/** * <center> * @mainpage APBS Programmers Guide * * APBS was written by Nathan A. Baker.<br> * Additional contributing authors listed in the code documentation. * </center> * * <hr width="100%"> * @section toc Table of Contents * <ul> * <li> @ref style * <li> @ref api * <ul> * <li> <a href="modules.html">Modules</a> * <li> <a href="annotated.html">Class list</a> * <li> <a href="functions.html">Class members</a> * <li> <a href="globals.html">Class methods</a> * </ul> * </ul> * * <hr width="100%"> * @section license License * * Primary author: <a href="http://agave.wustl.edu/">Nathan A. Baker</a> (<a href="mailto:baker@biochem.wustl.edu">baker@biochem.wustl.edu</a>)<br> * Department of Biochemistry and Molecular Biophysics<br> * Center for Computational Biology<br> * Washington University in St. Louis<br> * Additional contributing authors are listed in the code documentation.<br> * * <p> 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 * * <p> All rights reserved. * * <p> Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * <ul> * <li> Redistributions of source code must retain the above copyright notice, this * list of conditions and the following disclaimer. * * <li> 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. * * <li> 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. * </ul> * <p> * 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. * * <hr> * <p> * This documentation provides information about the programming interface * provided by the APBS software and a general guide to linking to the APBS * libraries. Information about installation, configuration, and general usage * can be found in the <a href="user.html">User's Guide</a>. * <hr> * * @section style Programming Style * * <p> * APBS was developed following the <a * href="http://scicomp.ucsd.edu/~mholst/codes/maloc/cleanc.html">Clean OO * C</a> style of Mike Holst. In short, Clean OO C code is written in a * object-oriented, ISO C-compliant fashion, and can be compiled with either a * C or C++ compiler. <p> Following this formalism, all public data is * enclosed in structures which resemble C++ classes. These structures and * member functions are then declared in a public header file which provides a * concise description of the interface for the class. Private functions and * data are included in private header files (or simply the source code files * themselves) which are not distributed. When using the library, the * end-user only sees the public header file and the compiled library and is * therefore (hopefully) oblivious to the private members and functions. Each * class is also equipped with a constructor and destructor function which is * responsible for allocating and freeing any memory required by the * instatiated objects. * * <p> * As mentioned above, public data members are enclosed in C structures which * are visible to the end-user. Public member functions are generated by * mangling the class and function names <i>and</i> passing a pointer to the * object on which the member function is supposed to act. For example, a * public member function with the C++ declaration * <pre> * public double Foo::bar(int i, double d) * </pre> * would be declared as * <pre> * VEXTERNC double Foo_bar(Foo *thee, int i, double d) * </pre> * where <code>VEXTERNC</code> is a compiler-dependent macro, the underscore * <code>_</code> replaces the C++ double-colon <code>::</code>, and * <code>thee</code> replaces the <code>this</code> variable implicit in all * C++ classes. Since they do not appear in public header files, private * functions could be declared in any format pleasing to the user, however, the * above declaration convention should generally be used for both public and * private functions. Within the source code, the public and private function * declarations/definitions are prefaced by the macros <code>VPUBLIC</code> and * <code>VPRIVATE</code>, respectively. These are macros which reduce global * name pollution, similar to encapsulating private data withing C++ classes. * * <p> * The only C++ functions not explicitly covered by the above declaration * scheme are the constructors (used to allocate and initialize class data * members) and destructors (used to free allocated memory). These are * declared in the following fashion: a constructor with the C++ declaration * <pre> * public void Foo::Foo(int i, double d) * </pre> * would be declared as * <pre> * VEXTERNC Foo* Foo_ctor(int i, double d) * </pre> * which returns a pointer to the newly constructed <code>Foo</code> object. * Likewise, a destructor declared as * <pre> * public void Foo::~Foo() * </pre> * in C++ would be * <pre> * VEXTERNC void Foo_dtor(Foo **thee) * </pre> * in Clean OO C. * <p> * Finally, inline functions in C++ are simply treated as macros in Clean OO C * and declared/defined using <code>#define</code> statements in the public * header file. * <p> * See any of the APBS header files for more information on Clean OO C * programming styles. * * @section api Application programming interface documentation * <p> * The API documentation for this code was generated by <a * href="http://www.doxygen.org">doxygen</a>. You can either view the API * documentation by using the links at the top of this page, or the slight * re-worded/re-interpreted list below: * <ul> * <li> <a href="modules.html">Class overview</a> * <li> <a href="annotated.html">Class declarations</a> * <li> <a href="functions.html">Class members</a> * <li> <a href="globals.html">Class methods</a> * </ul> * */
