| /** @defgroup PBSAMparm PBSAMparm class | |
| * @brief Parameter which holds useful parameters for Poisson-boltzmann | |
| * analytical method calculations | |
| */ | |
| /** | |
| * @file pbsamparm.h | |
| * @ingroup PBSAMparm | |
| * @brief Contains declarations for class PBSAMparm | |
| * @version $Id$ | |
| * @author Lisa Felberg | |
| * | |
| * @attention | |
| * @verbatim | |
| * | |
| * APBS -- Adaptive Poisson-Boltzmann Solver | |
| * | |
| * Nathan A. Baker (nathan.baker@pnnl.gov) | |
| * Pacific Northwest National Laboratory | |
| * | |
| * Additional contributing authors listed in the code documentation. | |
| * | |
| * Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the | |
| * Pacific Northwest National Laboratory, operated by Battelle Memorial | |
| * Institute, Pacific Northwest Division for the U.S. Department of Energy. | |
| * | |
| * Portions Copyright (c) 2002-2010, Washington University in St. Louis. | |
| * Portions Copyright (c) 2002-2010, 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 the developer 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. | |
| * | |
| * @endverbatim | |
| */ | |
| /* Generic header files */ | |
| /** @brief Number of things that can be written out in a single calculation | |
| * @ingroup PBSAMparm | |
| */ | |
| /** | |
| * @brief Calculation type | |
| * @ingroup PBSAMparm | |
| */ | |
| enum ePBSAMparm_CalcType { | |
| //other methods disabled for now only auto currently implemented. | |
| //PBSAMCT_MANUAL=0, /**< PBSAM-manual */ | |
| PBSAMCT_AUTO=1, /**< PBSAM-auto */ | |
| //PBSAMCT_NONE=2 /**< not defined */ | |
| }; | |
| /** | |
| * @brief Declare PBSAMparm_CalcType type | |
| * @ingroup PBSAMparm | |
| */ | |
| typedef enum ePBSAMparm_CalcType PBSAMparm_CalcType; | |
| /** | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @brief Parameter structure for PBSAM-specific variables from input files | |
| * @note If you add/delete/change something in this class, the member | |
| * functions -- especially PBSAMparm_copy -- must be modified | |
| * accordingly | |
| */ | |
| typedef struct sPBSAMparm { | |
| PBSAMparm_CalcType type; /**< What type of PBSAM calculation? */ | |
| int parsed; /**< Has this structure been filled? (0 = no, 1 = yes) */ | |
| /* The only parms in addition to PBAM would be | |
| IMAT and Selfpol */ | |
| int settolsp; | |
| double tolsp; | |
| double probe_radius; | |
| double density; | |
| int setsurf; | |
| int surfct; | |
| char surffil[PBSAMPARM_MAXMOL][CHR_MAXLEN]; | |
| int setimat; | |
| int imatct; | |
| char imatfil[PBSAMPARM_MAXMOL][CHR_MAXLEN]; | |
| int setexp; | |
| int expct; | |
| char expfil[PBSAMPARM_MAXMOL][CHR_MAXLEN]; | |
| } PBSAMparm; | |
| /** @brief Construct PBSAMparm object | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @param type Type of PBSAM calculation | |
| * @returns Newly allocated and initialized PBSAMparm object | |
| */ | |
| VEXTERNC PBSAMparm* PBSAMparm_ctor(PBSAMparm_CalcType type); | |
| /** @brief FORTRAN stub to construct PBSAMparm object ?????????!!!!!!! | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @param thee Space for PBSAMparm object | |
| * @param type Type of MG calculation | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes PBSAMparm_ctor2(PBSAMparm *thee, PBSAMparm_CalcType type); | |
| /** @brief Object destructor | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @param thee Pointer to memory location of PBSAMparm object | |
| */ | |
| VEXTERNC void PBSAMparm_dtor(PBSAMparm **thee); | |
| /** @brief FORTRAN stub for object destructor ?????????!!!!!!!!!!!! | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @param thee Pointer to PBSAMparm object | |
| */ | |
| VEXTERNC void PBSAMparm_dtor2(PBSAMparm *thee); | |
| /** @brief Consistency check for parameter values stored in object | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @param thee PBSAMparm object | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes PBSAMparm_check(PBSAMparm *thee); | |
| /** @brief Parse an MG keyword from an input file | |
| * @ingroup PBSAMparm | |
| * @author Lisa Felberg | |
| * @param thee PBSAMparm object | |
| * @param tok Token to parse | |
| * @param sock Stream for more tokens | |
| * @returns Success enumeration (1 if matched and assigned; -1 if matched, but there's some sort | |
| * of error (i.e., too few args); 0 if not matched) | |
| */ | |
| VEXTERNC Vrc_Codes PBSAMparm_parseToken(PBSAMparm *thee, char tok[VMAX_BUFSIZE], | |
| Vio *sock); | |
| /** | |
| * @brief copy PBSAMparm object int thee. | |
| * @ingroup PBSAMparm | |
| * @author | |
| * @param thee PBSAMparm object to be copied into | |
| * @param parm PBSAMparm object. | |
| */ | |
| VEXTERNC void PBSAMparm_copy(PBSAMparm *thee, PBSAMparm *parm); | |
| /** | |
| * @brief Find sphere tolerance for coarse-graining | |
| * @ingroup PBSAMparm | |
| * @author | |
| * @param thee PBSAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find vertex files for each molecule and save them | |
| * @ingroup PBSAMparm | |
| * @author | |
| * @param thee PBSAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find IMAT files for each molecule and save them | |
| * @ingroup PBSAMparm | |
| * @author | |
| * @param thee PBSAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find expansion files for each molecule and save them | |
| * @ingroup PBSAMparm | |
| * @author | |
| * @param thee PBSAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | |