Data Structures | Files | Typedefs | Functions | Variables

Vparam class

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

Data Structures

struct  sVparam_AtomData
 AtomData sub-class; stores atom data. More...
struct  Vparam_ResData
 ResData sub-class; stores residue data. More...
struct  Vparam
 Reads and assigns charge/radii parameters. More...

Files

file  vparam.h
 

Contains declarations for class Vparam.


file  vparam.c
 

Class Vparam methods.


Typedefs

typedef struct sVparam_AtomData Vparam_AtomData
 Declaration of the Vparam_AtomData class as the sVparam_AtomData structure.
typedef struct Vparam_ResData Vparam_ResData
 Declaration of the Vparam_ResData class as the Vparam_ResData structure.
typedef struct Vparam Vparam
 Declaration of the Vparam class as the Vparam structure.

Functions

VEXTERNC unsigned long int Vparam_memChk (Vparam *thee)
 Get number of bytes in this object and its members.
VEXTERNC Vparam_AtomDataVparam_AtomData_ctor ()
 Construct the object.
VEXTERNC int Vparam_AtomData_ctor2 (Vparam_AtomData *thee)
 FORTRAN stub to construct the object.
VEXTERNC void Vparam_AtomData_dtor (Vparam_AtomData **thee)
 Destroy object.
VEXTERNC void Vparam_AtomData_dtor2 (Vparam_AtomData *thee)
 FORTRAN stub to destroy object.
VEXTERNC void Vparam_AtomData_copyTo (Vparam_AtomData *thee, Vparam_AtomData *dest)
 Copy current atom object to destination.
VEXTERNC void Vparam_ResData_copyTo (Vparam_ResData *thee, Vparam_ResData *dest)
 Copy current residue object to destination.
VEXTERNC void Vparam_AtomData_copyFrom (Vparam_AtomData *thee, Vparam_AtomData *src)
 Copy current atom object from another.
VEXTERNC Vparam_ResDataVparam_ResData_ctor (Vmem *mem)
 Construct the object.
VEXTERNC int Vparam_ResData_ctor2 (Vparam_ResData *thee, Vmem *mem)
 FORTRAN stub to construct the object.
VEXTERNC void Vparam_ResData_dtor (Vparam_ResData **thee)
 Destroy object.
VEXTERNC void Vparam_ResData_dtor2 (Vparam_ResData *thee)
 FORTRAN stub to destroy object.
VEXTERNC VparamVparam_ctor ()
 Construct the object.
VEXTERNC int Vparam_ctor2 (Vparam *thee)
 FORTRAN stub to construct the object.
VEXTERNC void Vparam_dtor (Vparam **thee)
 Destroy object.
VEXTERNC void Vparam_dtor2 (Vparam *thee)
 FORTRAN stub to destroy object.
VEXTERNC Vparam_ResDataVparam_getResData (Vparam *thee, char resName[VMAX_ARGLEN])
 Get residue data.
VEXTERNC Vparam_AtomDataVparam_getAtomData (Vparam *thee, char resName[VMAX_ARGLEN], char atomName[VMAX_ARGLEN])
 Get atom data.
VEXTERNC int Vparam_readFlatFile (Vparam *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname)
 Read a flat-file format parameter database.
VEXTERNC 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:
sockSocket ready for reading
atomAtom to hold parsed data
Returns:
1 if successful, 0 otherwise

Definition at line 688 of file vparam.c.

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VPRIVATE int readXMLFileAtom ( Vio *  sock,
Vparam_AtomData atom 
)

Read atom information from an XML file.

Author:
Todd Dolinsky
Parameters:
sockSocket ready for reading
atomAtom to hold parsed data
Returns:
1 if successful, 0 otherwise

Definition at line 607 of file vparam.c.

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VEXTERNC void Vparam_AtomData_copyFrom ( Vparam_AtomData thee,
Vparam_AtomData src 
)

Copy current atom object from another.

Author:
Nathan Baker
Parameters:
theePointer to destination object
srcPointer to source object

Definition at line 604 of file vparam.c.

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VEXTERNC void Vparam_AtomData_copyTo ( Vparam_AtomData thee,
Vparam_AtomData dest 
)

Copy current atom object to destination.

