APBS 3.0.0
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Files | Data Structures | Typedefs | Functions | Variables
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_ResData
 ResData sub-class; stores residue data. More...
 
struct  Vparam
 Reads and assigns charge/radii parameters. More...
 

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

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.
 
VEXTERNC unsigned long int Vparam_memChk (Vparam *thee)
 Get number of bytes in this object and its members.
 
VEXTERNC Vparam_AtomData * Vparam_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_ResData * Vparam_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 Vparam * Vparam_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_ResData * Vparam_getResData (Vparam *thee, char resName[VMAX_ARGLEN])
 Get residue data.
 
VEXTERNC Vparam_AtomData * Vparam_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.
 

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.

Typedef Documentation

◆ Vparam

typedef struct Vparam Vparam

Declaration of the Vparam class as the Vparam structure.

Definition at line 147 of file vparam.h.

◆ Vparam_AtomData

typedef struct sVparam_AtomData Vparam_AtomData

Declaration of the Vparam_AtomData class as the sVparam_AtomData structure.

Definition at line 106 of file vparam.h.

◆ Vparam_ResData

typedef struct Vparam_ResData Vparam_ResData

Declaration of the Vparam_ResData class as the Vparam_ResData structure.

Definition at line 127 of file vparam.h.

Function Documentation

◆ readFlatFileLine()

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 691 of file vparam.c.

◆ readXMLFileAtom()

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 610 of file vparam.c.

◆ Vparam_AtomData_copyFrom()

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 607 of file vparam.c.

◆ Vparam_AtomData_copyTo()

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 571 of file vparam.c.

◆ Vparam_AtomData_ctor()

VEXTERNC Vparam_AtomData * Vparam_AtomData_ctor ( )

Construct the object.

Author
Nathan Baker
Returns
Newly allocated object

Definition at line 109 of file vparam.c.

◆ Vparam_AtomData_ctor2()

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 121 of file vparam.c.

◆ Vparam_AtomData_dtor()

VEXTERNC void Vparam_AtomData_dtor ( Vparam_AtomData ** thee)

Destroy object.

Author
Nathan Baker
Parameters
theePointer to memory location of object

Definition at line 123 of file vparam.c.

◆ Vparam_AtomData_dtor2()

VEXTERNC void Vparam_AtomData_dtor2 ( Vparam_AtomData * thee)

FORTRAN stub to destroy object.

Author
Nathan Baker
Parameters
theePointer to object

Definition at line 133 of file vparam.c.

◆ Vparam_ctor()

VEXTERNC Vparam * Vparam_ctor ( )

Construct the object.

Author
Nathan Baker
Returns
Newly allocated Vparam object

Definition at line 181 of file vparam.c.

◆ Vparam_ctor2()

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 193 of file vparam.c.

◆ Vparam_dtor()

VEXTERNC void Vparam_dtor ( Vparam ** thee)

Destroy object.

Author
Nathan Baker
Parameters
theePointer to memory location of object

Definition at line 213 of file vparam.c.

◆ Vparam_dtor2()

VEXTERNC void Vparam_dtor2 ( Vparam * thee)

FORTRAN stub to destroy object.

Author
Nathan Baker
Parameters
theePointer to object

Definition at line 223 of file vparam.c.

◆ Vparam_getAtomData()

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 267 of file vparam.c.

◆ Vparam_getResData()

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 241 of file vparam.c.

◆ Vparam_memChk()

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 102 of file vparam.c.

◆ Vparam_readFlatFile()

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 445 of file vparam.c.

◆ Vparam_readXMLFile()

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 306 of file vparam.c.

◆ Vparam_ResData_copyTo()

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 585 of file vparam.c.

◆ Vparam_ResData_ctor()

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 135 of file vparam.c.

◆ Vparam_ResData_ctor2()

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 147 of file vparam.c.

◆ Vparam_ResData_dtor()

VEXTERNC void Vparam_ResData_dtor ( Vparam_ResData ** thee)

Destroy object.

Author
Nathan Baker
Parameters
theePointer to memory location of object

Definition at line 160 of file vparam.c.

◆ Vparam_ResData_dtor2()

VEXTERNC void Vparam_ResData_dtor2 ( Vparam_ResData * thee)

FORTRAN stub to destroy object.

Author
Nathan Baker
Parameters
theePointer to object

Definition at line 170 of file vparam.c.

Variable Documentation

◆ MCcommChars

VPRIVATE char* MCcommChars = "#%"

Comment characters for socket reads.

Definition at line 71 of file vparam.c.

◆ MCwhiteChars

VPRIVATE char* MCwhiteChars = " =,;\t\n\r"

Whitespace characters for socket reads.

Definition at line 65 of file vparam.c.

◆ MCxmlwhiteChars

VPRIVATE char* MCxmlwhiteChars = " =,;\t\n\r<>"

Whitespace characters for XML socket reads.

Definition at line 77 of file vparam.c.