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nosh.h File Reference

Contains declarations for class NOsh. More...

#include "maloc/maloc.h"
#include "apbs/vhal.h"
#include "apbs/pbeparm.h"
#include "apbs/mgparm.h"
#include "apbs/femparm.h"
#include "apbs/apolparm.h"
#include "apbs/valist.h"

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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_calc NOsh_calc
 Declaration of the NOsh_calc class as the NOsh_calc structure.

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

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 (.

NOshNOsh_ctor (int rank, int size)
 Construct NOsh.

NOsh_calcNOsh_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

Contains declarations for class NOsh.

Version:
Id
nosh.h 1045 2007-01-02 16:16:42Z sdg0919
Author:
Nathan A. Baker
Attention:
 *
 * APBS -- Adaptive Poisson-Boltzmann Solver
 *
 * Nathan A. Baker (baker@biochem.wustl.edu)
 * Dept. of Biochemistry and Molecular Biophysics
 * Center for Computational Biology
 * Washington University in St. Louis
 *
 * Additional contributing authors listed in the code documentation.
 *
 * Copyright (c) 2002-2007.  Washington University in St. Louis.
 * All Rights Reserved.
 * Portions Copyright (c) 1999-2002.  The Regents of the University of
 * California.  
 * Portions Copyright (c) 1995.  Michael Holst.
 *
 * This file is part of APBS.
 *
 * APBS is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * APBS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with APBS; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
 *
 * Linking APBS statically or dynamically with other modules is making a
 * combined work based on APBS. Thus, the terms and conditions of the GNU
 * General Public License cover the whole combination.
 * 
 * SPECIAL GPL EXCEPTION
 * In addition, as a special exception, the copyright holders of APBS
 * give you permission to combine the APBS program with free software
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