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10f2621 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 | /** @defgroup Vatom Vatom class
* @brief Atom class for interfacing APBS with PDB files
*/
/**
* @file vatom.h
* @ingroup Vatom
* @brief Contains declarations for class Vatom
* @version $Id$
* @author Nathan A. Baker
*
* @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
*/
#ifndef _VATOM_H_
#define _VATOM_H_
#include "apbscfg.h"
#include "maloc/maloc.h"
#include "generic/vhal.h"
/**
* @ingroup Vatom
* @def VMAX_RECLEN
* @author Nathan Baker, David Gohara, Mike Schneiders
* @brief Residue name length
*/
#define VMAX_RECLEN 64
/**
* @ingroup Vatom
* @author Nathan Baker, David Gohara, Mike Schneiders
* @brief Contains public data members for Vatom class/module
*/
struct sVatom {
double position[3]; /**< Atomic position */
double radius; /**< Atomic radius */
double charge; /**< Atomic charge */
double partID; /**< Partition value for assigning atoms to particular
* processors and/or partitions */
double epsilon; /**< Epsilon value for WCA calculations */
int id; /**< Atomic ID; this should be a unique non-negative integer
* assigned based on the index of the atom in a Valist atom
* array */
char resName[VMAX_RECLEN]; /**< Residue name from PDB/PQR file */
char atomName[VMAX_RECLEN]; /**< Atom name from PDB/PDR file */
};
/**
* @ingroup Vatom
* @brief Declaration of the Vatom class as the Vatom structure
*/
typedef struct sVatom Vatom;
#if !defined(VINLINE_VATOM)
/** @brief Get atomic position
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @returns Pointer to 3*double array of atomic coordinates (in Å)
*/
VEXTERNC double* Vatom_getPosition(Vatom *thee);
/** @brief Set atomic radius
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @param radius Atomic radius (in Å)
*/
VEXTERNC void Vatom_setRadius(Vatom *thee, double radius);
/** @brief Get atomic position
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @returns Atomic radius (in Å)
*/
VEXTERNC double Vatom_getRadius(Vatom *thee);
/** @brief Set partition ID
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @param partID Partition ID; a negative value means this atom is not
* assigned to any partition
*/
VEXTERNC void Vatom_setPartID(Vatom *thee, int partID);
/** @brief Get partition ID
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @return Partition ID; a negative value means this atom is not
* assigned to any partition
*/
VEXTERNC double Vatom_getPartID(Vatom *thee);
/** @brief Set atom ID
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @param id Unique non-negative number
*/
VEXTERNC void Vatom_setAtomID(Vatom *thee, int id);
/** @brief Get atom ID
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @return Unique non-negative number
*/
VEXTERNC double Vatom_getAtomID(Vatom *thee);
/** @brief Set atomic charge
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @param charge Atom partial charge (in e)
*/
VEXTERNC void Vatom_setCharge(Vatom *thee, double charge);
/** @brief Get atomic charge
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object
* @return Atom partial charge (in e)
*/
VEXTERNC double Vatom_getCharge(Vatom *thee);
/** @brief Set atomic epsilon
* @ingroup Vatom
* @author David Gohara
* @param thee Vatom object
* @param epsilon Atomic epsilon (in Å)
*/
VEXTERNC void Vatom_setEpsilon(Vatom *thee, double epsilon);
/** @brief Get atomic epsilon
* @ingroup Vatom
* @author David Gohara
* @param thee Vatom object
* @returns Atomic epsilon (in Å)
*/
VEXTERNC double Vatom_getEpsilon(Vatom *thee);
