads.

VPRIVATE char * MCcommChars = "#%"
 Comment characters for socket reads.

VPRIVATE char * MCxmlwhiteChars = " =,;\t\n\r<>"
 Whitespace characters for XML socket reads.


Detailed Description

Reads and assigns charge/radii parameters.


Function Documentation

VPRIVATE int readFlatFileLine Vio *  sock,
Vparam_AtomData atom
 

Read a single line of the flat file database.

Author:
Nathan Baker
Parameters:
sock Socket ready for reading
atom Atom to hold parsed data
Returns:
1 if successful, 0 otherwise

VPRIVATE int readXMLFileAtom Vio *  sock,
Vparam_AtomData atom
 

Read atom information from an XML file.

Author:
Todd Dolinsky
Parameters:
sock Socket ready for reading
atom Atom to hold parsed data
Returns:
1 if successful, 0 otherwise

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void Vparam_AtomData_copyFrom Vparam_AtomData thee,
Vparam_AtomData src
 

Copy current atom object from another.

Author:
Nathan Baker
Parameters:
thee Pointer to destination object
src Pointer to source object

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void Vparam_AtomData_copyTo Vparam_AtomData thee,
Vparam_AtomData dest
 

Copy current atom object to destination.

Author:
Nathan Baker
Parameters:
thee Pointer to source object
dest Pointer to destination object

Vparam_AtomData* Vparam_AtomData_ctor  ) 
 

Construct the object.

Author:
Nathan Baker
Returns:
Newly allocated object

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int Vparam_AtomData_ctor2 Vparam_AtomData thee  ) 
 

FORTRAN stub to construct the object.

Author:
Nathan Baker
Parameters:
thee Allocated memory
Returns:
1 if successful, 0 otherwise

void Vparam_AtomData_dtor Vparam_AtomData **  thee  ) 
 

Destroy object.

Author:
Nathan Baker
Parameters:
thee Pointer to memory location of object

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void Vparam_AtomData_dtor2 Vparam_AtomData thee  ) 
 

FORTRAN stub to destroy object.

Author:
Nathan Baker
Parameters:
thee Pointer to object

Vparam* Vparam_ctor  ) 
 

Construct the object.

Author:
Nathan Baker
Returns:
Newly allocated Vparam object

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int Vparam_ctor2 Vparam thee  ) 
 

FORTRAN stub to construct the object.

Author:
Nathan Baker
Parameters:
thee Allocated Vparam memory
Returns:
1 if successful, 0 otherwise

void Vparam_dtor Vparam **  thee  ) 
 

Destroy object.

Author:
Nathan Baker
Parameters:
thee Pointer to memory location of object

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void Vparam_dtor2 Vparam thee  ) 
 

FORTRAN stub to destroy object.

Author:
Nathan Baker
Parameters:
thee Pointer to object

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Vparam_AtomData* Vparam_getAtomData Vparam thee,
char  resName[VMAX_ARGLEN],
char  atomName[VMAX_ARGLEN]
 

Get atom data.

Author:
Nathan Baker
Parameters:
thee Vparam object
resName Residue name
atomName Atom name
Returns:
Pointer to the desired atom object or VNULL if residue not found
Note:
Some method to initialize the database must be called before this method (e.g.,
See also:
Vparam_readFlatFile)

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Vparam_ResData* Vparam_getResData Vparam thee,
char  resName[VMAX_ARGLEN]
 

Get residue data.

Author:
Nathan Baker
Parameters:
thee Vparam object
resName Residue name
Returns:
Pointer to the desired residue object or VNULL if residue not found
Note:
Some method to initialize the database must be called before this method (e.g.,
See also:
Vparam_readFlatFile)

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unsigned long int Vparam_memChk Vparam thee  ) 
 

Get number of bytes in this object and its members.

Author:
Nathan Baker
Parameters:
thee Vparam object
Returns:
Number of bytes allocated for object

int Vparam_readFlatFile Vparam thee,
const char *  iodev,
const char *  iofmt,
const char *  thost,
const char *  fname
 

Read a flat-file format parameter database.

Author:
Nathan Baker
Parameters:
thee Vparam 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 (see note below for format)
Returns:
1 if successful, 0 otherwise
Note:
The database file should have the following format:
RESIDUE ATOM CHARGE RADIUS EPSILON
where RESIDUE is the residue name string, ATOM is the atom name string, CHARGE is the charge in e, RADIUS is the van der Waals radius ($\sigma_i$) in Å, and EPSILON is the van der Waals well-depth ($\epsilon_i$) in kJ/mol. See the Vparam structure documentation for the precise definitions of $\sigma_i$ and $\epsilon_i$.
ASCII-format flat files are provided with the APBS source code:
tools/conversion/vparam-amber-parm94.dat
AMBER parm94 parameters
tools/conversion/vparam-charmm-par_all27.dat
CHARMM par_all27_prot_na parameters

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int Vparam_readXMLFile Vparam thee,
const char *  iodev,
const char *  iofmt,
const char *  thost,
const char *  fname
 

Read an XML format parameter database.

Author:
Todd Dolinsky
Parameters:
thee Vparam 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

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void Vparam_ResData_copyTo Vparam_ResData thee,
Vparam_ResData dest
 

Copy current residue object to destination.

Author:
Todd Dolinsky
Parameters:
thee Pointer to source object
dest Pointer to destination object

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Vparam_ResData* Vparam_ResData_ctor Vmem *  mem  ) 
 

Construct the object.

Author:
Nathan Baker
Parameters:
mem Memory object of Vparam master class
Returns:
Newly allocated object

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int Vparam_ResData_ctor2 Vparam_ResData thee,
Vmem *  mem
 

FORTRAN stub to construct the object.

Author:
Nathan Baker
Parameters:
thee Allocated memory
mem Memory object of Vparam master class
Returns:
1 if successful, 0 otherwise

void Vparam_ResData_dtor Vparam_ResData **  thee  ) 
 

Destroy object.

Author:
Nathan Baker
Parameters:
thee Pointer to memory location of object

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void Vparam_ResData_dtor2 Vparam_ResData thee  ) 
 

FORTRAN stub to destroy object.

Author:
Nathan Baker
Parameters:
thee Pointer to object


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