APBS
1.4.1
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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. More... | |
VPRIVATE int | readXMLFileAtom (Vio *sock, Vparam_AtomData *atom) |
Read atom information from an XML file. More... | |
VEXTERNC unsigned long int | Vparam_memChk (Vparam *thee) |
Get number of bytes in this object and its members. More... | |
VEXTERNC Vparam_AtomData * | Vparam_AtomData_ctor () |
Construct the object. More... | |
VEXTERNC int | Vparam_AtomData_ctor2 (Vparam_AtomData *thee) |
FORTRAN stub to construct the object. More... | |
VEXTERNC void | Vparam_AtomData_dtor (Vparam_AtomData **thee) |
Destroy object. More... | |
VEXTERNC void | Vparam_AtomData_dtor2 (Vparam_AtomData *thee) |
FORTRAN stub to destroy object. More... | |
VEXTERNC void | Vparam_AtomData_copyTo (Vparam_AtomData *thee, Vparam_AtomData *dest) |
Copy current atom object to destination. More... | |
VEXTERNC void | Vparam_ResData_copyTo (Vparam_ResData *thee, Vparam_ResData *dest) |
Copy current residue object to destination. More... | |
VEXTERNC void | Vparam_AtomData_copyFrom (Vparam_AtomData *thee, Vparam_AtomData *src) |
Copy current atom object from another. More... | |
VEXTERNC Vparam_ResData * | Vparam_ResData_ctor (Vmem *mem) |
Construct the object. More... | |
VEXTERNC int | Vparam_ResData_ctor2 (Vparam_ResData *thee, Vmem *mem) |
FORTRAN stub to construct the object. More... | |
VEXTERNC void | Vparam_ResData_dtor (Vparam_ResData **thee) |
Destroy object. More... | |
VEXTERNC void | Vparam_ResData_dtor2 (Vparam_ResData *thee) |
FORTRAN stub to destroy object. More... | |
VEXTERNC Vparam * | Vparam_ctor () |
Construct the object. More... | |
VEXTERNC int | Vparam_ctor2 (Vparam *thee) |
FORTRAN stub to construct the object. More... | |
VEXTERNC void | Vparam_dtor (Vparam **thee) |
Destroy object. More... | |
VEXTERNC void | Vparam_dtor2 (Vparam *thee) |
FORTRAN stub to destroy object. More... | |
VEXTERNC Vparam_ResData * | Vparam_getResData (Vparam *thee, char resName[VMAX_ARGLEN]) |
Get residue data. More... | |
VEXTERNC Vparam_AtomData * | Vparam_getAtomData (Vparam *thee, char resName[VMAX_ARGLEN], char atomName[VMAX_ARGLEN]) |
Get atom data. More... | |
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. More... | |
VEXTERNC int | Vparam_readXMLFile (Vparam *thee, const char *iodev, const char *iofmt, const char *thost, const char *fname) |
Read an XML format parameter database. More... | |
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. | |
Reads and assigns charge/radii parameters.
VPRIVATE int readFlatFileLine | ( | Vio * | sock, |
Vparam_AtomData * | atom | ||
) |
VPRIVATE int readXMLFileAtom | ( | Vio * | sock, |
Vparam_AtomData * | atom | ||
) |
VEXTERNC void Vparam_AtomData_copyFrom | ( | Vparam_AtomData * | thee, |
Vparam_AtomData * | src | ||
) |
VEXTERNC void Vparam_AtomData_copyTo | ( | Vparam_AtomData * | thee, |
Vparam_AtomData * | dest | ||
) |
VEXTERNC Vparam_AtomData* Vparam_AtomData_ctor | ( | ) |
VEXTERNC int Vparam_AtomData_ctor2 | ( | Vparam_AtomData * | thee | ) |
VEXTERNC void Vparam_AtomData_dtor | ( | Vparam_AtomData ** | thee | ) |
VEXTERNC void Vparam_AtomData_dtor2 | ( | Vparam_AtomData * | thee | ) |
VEXTERNC Vparam* Vparam_ctor | ( | ) |
VEXTERNC int Vparam_ctor2 | ( | Vparam * | thee | ) |
VEXTERNC void Vparam_dtor | ( | Vparam ** | thee | ) |
VEXTERNC void Vparam_dtor2 | ( | Vparam * | thee | ) |
VEXTERNC Vparam_AtomData* Vparam_getAtomData | ( | Vparam * | thee, |
char | resName[VMAX_ARGLEN], | ||
char | atomName[VMAX_ARGLEN] | ||
) |
Get atom data.
thee | Vparam object |
resName | Residue name |
atomName | Atom name |
VEXTERNC Vparam_ResData* Vparam_getResData | ( | Vparam * | thee, |
char | resName[VMAX_ARGLEN] | ||
) |
Get residue data.
thee | Vparam object |
resName | Residue name |
VEXTERNC unsigned long int Vparam_memChk | ( | Vparam * | thee | ) |
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.
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) |
RESIDUE ATOM CHARGE RADIUS EPSILONwhere 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 (
ASCII-format flat files are provided with the APBS source code:
VEXTERNC int Vparam_readXMLFile | ( | Vparam * | thee, |
const char * | iodev, | ||
const char * | iofmt, | ||
const char * | thost, | ||
const char * | fname | ||
) |
VEXTERNC void Vparam_ResData_copyTo | ( | Vparam_ResData * | thee, |
Vparam_ResData * | dest | ||
) |
VEXTERNC Vparam_ResData* Vparam_ResData_ctor | ( | Vmem * | mem | ) |
VEXTERNC int Vparam_ResData_ctor2 | ( | Vparam_ResData * | thee, |
Vmem * | mem | ||
) |
VEXTERNC void Vparam_ResData_dtor | ( | Vparam_ResData ** | thee | ) |
VEXTERNC void Vparam_ResData_dtor2 | ( | Vparam_ResData * | thee | ) |