/** @brief Return the memory used by this structure (and its contents)
* in bytes
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vpmg object
* @return The memory used by this structure and its contents in bytes
*/
VEXTERNC unsigned long int Vatom_memChk(Vatom *thee);
#else /* if defined(VINLINE_VATOM) */
# define Vatom_getPosition(thee) ((thee)->position)
# define Vatom_setRadius(thee, tRadius) ((thee)->radius = (tRadius))
# define Vatom_getRadius(thee) ((thee)->radius)
# define Vatom_setPartID(thee, tpartID) ((thee)->partID = (double)(tpartID))
# define Vatom_getPartID(thee) ((thee)->partID)
# define Vatom_setAtomID(thee, tatomID) ((thee)->id = (tatomID))
# define Vatom_getAtomID(thee) ((thee)->id)
# define Vatom_setCharge(thee, tCharge) ((thee)->charge = (tCharge))
# define Vatom_getCharge(thee) ((thee)->charge)
# define Vatom_setEpsilon(thee, tEpsilon) ((thee)->epsilon = (tEpsilon))
# define Vatom_getEpsilon(thee) ((thee)->epsilon)
# define Vatom_memChk(thee) (sizeof(Vatom))
#endif /* if !defined(VINLINE_VATOM) */
/* ///////////////////////////////////////////////////////////////////////////
// Class Vatom: Non-Inlineable methods (vatom.c)
/////////////////////////////////////////////////////////////////////////// */
/** @brief Set residue name
* @ingroup Vatom
* @author Jason Wagoner
* @param thee Vatom object
* @param resName Residue Name
*/
VEXTERNC void Vatom_setResName(Vatom *thee, char resName[VMAX_RECLEN]);
/** @brief Set atom name
* @ingroup Vatom
* @author Jason Wagoner
*/
VEXTERNC void Vatom_setAtomName(
Vatom *thee, /**< Vatom object */
char atomName[VMAX_RECLEN] /**< Atom name */
);
/** @brief Retrieve residue name
* @ingroup Vatom
* @author Jason Wagoner
* @param thee Vatom object
* @param resName Residue Name
*/
VEXTERNC void Vatom_getResName(Vatom *thee, char resName[VMAX_RECLEN]);
/** @brief Retrieve atom name
* @ingroup Vatom
* @author Jason Wagoner
*/
VEXTERNC void Vatom_getAtomName(
Vatom *thee, /**< Vatom object */
char atomName[VMAX_RECLEN] /**< Atom name */
);
/** @brief Constructor for the Vatom class
* @author Nathan Baker
* @ingroup Vatom
* @returns Pointer to newly allocated Vatom object
*/
VEXTERNC Vatom* Vatom_ctor();
/** @brief FORTRAN stub constructor for the Vatom class
* @author Nathan Baker
* @ingroup Vatom
* @param thee Pointer to Vatom allocated memory location
* @returns 1 if succesful, 0 otherwise
*/
VEXTERNC int Vatom_ctor2(Vatom *thee);
/** @brief Object destructor
* @ingroup Vatom
* @author Nathan Baker
* @param thee Pointer to memory location of object to be destroyed
*/
VEXTERNC void Vatom_dtor(Vatom **thee);
/** @brief FORTRAN stub object destructor
* @ingroup Vatom
* @author Nathan Baker
* @param thee Pointer to object to be destroyed
*/
VEXTERNC void Vatom_dtor2(Vatom *thee);
/** @brief Set the atomic position
* @ingroup Vatom
* @author Nathan Baker
* @param thee Vatom object to be modified
* @param position Coordinates (in Å)
*/
VEXTERNC void Vatom_setPosition(Vatom *thee, double position[3]);
/**
* @brief Copy information to another atom
* @ingroup Vatom
* @author Nathan Baker
* @param thee Source for atom information
* @param dest Destination for atom information
*/
VEXTERNC void Vatom_copyTo(Vatom *thee, Vatom *dest);
/**
* @brief Copy information to another atom
* @ingroup Vatom
* @author Nathan Baker
* @param thee Destination for atom information
* @param src Source for atom information
*/
VEXTERNC void Vatom_copyFrom(Vatom *thee, Vatom *src);
#endif /* ifndef _VATOM_H_ */
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