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NOsh class

Class for parsing for fixed format input files. More...


Files

file  nosh.h
 Contains declarations for class NOsh.


Data Structures

struct  sNOsh
 Class for parsing fixed format input files. More...

struct  sNOsh_calc
 Calculation class for use when parsing fixed format input files. More...


Defines

#define NOSH_MAXMOL   20
 Maximum number of molecules in a run.

#define NOSH_MAXCALC   20
 Maximum number of calculations in a run.

#define NOSH_MAXPRINT   20
 Maximum number of PRINT statements in a run.

#define NOSH_MAXPOP   20
 Maximum number of operations in a PRINT statement.


Typedefs

typedef enum eNOsh_MolFormat NOsh_MolFormat
 Declare NOsh_MolFormat type.

typedef enum eNOsh_ParmFormat NOsh_ParmFormat
 Declare NOsh_ParmFormat type.

typedef sNOsh NOsh
 Declaration of the NOsh class as the NOsh structure.

typedef sNOsh_calc NOsh_calc
 Declaration of the NOsh_calc class as the NOsh_calc structure.


Enumerations

enum  eNOsh_MolFormat {
  NMF_PQR = 0,
  NMF_PDB = 1
}
 Molecule file format types. More...

enum  eNOsh_ParmFormat { NPF_FLAT = 0 }
 Parameter file format types. More...


Functions

char * NOsh_getMolpath (NOsh *thee, int imol)
 Returns path to specified molecule.

char * NOsh_getDielXpath (NOsh *thee, int imap)
 Returns path to specified x-shifted dielectric map.

char * NOsh_getDielYpath (NOsh *thee, int imap)
 Returns path to specified y-shifted dielectric map.

char * NOsh_getDielZpath (NOsh *thee, int imap)
 Returns path to specified z-shifted dielectric map.

char * NOsh_getKappapath (NOsh *thee, int imap)
 Returns path to specified kappa map.

char * NOsh_getChargepath (NOsh *thee, int imap)
 Returns path to specified charge distribution map.

NOsh_calcNOsh_getCalc (NOsh *thee, int icalc)
 Returns specified calculation object.

int NOsh_getDielfmt (NOsh *thee, int imap)
 Returns format of specified dielectric map.

int NOsh_getKappafmt (NOsh *thee, int imap)
 Returns format of specified kappa map.

int NOsh_getChargefmt (NOsh *thee, int imap)
 Returns format of specified charge map.

int NOsh_printWhat (NOsh *thee, int iprint)
 Return an integer ID of the observable to print (
See also:
printwhat).


char * NOsh_elecname (NOsh *thee, int ielec)
 Return an integer mapping of an ELEC statement to a calculation ID (
See also:
elec2calc).


int NOsh_elec2calc (NOsh *thee, int icalc)
 Return the name of an elec statement.

int NOsh_printNarg (NOsh *thee, int iprint)
 Return number of arguments to PRINT statement (
See also:
printnarg).


int NOsh_printOp (NOsh *thee, int iprint, int iarg)
 Return integer ID for specified operation (
See also:
printop).


int NOsh_printCalc (NOsh *thee, int iprint, int iarg)
 Return calculation ID for specified PRINT statement (
See also:
printcalc).


NOsh * NOsh_ctor (int rank, int size)
 Construct NOsh.

int NOsh_ctor2 (NOsh *thee, int rank, int size)
 FORTRAN stub to construct NOsh.

void NOsh_dtor (NOsh **thee)
 Object destructor.

void NOsh_dtor2 (NOsh *thee)
 FORTRAN stub for object destructor.

int NOsh_parse (NOsh *thee, Vio *sock)
 Parse an input file from a socket.

int NOsh_parseFile (NOsh *thee, char *filename)
 Parse an input file only from a file.

int NOsh_setupMGMANUAL (NOsh *thee, MGparm *mgparm, PBEparm *pbeparm)
 Setup NOsh, MGparm, and PBEparm objects for a MG-MANUAL ELEC calculation.

int NOsh_setupMGAUTO (NOsh *thee, MGparm *mgparm, PBEparm *pbeparm)
 Setup NOsh, MGparm, and PBEparm objects for a MG-AUTO ELEC calculation.

int NOsh_setupMGPARA (NOsh *thee, MGparm *mgparm, PBEparm *pbeparm)
 Setup NOsh, MGparm, and PBEparm objects for a MG-PARA ELEC calculation.


Detailed Description

Class for parsing for fixed format input files.


Enumeration Type Documentation

enum eNOsh_MolFormat
 

Molecule file format types.

Enumeration values:
NMF_PQR  PQR format
NMF_PDB  PDB format

enum eNOsh_ParmFormat
 

Parameter file format types.

Enumeration values:
NPF_FLAT  Flat-file format


Function Documentation

NOsh* NOsh_ctor int    rank,
int    size
 

Construct NOsh.

Author:
Nathan Baker
Parameters:
rank  Rank of current processor in parallel calculation (0 if not parallel)
size  Number of processors in parallel calculation (1 if not parallel)
Returns:
Newly allocated and initialized NOsh object

int NOsh_ctor2 NOsh   thee,
int    rank,
int    size
 

FORTRAN stub to construct NOsh.

Author:
Nathan Baker
Parameters:
thee  Space for NOsh objet
rank  Rank of current processor in parallel calculation (0 if not parallel)
size  Number of processors in parallel calculation (1 if not parallel)
Returns:
1 if successful, 0 otherwise

void NOsh_dtor NOsh **    thee
 

Object destructor.

