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NOsh class

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


Files

file  nosh.c
 Class NOsh methods.

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_CalcType NOsh_CalcType
 Declare NOsh_CalcType type.

typedef enum eNOsh_ParmFormat NOsh_ParmFormat
 Declare NOsh_ParmFormat type.

typedef enum eNOsh_PrintType NOsh_PrintType
 Declare NOsh_PrintType 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,
  NMF_XML = 2
}
 Molecule file format types. More...

enum  eNOsh_CalcType {
  NCT_MG = 0,
  NCT_FEM = 1,
  NCT_APOL = 2
}
 NOsh calculation types. More...

enum  eNOsh_ParmFormat {
  NPF_FLAT = 0,
  NPF_XML = 1
}
 Parameter file format types. More...

enum  eNOsh_PrintType {
  NPT_ENERGY = 0,
  NPT_FORCE = 1,
  NPT_ELECENERGY,
  NPT_ELECFORCE,
  NPT_APOLENERGY,
  NPT_APOLFORCE
}
 NOsh print 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_calc * NOsh_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.

NOsh_PrintType NOsh_printWhat (NOsh *thee, int iprint)
 Return an integer ID of the observable to print (.

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

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

int NOsh_apol2calc (NOsh *thee, int icalc)
 Return the name of an apol statement.

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

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

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

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

NOsh_calc * NOsh_calc_ctor (NOsh_CalcType calcType)
 Construct NOsh_calc.

int NOsh_calc_copy (NOsh_calc *thee, NOsh_calc *source)
 Copy NOsh_calc object into thee.

void NOsh_calc_dtor (NOsh_calc **thee)
 Object destructor.

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

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

int NOsh_setupElecCalc (NOsh *thee, Valist *alist[NOSH_MAXMOL])
 Setup the series of electrostatics calculations.

int NOsh_setupApolCalc (NOsh *thee, Valist *alist[NOSH_MAXMOL])
 Setup the series of non-polar calculations.

Detailed Description

Class for parsing for fixed format input files.

Enumeration Type Documentation

enum eNOsh_CalcType
 

NOsh calculation types.

Enumeration values:
NCT_MG  Multigrid
NCT_FEM  Finite element
NCT_APOL  non-polar

enum eNOsh_MolFormat
 

Molecule file format types.

Enumeration values:
NMF_PQR  PQR format
NMF_PDB  PDB format
NMF_XML  XML format

enum eNOsh_ParmFormat
 

Parameter file format types.

Enumeration values:
NPF_FLAT  Flat-file format
NPF_XML  XML format

enum eNOsh_PrintType
 

NOsh print types.

Enumeration values:
NPT_ENERGY  Energy (deprecated)
NPT_FORCE  Force (deprecated)
NPT_ELECENERGY  Elec Energy
NPT_ELECFORCE  Elec Force
NPT_APOLENERGY  Apol Energy
NPT_APOLFORCE  Apol Force

Function Documentation

int NOsh_apol2calc (  NOsh *  thee,
int  icalc
) 
 

Return the name of an apol statement.

Author:
David Gohara
Parameters:
thee NOsh object to use
icalc ID of CALC statement
Returns:
The name (if present) of an APOL statement

int NOsh_calc_copy (  NOsh_calc *  thee,
NOsh_calc *  source
) 
 

Copy NOsh_calc object into thee.

Author:
Nathan Baker
Parameters:
thee Target object
source Source object

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NOsh_calc* NOsh_calc_ctor (  NOsh_CalcType  calcType  ) 
 

Construct NOsh_calc.

Author:
Nathan Baker
Parameters:
calcType Calculation type
Returns:
Newly allocated and initialized NOsh object

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void NOsh_calc_dtor (  NOsh_calc **  thee  ) 
 

Object destructor.

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

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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

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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

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void NOsh_dtor2 (  NOsh *  thee  ) 
 

FORTRAN stub for object destructor.

Author:
Nathan Baker
Parameters:
thee Pointer to NOsh object

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int NOsh_elec2calc (  NOsh *  thee,
int  icalc
) 
 

Return the name of an elec statement.

Author:
Todd Dolinsky
Parameters:
thee NOsh object to use
icalc ID of CALC 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
ielec ID of ELEC 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_parseInput (  NOsh *  thee,
Vio *  sock
) 
 

Parse an input file from a socket.

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

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int NOsh_parseInputFile (  NOsh *  thee,
char *  filename
) 
 

Parse an input file only from a file.

Note:
Included for SWIG wrapper compatibility

Should be called before NOsh_setupCalc

Author:
Nathan Baker and Todd Dolinsky
Parameters:
thee Pointer to NOsh object
filename Name/path of readable file
Returns:
1 if successful, 0 otherwise

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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)

NOsh_PrintType 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_setupApolCalc (  NOsh *  thee,
Valist *  alist[NOSH_MAXMOL]
) 
 

Setup the series of non-polar calculations.

Note:
Should be called after NOsh_parseInput*
Author:
Nathan Baker and Todd Dolinsky
Parameters:
thee Pointer to NOsh object
alist Array of pointers to Valist objects (molecules used to center mesh);
Returns:
1 if successful, 0 otherwise
Parameters:
thee  NOsh object
alist  Atom list for calculation

int NOsh_setupElecCalc (  NOsh *  thee,
Valist *  alist[NOSH_MAXMOL]
) 
 

Setup the series of electrostatics calculations.

Note:
Should be called after NOsh_parseInput*
Author:
Nathan Baker and Todd Dolinsky
Parameters:
thee Pointer to NOsh object
alist Array of pointers to Valist objects (molecules used to center mesh);
Returns:
1 if successful, 0 otherwise
Parameters:
thee  NOsh object
alist  Atom list for calculation

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