NOsh class

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

Data Structures
struct	sNOsh_calc
	Calculation class for use when parsing fixed format input files. More...
struct	sNOsh
	Class for parsing fixed format input files. More...
Files
file	nosh.h
	Contains declarations for class NOsh.
file	nosh.c
	Class NOsh methods.
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 struct sNOsh	NOsh
	Declaration of the NOsh class as the NOsh structure.
typedef struct 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.

Enumerator:

NCT_MG	Multigrid
NCT_FEM	Finite element
NCT_APOL	non-polar

enum eNOsh_MolFormat

Molecule file format types.

Enumerator:

NMF_PQR	PQR format
NMF_PDB	PDB format
NMF_XML	XML format

enum eNOsh_ParmFormat

Parameter file format types.

Enumerator:

NPF_FLAT	Flat-file format
NPF_XML	XML format

enum eNOsh_PrintType

NOsh print types.

Enumerator:

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

References sNOsh::apol2calc.

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

References sNOsh_calc::apolparm, APOLparm_copy(), sNOsh_calc::calctype, sNOsh_calc::femparm, FEMparm_copy(), sNOsh_calc::mgparm, MGparm_copy(), sNOsh_calc::pbeparm, and PBEparm_copy().

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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

References sNOsh_calc::apolparm, APOLparm_ctor(), sNOsh_calc::calctype, FCT_NONE, sNOsh_calc::femparm, FEMparm_ctor(), MCT_NONE, sNOsh_calc::mgparm, MGparm_ctor(), NCT_APOL, NCT_FEM, NCT_MG, sNOsh_calc::pbeparm, and PBEparm_ctor().

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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

References sNOsh_calc::apolparm, APOLparm_dtor(), sNOsh_calc::calctype, sNOsh_calc::femparm, FEMparm_dtor(), sNOsh_calc::mgparm, MGparm_dtor(), NCT_APOL, NCT_FEM, NCT_MG, sNOsh_calc::pbeparm, and PBEparm_dtor().

Referenced by NOsh_dtor2().

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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

References NOsh_ctor2().

Referenced by main().

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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

References sNOsh::alist, sNOsh::apol, sNOsh::calc, sNOsh::elec, sNOsh::gotparm, sNOsh::ispara, sNOsh::napol, sNOsh::ncalc, sNOsh::ncharge, sNOsh::ndiel, sNOsh::nelec, sNOsh::nkappa, sNOsh::nmol, NOSH_MAXCALC, NOSH_MAXMOL, sNOsh::nprint, sNOsh::parsed, sNOsh::proc_rank, and sNOsh::proc_size.

Referenced by NOsh_ctor().

void NOsh_dtor ( NOsh ** thee )

Object destructor.

Author:: Nathan Baker

Parameters:

thee

Pointer to memory location of NOsh object

References NOsh_dtor2().

Referenced by main().

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void NOsh_dtor2 ( NOsh * thee )

FORTRAN stub for object destructor.

Author:: Nathan Baker

Parameters:

thee

Pointer to NOsh object

References sNOsh::apol, sNOsh::calc, sNOsh::elec, sNOsh::napol, sNOsh::ncalc, sNOsh::nelec, and NOsh_calc_dtor().

Referenced by NOsh_dtor().

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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

References sNOsh::elec2calc.

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)

References sNOsh::elecname.

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

References sNOsh::calc.

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

References sNOsh::chargefmt.

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

References sNOsh::chargepath.

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

References sNOsh::dielfmt.

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

References sNOsh::dielXpath.

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

References sNOsh::dielYpath.

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

References sNOsh::dielZpath.

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

References sNOsh::kappafmt.

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

References sNOsh::kappapath.

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

References sNOsh::molpath.

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

References MCcommChars, MCwhiteChars, sNOsh::ncharge, sNOsh::ndiel, sNOsh::nelec, sNOsh::nkappa, sNOsh::nmol, sNOsh::parsed, and Vstring_strcasecmp().

Referenced by main(), and NOsh_parseInputFile().

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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

References NOsh_parseInput().

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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)

References sNOsh::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)

References sNOsh::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)

References sNOsh::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)

References sNOsh::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

References ACD_ERROR, ACD_NO, ACD_YES, sNOsh::alist, sNOsh::apol, sNOsh::apol2calc, sNOsh_calc::calctype, sNOsh::napol, sNOsh::ncalc, NCT_APOL, and sNOsh::nmol.

Referenced by main().

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

References sNOsh::alist, sPBEparm::calcforce, sNOsh_calc::calctype, sMGparm::ccenter, sMGparm::ccentmol, sMGparm::ccmeth, sValist::center, sMGparm::center, sMGparm::centmol, sMGparm::cmeth, sNOsh::elec, sNOsh::elec2calc, sMGparm::fcenter, sMGparm::fcentmol, sMGparm::fcmeth, MCM_MOLECULE, sNOsh_calc::mgparm, sNOsh::ncalc, sNOsh::ncharge, NCT_FEM, NCT_MG, sNOsh::ndiel, sNOsh::nelec, sNOsh::nkappa, sNOsh::nmol, sNOsh_calc::pbeparm, and PCF_NO.

Referenced by main().

NOsh class

Data Structures

Files

Defines

Typedefs

Enumerations

Functions

Detailed Description

Enumeration Type Documentation

Function Documentation