Author:
Nathan Baker
Parameters:
thee  Pointer to memory location of NOsh object

void NOsh_dtor2 NOsh   thee
 

FORTRAN stub for object destructor.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object

int NOsh_elec2calc NOsh   thee,
int    icalc
 

Return the name of an elec statement.

Author:
Todd Dolinsky
Parameters:
thee  NOsh object to use
ielec  ID of ELEC statement
Returns:
The name (if present) of an ELEC statement

char* NOsh_elecname NOsh   thee,
int    ielec
 

Return an integer mapping of an ELEC statement to a calculation ID (

See also:
elec2calc).

Author:
Nathan Baker
Parameters:
thee  NOsh object to use
icalc  ID of CALC statement
Returns:
An integer mapping of an ELEC statement to a calculation ID (
See also:
elec2calc)

NOsh_calc* NOsh_getCalc NOsh   thee,
int    icalc
 

Returns specified calculation object.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
icalc  Calculation ID of interest
Returns:
Pointer to specified calculation object

int NOsh_getChargefmt NOsh   thee,
int    imap
 

Returns format of specified charge map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Calculation ID of interest
Returns:
Format of charge map

char* NOsh_getChargepath NOsh   thee,
int    imap
 

Returns path to specified charge distribution map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Map ID of interest
Returns:
Path string

int NOsh_getDielfmt NOsh   thee,
int    imap
 

Returns format of specified dielectric map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Calculation ID of interest
Returns:
Format of dielectric map

char* NOsh_getDielXpath NOsh   thee,
int    imap
 

Returns path to specified x-shifted dielectric map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Map ID of interest
Returns:
Path string

char* NOsh_getDielYpath NOsh   thee,
int    imap
 

Returns path to specified y-shifted dielectric map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Map ID of interest
Returns:
Path string

char* NOsh_getDielZpath NOsh   thee,
int    imap
 

Returns path to specified z-shifted dielectric map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Map ID of interest
Returns:
Path string

int NOsh_getKappafmt NOsh   thee,
int    imap
 

Returns format of specified kappa map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Calculation ID of interest
Returns:
Format of kappa map

char* NOsh_getKappapath NOsh   thee,
int    imap
 

Returns path to specified kappa map.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imap  Map ID of interest
Returns:
Path string

char* NOsh_getMolpath NOsh   thee,
int    imol
 

Returns path to specified molecule.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
imol  Molecule ID of interest
Returns:
Path string

int NOsh_parse NOsh   thee,
Vio *    sock
 

Parse an input file from a socket.

Author:
Nathan Baker and Todd Dolinsky
Parameters:
thee  Pointer to NOsh object
sock  Stream of tokens to parse
Returns:
1 if successful, 0 otherwise

int NOsh_parseFile NOsh   thee,
char *    filename
 

Parse an input file only from a file.

Note:
Included for SWIG wrapper compatibility
Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
filename  Name/path of readable file
Returns:
1 if successful, 0 otherwise

int NOsh_printCalc NOsh   thee,
int    iprint,
int    iarg
 

Return calculation ID for specified PRINT statement (

See also:
printcalc).

Author:
Nathan Baker
Parameters:
thee  NOsh object to use
iprint  ID of PRINT statement
iarg  ID of operation in PRINT statement
Returns:
Calculation ID for specified PRINT statement (
See also:
printcalc)

int NOsh_printNarg NOsh   thee,
int    iprint
 

Return number of arguments to PRINT statement (

See also:
printnarg).

Author:
Nathan Baker
Parameters:
thee  NOsh object to use
iprint  ID of PRINT statement
Returns:
Number of arguments to PRINT statement (
See also:
printnarg)

int NOsh_printOp NOsh   thee,
int    iprint,
int    iarg
 

Return integer ID for specified operation (

See also:
printop).

Author:
Nathan Baker
Parameters:
thee  NOsh object to use
iprint  ID of PRINT statement
iarg  ID of operation in PRINT statement
Returns:
Integer ID for specified operation (
See also:
printop)

int NOsh_printWhat NOsh   thee,
int    iprint
 

Return an integer ID of the observable to print (

See also:
printwhat).

Author:
Nathan Baker
Parameters:
thee  NOsh object to use
iprint  ID of PRINT statement
Returns:
An integer ID of the observable to print (
See also:
printwhat)

int NOsh_setupMGAUTO NOsh   thee,
MGparm   mgparm,
PBEparm   pbeparm
 

Setup NOsh, MGparm, and PBEparm objects for a MG-AUTO ELEC calculation.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
mgparm  Pointer to base MGparm object containing parameters for the run; these will be used to construct the MGparm objects inside the NOsh object (for actual use by the code during calculations)
pbeparm  Pointer to PBEparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function
Returns:
1 if successful, 0 otherwise

int NOsh_setupMGMANUAL NOsh   thee,
MGparm   mgparm,
PBEparm   pbeparm
 

Setup NOsh, MGparm, and PBEparm objects for a MG-MANUAL ELEC calculation.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
mgparm  Pointer to MGparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function
pbeparm  Pointer to PBEparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function
Returns:
1 if successful, 0 otherwise

int NOsh_setupMGPARA NOsh   thee,
MGparm   mgparm,
PBEparm   pbeparm
 

Setup NOsh, MGparm, and PBEparm objects for a MG-PARA ELEC calculation.

Author:
Nathan Baker
Parameters:
thee  Pointer to NOsh object
mgparm  Pointer to base MGparm object containing parameters for the run; these will be used to construct the MGparm objects inside the NOsh object (for actual use by the code during calculations)
pbeparm  Pointer to PBEparm object containing basic parameters for run; these will be supplemented and modified (for consistency, etc.) by this function
Returns:
1 if successful, 0 otherwise


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