APBS
1.5
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Primary author: Nathan A. Baker (nathan.baker@pnnl.gov)
Pacific Northwest National Laboratory
Additional contributing authors are listed in the code documentation.
Copyright (c) 2010-2014 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:
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.
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 User's Guide.
APBS was developed following the Clean OO C 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.
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.
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 and 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
public double Foo::bar(int i, double d)
would be declared as
VEXTERNC double Foo_bar(Foo *thee, int i, double d)
where VEXTERNC
is a compiler-dependent macro, the underscore _
replaces the C++ double-colon ::
, and thee
replaces the this
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 VPUBLIC
and VPRIVATE
, respectively. These are macros which reduce global name pollution, similar to encapsulating private data withing C++ classes.
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
public void Foo::Foo(int i, double d)
would be declared as
VEXTERNC Foo* Foo_ctor(int i, double d)
which returns a pointer to the newly constructed Foo
object. Likewise, a destructor declared as
public void Foo::~Foo()
in C++ would be
VEXTERNC void Foo_dtor(Foo **thee)
in Clean OO C.
Finally, inline functions in C++ are simply treated as macros in Clean OO C and declared/defined using define
statements in the public header file.
See any of the APBS header files for more information on Clean OO C programming styles.
The API documentation for this code was generated by doxygen. 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: