/** @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_ */