APBS 3.0.0
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Parameter which holds useful parameters for Poisson-boltzmann analytical method calculations. More...
Files | |
file | pbamparm.c |
Class PBAMparm methods. | |
file | pbamparm.h |
Contains declarations for class PBAMparm. | |
Data Structures | |
struct | sPBAMparm |
Parameter structure for PBAM-specific variables from input files. More... | |
Macros | |
#define | CHR_MAXLEN 1000 |
Number of things that can be written out in a single calculation. | |
Typedefs | |
typedef enum ePBAMparm_CalcType | PBAMparm_CalcType |
Declare PBAMparm_CalcType type. | |
typedef struct sPBAMparm | PBAMparm |
Parameter structure for PBAM-specific variables from input files. | |
Enumerations | |
enum | ePBAMparm_CalcType { PBAMCT_AUTO =1 } |
Calculation type. More... | |
Functions | |
VEXTERNC PBAMparm * | PBAMparm_ctor (PBAMparm_CalcType type) |
Construct PBAMparm object. | |
VEXTERNC Vrc_Codes | PBAMparm_ctor2 (PBAMparm *thee, PBAMparm_CalcType type) |
FORTRAN stub to construct PBAMparm object ?????????!!!!!!! | |
VEXTERNC void | PBAMparm_dtor (PBAMparm **thee) |
Object destructor. | |
VEXTERNC void | PBAMparm_dtor2 (PBAMparm *thee) |
FORTRAN stub for object destructor ?????????!!!!!!!!!!!! | |
VEXTERNC Vrc_Codes | PBAMparm_check (PBAMparm *thee) |
Consistency check for parameter values stored in object. | |
VEXTERNC Vrc_Codes | PBAMparm_parseToken (PBAMparm *thee, char tok[VMAX_BUFSIZE], Vio *sock) |
Parse an MG keyword from an input file. | |
VEXTERNC void | PBAMparm_copy (PBAMparm *thee, PBAMparm *parm) |
copy PBAMparm object int thee. | |
VPRIVATE Vrc_Codes | PBAMparm_parseSalt (PBAMparm *thee, Vio *sock) |
Find salt conc and save it as a structure variable. | |
VPRIVATE Vrc_Codes | PBAMparm_parseRunType (PBAMparm *thee, Vio *sock) |
Find runType and save it as a structure variable. | |
VPRIVATE Vrc_Codes | PBAMparm_parseRunName (PBAMparm *thee, Vio *sock) |
Find runName and save it as a structure variable. | |
VPRIVATE Vrc_Codes | PBAMparm_parseRandorient (PBAMparm *thee, Vio *sock) |
Find randomorientation flag and save it as a boolean. | |
VPRIVATE Vrc_Codes | PBAMparm_parsePBCS (PBAMparm *thee, Vio *sock) |
Find PBC flag and save the type and the boxlength. | |
VPRIVATE Vrc_Codes | PBAMparm_parseUnits (PBAMparm *thee, Vio *sock) |
Find units flag and save units. | |
VPRIVATE Vrc_Codes | PBAMparm_parse3Dmap (PBAMparm *thee, Vio *sock) |
Find 3D map filename and save it. | |
VPRIVATE Vrc_Codes | PBAMparm_parseGrid2D (PBAMparm *thee, Vio *sock) |
Find 2D grid filename and save it. | |
VPRIVATE Vrc_Codes | PBAMparm_parseDX (PBAMparm *thee, Vio *sock) |
Find DX filename and save it. | |
VPRIVATE Vrc_Codes | PBAMparm_parseGridPts (PBAMparm *thee, Vio *sock) |
Find Grid points and save them. | |
VPRIVATE Vrc_Codes | PBAMparm_parseTermcombine (PBAMparm *thee, Vio *sock) |
Find Termination logic and save it. | |
VPRIVATE Vrc_Codes | PBAMparm_parseDiff (PBAMparm *thee, Vio *sock) |
Find diffusion coeffs for each molecule and save them. | |
VPRIVATE Vrc_Codes | PBAMparm_parseXYZ (PBAMparm *thee, Vio *sock) |
Find xyz files for each molecule for each traj and save them. | |
Parameter which holds useful parameters for Poisson-boltzmann analytical method calculations.
#define CHR_MAXLEN 1000 |
Number of things that can be written out in a single calculation.
Definition at line 76 of file pbamparm.h.
Parameter structure for PBAM-specific variables from input files.
typedef enum ePBAMparm_CalcType PBAMparm_CalcType |
Declare PBAMparm_CalcType type.
Definition at line 95 of file pbamparm.h.
enum ePBAMparm_CalcType |
VEXTERNC Vrc_Codes PBAMparm_check | ( | PBAMparm * | thee | ) |
Consistency check for parameter values stored in object.
thee | PBAMparm object |
Definition at line 132 of file pbamparm.c.
copy PBAMparm object int thee.
thee | PBAMparm object to be copied into |
parm | PBAMparm object. |
Definition at line 157 of file pbamparm.c.
VEXTERNC PBAMparm * PBAMparm_ctor | ( | PBAMparm_CalcType | type | ) |
Construct PBAMparm object.
type | Type of PBAM calculation |
Definition at line 66 of file pbamparm.c.
VEXTERNC Vrc_Codes PBAMparm_ctor2 | ( | PBAMparm * | thee, |
PBAMparm_CalcType | type ) |
FORTRAN stub to construct PBAMparm object ?????????!!!!!!!
thee | Space for PBAMparm object |
type | Type of MG calculation |
Definition at line 77 of file pbamparm.c.
VEXTERNC void PBAMparm_dtor | ( | PBAMparm ** | thee | ) |
Object destructor.
thee | Pointer to memory location of PBAMparm object |
Definition at line 122 of file pbamparm.c.
VEXTERNC void PBAMparm_dtor2 | ( | PBAMparm * | thee | ) |
FORTRAN stub for object destructor ?????????!!!!!!!!!!!!
thee | Pointer to PBAMparm object |
Definition at line 130 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parse3Dmap | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find 3D map filename and save it.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 371 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseDiff | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find diffusion coeffs for each molecule and save them.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 477 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseDX | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find DX filename and save it.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 426 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseGrid2D | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find 2D grid filename and save it.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 391 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseGridPts | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find Grid points and save them.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 351 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parsePBCS | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find PBC flag and save the type and the boxlength.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 310 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseRandorient | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find randomorientation flag and save it as a boolean.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 304 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseRunName | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find runName and save it as a structure variable.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 289 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseRunType | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find runType and save it as a structure variable.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 271 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseSalt | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find salt conc and save it as a structure variable.
thee | PBAMparm object to be copied into |
parm | The stream from which parameter is taken |
Definition at line 252 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseTermcombine | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find Termination logic and save it.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 444 of file pbamparm.c.
VEXTERNC Vrc_Codes PBAMparm_parseToken | ( | PBAMparm * | thee, |
char | tok[VMAX_BUFSIZE], | ||
Vio * | sock ) |
Parse an MG keyword from an input file.
thee | PBAMparm object |
tok | Token to parse |
sock | Stream for more tokens |
Definition at line 662 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseUnits | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find units flag and save units.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 336 of file pbamparm.c.
VPRIVATE Vrc_Codes PBAMparm_parseXYZ | ( | PBAMparm * | thee, |
Vio * | sock ) |
Find xyz files for each molecule for each traj and save them.
thee | PBAMparm object to be copied into |
sock | The stream from which parameter is taken |
Definition at line 632 of file pbamparm.c.