Author:
Nathan Baker
Parameters:
theePointer to source object
destPointer to destination object

Definition at line 568 of file vparam.c.

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VEXTERNC Vparam_AtomData* Vparam_AtomData_ctor (  )

Construct the object.

Author:
Nathan Baker
Returns:
Newly allocated object

Definition at line 106 of file vparam.c.

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VEXTERNC int Vparam_AtomData_ctor2 ( Vparam_AtomData thee )

FORTRAN stub to construct the object.

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

Definition at line 118 of file vparam.c.

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VEXTERNC void Vparam_AtomData_dtor ( Vparam_AtomData **  thee )

Destroy object.

Author:
Nathan Baker
Parameters:
theePointer to memory location of object

Definition at line 120 of file vparam.c.

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VEXTERNC void Vparam_AtomData_dtor2 ( Vparam_AtomData thee )

FORTRAN stub to destroy object.

Author:
Nathan Baker
Parameters:
theePointer to object

Definition at line 130 of file vparam.c.

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VEXTERNC Vparam* Vparam_ctor (  )

Construct the object.

Author:
Nathan Baker
Returns:
Newly allocated Vparam object

Definition at line 178 of file vparam.c.

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VEXTERNC int Vparam_ctor2 ( Vparam thee )

FORTRAN stub to construct the object.

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

Definition at line 190 of file vparam.c.

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VEXTERNC void Vparam_dtor ( Vparam **  thee )

Destroy object.

Author:
Nathan Baker
Parameters:
theePointer to memory location of object

Definition at line 210 of file vparam.c.

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VEXTERNC void Vparam_dtor2 ( Vparam thee )

FORTRAN stub to destroy object.

Author:
Nathan Baker
Parameters:
theePointer to object

Definition at line 220 of file vparam.c.

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

Get atom data.

Author:
Nathan Baker
Parameters:
theeVparam object
resNameResidue name
atomNameAtom 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)

Definition at line 264 of file vparam.c.

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VEXTERNC Vparam_ResData* Vparam_getResData ( Vparam thee,
char  resName[VMAX_ARGLEN] 
)

Get residue data.

Author:
Nathan Baker
Parameters:
theeVparam object
resNameResidue 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)

Definition at line 238 of file vparam.c.

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VEXTERNC unsigned long int Vparam_memChk ( Vparam thee )

Get number of bytes in this object and its members.

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

Definition at line 99 of file vparam.c.

VEXTERNC 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:
theeVparam object
iodevInput device type (FILE/BUFF/UNIX/INET)
iofmtInput device format (ASCII/XDR)
thostInput hostname (for sockets)
fnameInput 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

Definition at line 442 of file vparam.c.

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VEXTERNC 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:
theeVparam object
iodevInput device type (FILE/BUFF/UNIX/INET)
iofmtInput device format (ASCII/XDR)
thostInput hostname (for sockets)
fnameInput FILE/BUFF/UNIX/INET name
Returns:
1 if successful, 0 otherwise

Definition at line 303 of file vparam.c.

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VEXTERNC void Vparam_ResData_copyTo ( Vparam_ResData thee,
Vparam_ResData dest 
)

Copy current residue object to destination.

Author:
Todd Dolinsky
Parameters:
theePointer to source object
destPointer to destination object

Definition at line 582 of file vparam.c.

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VEXTERNC Vparam_ResData* Vparam_ResData_ctor ( Vmem *  mem )

Construct the object.

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

Definition at line 132 of file vparam.c.

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VEXTERNC int Vparam_ResData_ctor2 ( Vparam_ResData thee,
Vmem *  mem 
)

FORTRAN stub to construct the object.

Author:
Nathan Baker
Parameters:
theeAllocated memory
memMemory object of Vparam master class
Returns:
1 if successful, 0 otherwise

Definition at line 144 of file vparam.c.

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VEXTERNC void Vparam_ResData_dtor ( Vparam_ResData **  thee )

Destroy object.

Author:
Nathan Baker
Parameters:
theePointer to memory location of object

Definition at line 157 of file vparam.c.

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VEXTERNC void Vparam_ResData_dtor2 ( Vparam_ResData thee )

FORTRAN stub to destroy object.

Author:
Nathan Baker
Parameters:
theePointer to object

Definition at line 167 of file vparam.c.

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