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_calc |
| Calculation class for use when parsing fixed format input files. More... | |
| struct | sNOsh |
| Class for 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 struct sNOsh_calc | NOsh_calc |
| Declaration of the NOsh_calc class as the NOsh_calc structure. | |
| typedef struct 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_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
Contains declarations for class NOsh.
- Version:
- Id
- nosh.h 1350 2009-02-12 00:38:48Z yhuang01
- 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) 2002-2009, Washington University in St. Louis. * Portions Copyright (c) 2002-2009. Nathan A. Baker * Portions Copyright (c) 1999-2002. The Regents of the University of California. * Portions Copyright (c) 1995. Michael Holst * * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * - Redistributions of source code must retain the above copyright notice, this * list of conditions and the following disclaimer. * * - Redistributions in binary form must reproduce the above copyright notice, * this list of conditions and the following disclaimer in the documentation * and/or other materials provided with the distribution. * * - Neither the name of Washington University in St. Louis nor the names of its * contributors may be used to endorse or promote products derived from this * software without specific prior written permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * *
