APBS 3.0.0
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PBAMparm class

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 PBAMparmPBAMparm_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.
 

Detailed Description

Parameter which holds useful parameters for Poisson-boltzmann analytical method calculations.

Macro Definition Documentation

◆ CHR_MAXLEN

#define CHR_MAXLEN   1000

Number of things that can be written out in a single calculation.

Definition at line 76 of file pbamparm.h.

Typedef Documentation

◆ PBAMparm

typedef struct sPBAMparm PBAMparm

Parameter structure for PBAM-specific variables from input files.

Author
Andrew Stevens, Kyle Monson
Note
If you add/delete/change something in this class, the member functions – especially PBAMparm_copy – must be modified accordingly

◆ PBAMparm_CalcType

Declare PBAMparm_CalcType type.

Definition at line 95 of file pbamparm.h.

Enumeration Type Documentation

◆ ePBAMparm_CalcType

Calculation type.

Enumerator
PBAMCT_AUTO 

PBAM-auto

Definition at line 84 of file pbamparm.h.

Function Documentation

◆ PBAMparm_check()

VEXTERNC Vrc_Codes PBAMparm_check ( PBAMparm * thee)

Consistency check for parameter values stored in object.

Author
Andrew Stevens, Kyle Monson
Parameters
theePBAMparm object
Returns
Success enumeration

Definition at line 132 of file pbamparm.c.

◆ PBAMparm_copy()

VEXTERNC void PBAMparm_copy ( PBAMparm * thee,
PBAMparm * parm )

copy PBAMparm object int thee.

Author
Parameters
theePBAMparm object to be copied into
parmPBAMparm object.

Definition at line 157 of file pbamparm.c.

◆ PBAMparm_ctor()

VEXTERNC PBAMparm * PBAMparm_ctor ( PBAMparm_CalcType type)

Construct PBAMparm object.

Author
Andrew Stevens, Kyle Monson
Parameters
typeType of PBAM calculation
Returns
Newly allocated and initialized PBAMparm object

Definition at line 66 of file pbamparm.c.

◆ PBAMparm_ctor2()

VEXTERNC Vrc_Codes PBAMparm_ctor2 ( PBAMparm * thee,
PBAMparm_CalcType type )

FORTRAN stub to construct PBAMparm object ?????????!!!!!!!

Author
Andrew Stevens, Kyle Monson
Parameters
theeSpace for PBAMparm object
typeType of MG calculation
Returns
Success enumeration

Definition at line 77 of file pbamparm.c.

◆ PBAMparm_dtor()

VEXTERNC void PBAMparm_dtor ( PBAMparm ** thee)

Object destructor.

Author
Andrew Stevens, Kyle Monson
Parameters
theePointer to memory location of PBAMparm object

Definition at line 122 of file pbamparm.c.

◆ PBAMparm_dtor2()

VEXTERNC void PBAMparm_dtor2 ( PBAMparm * thee)

FORTRAN stub for object destructor ?????????!!!!!!!!!!!!

Author
Andrew Stevens, Kyle Monson
Parameters
theePointer to PBAMparm object

Definition at line 130 of file pbamparm.c.

◆ PBAMparm_parse3Dmap()

VPRIVATE Vrc_Codes PBAMparm_parse3Dmap ( PBAMparm * thee,
Vio * sock )

Find 3D map filename and save it.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 371 of file pbamparm.c.

◆ PBAMparm_parseDiff()

VPRIVATE Vrc_Codes PBAMparm_parseDiff ( PBAMparm * thee,
Vio * sock )

Find diffusion coeffs for each molecule and save them.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 477 of file pbamparm.c.

◆ PBAMparm_parseDX()

VPRIVATE Vrc_Codes PBAMparm_parseDX ( PBAMparm * thee,
Vio * sock )

Find DX filename and save it.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 426 of file pbamparm.c.

◆ PBAMparm_parseGrid2D()

VPRIVATE Vrc_Codes PBAMparm_parseGrid2D ( PBAMparm * thee,
Vio * sock )

Find 2D grid filename and save it.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 391 of file pbamparm.c.

◆ PBAMparm_parseGridPts()

VPRIVATE Vrc_Codes PBAMparm_parseGridPts ( PBAMparm * thee,
Vio * sock )

Find Grid points and save them.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 351 of file pbamparm.c.

◆ PBAMparm_parsePBCS()

VPRIVATE Vrc_Codes PBAMparm_parsePBCS ( PBAMparm * thee,
Vio * sock )

Find PBC flag and save the type and the boxlength.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 310 of file pbamparm.c.

◆ PBAMparm_parseRandorient()

VPRIVATE Vrc_Codes PBAMparm_parseRandorient ( PBAMparm * thee,
Vio * sock )

Find randomorientation flag and save it as a boolean.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 304 of file pbamparm.c.

◆ PBAMparm_parseRunName()

VPRIVATE Vrc_Codes PBAMparm_parseRunName ( PBAMparm * thee,
Vio * sock )

Find runName and save it as a structure variable.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 289 of file pbamparm.c.

◆ PBAMparm_parseRunType()

VPRIVATE Vrc_Codes PBAMparm_parseRunType ( PBAMparm * thee,
Vio * sock )

Find runType and save it as a structure variable.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 271 of file pbamparm.c.

◆ PBAMparm_parseSalt()

VPRIVATE Vrc_Codes PBAMparm_parseSalt ( PBAMparm * thee,
Vio * sock )

Find salt conc and save it as a structure variable.

Author
Parameters
theePBAMparm object to be copied into
parmThe stream from which parameter is taken

Definition at line 252 of file pbamparm.c.

◆ PBAMparm_parseTermcombine()

VPRIVATE Vrc_Codes PBAMparm_parseTermcombine ( PBAMparm * thee,
Vio * sock )

Find Termination logic and save it.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 444 of file pbamparm.c.

◆ PBAMparm_parseToken()

VEXTERNC Vrc_Codes PBAMparm_parseToken ( PBAMparm * thee,
char tok[VMAX_BUFSIZE],
Vio * sock )

Parse an MG keyword from an input file.

Author
Andrew Stevens, Kyle Monson
Parameters
theePBAMparm object
tokToken to parse
sockStream for more tokens
Returns
Success enumeration (1 if matched and assigned; -1 if matched, but there's some sort of error (i.e., too few args); 0 if not matched)

Definition at line 662 of file pbamparm.c.

◆ PBAMparm_parseUnits()

VPRIVATE Vrc_Codes PBAMparm_parseUnits ( PBAMparm * thee,
Vio * sock )

Find units flag and save units.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 336 of file pbamparm.c.

◆ PBAMparm_parseXYZ()

VPRIVATE Vrc_Codes PBAMparm_parseXYZ ( PBAMparm * thee,
Vio * sock )

Find xyz files for each molecule for each traj and save them.

Author
Parameters
theePBAMparm object to be copied into
sockThe stream from which parameter is taken

Definition at line 632 of file pbamparm.c.